diff --git a/README.TXT b/README.TXT
index fb0539affa82b591ff445fcf1594f0e4ef66f264..3cf7008ac7e36a2db94a847f77de9c687d203ad7 100644
--- a/README.TXT
+++ b/README.TXT
@@ -1,6 +1,6 @@
#######################################################################
# Ontology alignment API and implementation #
-# 23/10/2015, version 4.7+ #
+# 20/11/2015, version 4.8 #
# http://alignapi.gforge.inria.fr #
#######################################################################
@@ -51,7 +51,7 @@ For a better introduction, see the tutorial at
http://alignapi.gforge.inria.fr/tutorial
or find it as a script in html/tutorial/script.sh
-$ setenv CWD `pwd`
+$ export CWD=`pwd`
$ java -jar lib/procalign.jar --help
@@ -82,7 +82,7 @@ Using with JWNL (Wordnet)
- jwnl.jar commons-logging.jar must be in lib.
(file_properties.xml need not anymore to be in current directory)
-$ setenv WNDIR ../WordNet-3.0/dict
+$ export WNDIR=../WordNet-3.0/dict
$ java -jar lib/procalign.jar -Dwndict=$WNDIR file://$CWD/examples/rdf/edu.umbc.ebiquity.publication.owl file://$CWD/examples/rdf/edu.mit.visus.bibtex.owl -i fr.inrialpes.exmo.align.ling.JWNLAlignment -o examples/rdf/JWNL.rdf
diff --git a/examples/omwg/transf.rdf b/examples/omwg/transf.rdf
index 17e5d986648dcd25ef2d792d85aa8234d7783aff..01981b10f2e5c94784d8a5f0061540a2a8f8dc2f 100644
--- a/examples/omwg/transf.rdf
+++ b/examples/omwg/transf.rdf
@@ -32,19 +32,19 @@ it only illustrates transformations
<align:level>2EDOAL</align:level>
<align:type>**</align:type>
<align:onto1>
- <align:Ontology rdf:about="&im;">
+ <align:Ontology rdf:about="&im;">
<align:formalism>
<align:Formalism align:name="OWL1.0" align:uri="http://www.w3.org/2002/07/owl#"/>
</align:formalism>
- </align:Ontology>
+ </align:Ontology>
</align:onto1>
<align:onto2>
- <align:Ontology rdf:about="&me;">
+ <align:Ontology rdf:about="&me;">
<align:location>http://www.scharffe.fr/ontologies/OntologieDuVin.wsml</align:location>
<align:formalism>
<align:Formalism align:uri="http://www.wsmo.org/wsml/wsml-syntax/wsml-dl" align:name="wsml" />
</align:formalism>
- </align:Ontology>
+ </align:Ontology>
</align:onto2>
<align:map>
<align:Cell rdf:about="#M11b">
diff --git a/src/fr/inrialpes/exmo/align/cli/ExtGroupEval.java b/src/fr/inrialpes/exmo/align/cli/ExtGroupEval.java
index 481f37b462ef483527ec175355a7cdbbe640f503..eb1365e44c5a7382464e341596d36e855d6aa70c 100644
--- a/src/fr/inrialpes/exmo/align/cli/ExtGroupEval.java
+++ b/src/fr/inrialpes/exmo/align/cli/ExtGroupEval.java
@@ -230,6 +230,8 @@ public class ExtGroupEval extends CommonCLI {
/**
* This does not only print the results but compute the average as well
+ *
+ * @param result: the vector of vector result to be printed
*/
public void print( Vector<Vector<Object>> result ) {
PrintStream writer = null;
diff --git a/src/fr/inrialpes/exmo/align/cli/GroupEval.java b/src/fr/inrialpes/exmo/align/cli/GroupEval.java
index c2f90518475e549d806715ccac5d3b72312419bd..aa5bada4086c4f2e6e565bbb3f933bd08d764ab0 100644
--- a/src/fr/inrialpes/exmo/align/cli/GroupEval.java
+++ b/src/fr/inrialpes/exmo/align/cli/GroupEval.java
@@ -251,6 +251,8 @@ public class GroupEval extends CommonCLI {
/**
* This does not only print the results but compute the average as well
+ *
+ * @param result: the vector of vector result to be printed
*/
public void print( Vector<Vector<Object>> result ) {
PrintStream writer = null;
@@ -274,6 +276,9 @@ public class GroupEval extends CommonCLI {
* A plot of the precision recall points on a triangular space
* Added level lines provides by Christian Meilicke (U. Mannheim)
* See his program in comment below
+ *
+ * @param result: the vector of vector result to be printed
+ * @param writer: the writer in which to print it
*/
public void printTRIANGLE( Vector<Vector<Object>> result, PrintStream writer ) {
// variables for computing iterative harmonic means
diff --git a/src/fr/inrialpes/exmo/align/cli/WGroupEval.java b/src/fr/inrialpes/exmo/align/cli/WGroupEval.java
index 795847f645b0befca802210cd2358e1d7c91a5c1..c99a157a05fb0e23543c059bb2cf55b7ac1db685 100644
--- a/src/fr/inrialpes/exmo/align/cli/WGroupEval.java
+++ b/src/fr/inrialpes/exmo/align/cli/WGroupEval.java
@@ -232,6 +232,8 @@ public class WGroupEval extends CommonCLI {
/**
* This does not only print the results but compute the average as well
+ *
+ * @param result: the vector of vector result to be printed
*/
public void print( Vector<Vector<Object>> result ) {
PrintStream writer = null;
diff --git a/src/fr/inrialpes/exmo/align/gen/Alterator.java b/src/fr/inrialpes/exmo/align/gen/Alterator.java
index 3f3d6f4f1effda06f13e50a694b46485b0a79471..d357f59aaaae710567dbfcafded683eb16970b69 100644
--- a/src/fr/inrialpes/exmo/align/gen/Alterator.java
+++ b/src/fr/inrialpes/exmo/align/gen/Alterator.java
@@ -46,17 +46,20 @@ public interface Alterator {
//public Alterator( Alterator om );
/**
- * the namespace of the input ontology
+ * @return the namespace of the input ontology
*/
public String getNamespace();
/**
- * the namespace of the source ontology in the input alignment
+ * @return the namespace of the source ontology in the input alignment
*/
public String getBase();
/**
* modify applies the alteration to the input (the results are kept in
* internal structures.
+ *
+ * @param params: the alteration to be performed
+ * @return the Alterator object with alterations performed
*/
public Alterator modify( Properties params );
@@ -64,6 +67,8 @@ public interface Alterator {
/**
* getProtoAlignment, getProtoOntology, getHierarchy
* are used for accessing these internal structure at creation time.
+ *
+ * @return properties representing a currect alignment
*/
public Properties getProtoAlignment();
public OntModel getProtoOntology();
@@ -72,14 +77,20 @@ public interface Alterator {
/**
* Modifies the namespaces of source and target ontologies
* (for the main purpose of outputing them)
+ *
+ * @param namespace1 and
+ * @param namespace2: the namespaces to be given to source and target ontologies
*/
public void relocateTest( String namespace1, String namespace2 );
public void relocateTest( String namespace2 );
/**
- * Returns the altered Alignment and Ontology in output form
+ * @return the altered Alignment in output form
*/
public Alignment getAlignment();
+ /**
+ * @return the altered Ontology in output form
+ */
public OntModel getModifiedOntology();
}
diff --git a/src/fr/inrialpes/exmo/align/gen/OntologyNetworkGenerator.java b/src/fr/inrialpes/exmo/align/gen/OntologyNetworkGenerator.java
index c04d361d61defbd97b1927dedefc2cc2036ab072..2e6e9fc4d4f8d27b78260fa4bfce862413134fd3 100644
--- a/src/fr/inrialpes/exmo/align/gen/OntologyNetworkGenerator.java
+++ b/src/fr/inrialpes/exmo/align/gen/OntologyNetworkGenerator.java
@@ -40,6 +40,12 @@ public interface OntologyNetworkGenerator {
* Returns an ontology network of size n (the number of ontologies)
* starting from an ontology o.
* Parameters may further specify the requirements.
+ *
+ * @param n: the size of the generated network of ontologies
+ * @param o: the initial ontology
+ * @param params: generator parameters
+ * //@throws AlignmentException whenever something goes wrong
+ * @return the generated network
*/
public OntologyNetwork generate( int n, Ontology<Object> o, Properties params );
diff --git a/src/fr/inrialpes/exmo/align/gen/OntologyNetworkWeakener.java b/src/fr/inrialpes/exmo/align/gen/OntologyNetworkWeakener.java
index 8293adc282621108a61badca8996168886bf8872..724506f14d3ebc1a513f57aa9040df902e66e7e5 100644
--- a/src/fr/inrialpes/exmo/align/gen/OntologyNetworkWeakener.java
+++ b/src/fr/inrialpes/exmo/align/gen/OntologyNetworkWeakener.java
@@ -38,11 +38,23 @@ public interface OntologyNetworkWeakener {
/**
* Weakens the ontology network of n units
+ *
+ * @param on: the network of ontologies to weaken
+ * @param n: the extent of the weakening in units
+ * @param p: weakening parameters
+ * @throws AlignmentException whenever something goes wrong
+ * @return the weakened network
*/
public OntologyNetwork weaken( OntologyNetwork on, int n, Properties p ) throws AlignmentException;
/**
* Weakens the ontology network of n%
+ *
+ * @param on: the network of ontologies to weaken
+ * @param n: the extent of the weakening in percentage
+ * @param p: weakening parameters
+ * @throws AlignmentException whenever something goes wrong
+ * @return the weakened network
*/
public OntologyNetwork weaken( OntologyNetwork on, double n, Properties p ) throws AlignmentException;
diff --git a/src/fr/inrialpes/exmo/align/gen/TestGenerator.java b/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
index ff47e1caa59a87747cd8f8badd6de1fe20f2ee49..071a3ba8d88db345ed5dd024b62dbcb228b2539e 100644
--- a/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
+++ b/src/fr/inrialpes/exmo/align/gen/TestGenerator.java
@@ -172,6 +172,14 @@ public class TestGenerator {
/**
* Generate a test by altering an existing test
+ *
+ * @param pKey: type of the alteration to perform
+ * @param pVal: extent (percentage?) of the alteration to perform
+ * @param suffix: suffix of the test
+ * @param prevTest: name of the prevous test
+ * @param al: an input protoalignment
+ * @param testNb: name (number) of the test to be generated
+ * @return the protoalignment expressed as properties
*/
public Properties incrementModifyOntology( String pKey, String pVal, String suffix, String prevTest, Properties al, String testNb ) {
Properties p = new Properties();
@@ -183,6 +191,12 @@ public class TestGenerator {
/**
* Generate a test by altering an existing test
+ *
+ * @param prevTestDir: the directory of the initial test
+ * @param al: an input protoalignment
+ * @param testDir: the directory of the final test
+ * @param params: parameters describing the test alterations
+ * @return the protoalignment expressed as properties
*/
public Properties incrementModifyOntology( String prevTestDir, Properties al, String testDir, Properties params ) {
return modifyOntology( dirprefix+"/"+prevTestDir+"/"+ontoname, al, testDir, params );
@@ -191,6 +205,12 @@ public class TestGenerator {
//modifies an ontology
/**
* Generate a test from an ontology
+ *
+ * @param file: the file containing the initial ontology
+ * @param al: an input protoalignment
+ * @param dirName: the name of the directory in which the test will be relocated
+ * @param params: parameters describing the test alterations
+ * @return the protoalignment expressed as properties
*/
public Properties modifyOntology( String file, Properties al, String dirName, Properties params) {
logger.trace( "Source: {}; Target {}", file, dirName );
@@ -209,7 +229,7 @@ public class TestGenerator {
// ******************************************************* GENERATOR
- //generate the alingnment
+ //generate the alignment
public Alterator generate( OntModel onto, Properties params, Properties initalign ) {
logger.debug( "[-------------------------------------------------]" );
logger.debug( "{} / {} / {} / {}", urlprefix, dirprefix, ontoname, alignname );
diff --git a/src/fr/inrialpes/exmo/align/gen/alt/BasicAlterator.java b/src/fr/inrialpes/exmo/align/gen/alt/BasicAlterator.java
index 53357f3dbfefff7f58a3805235fec7fd7569ff44..b34d9f49ab3dc8c9982dfd8f195d058583521ac5 100644
--- a/src/fr/inrialpes/exmo/align/gen/alt/BasicAlterator.java
+++ b/src/fr/inrialpes/exmo/align/gen/alt/BasicAlterator.java
@@ -407,6 +407,9 @@ public abstract class BasicAlterator implements Alterator {
* Modifies the namespace of the generated ontology
* This is the initial implementation.
* However... it has some problem with Jena treating fragments (containing numbers and / in them).
+ *
+ * @param ns: the namespace under which to relocate the ontology
+ * @return the relocated ontology
*/
public OntModel changeNamespace ( String ns ) {
OntModel newModel = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM ); //create new Model
@@ -443,6 +446,9 @@ public abstract class BasicAlterator implements Alterator {
* OntModel.write( OutputStream out ) / OntModel.write( Writer writer )
* new Model().read( InputStream in, String base ) / new Model().read(Reader reader, String base)
* So far this is less efficient (and less elegant) than the modifications above
+ *
+ * @param base2: the namespace under which to relocate the ontology
+ * @return the relocated ontology
*/
public OntModel changeNamespace2( String base2 ) {
OntModel model = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM );
@@ -481,6 +487,10 @@ public abstract class BasicAlterator implements Alterator {
* Rename the ontology, just in case it does not have the same URI as its content...
* This happens
* oldURI should be useless
+ *
+ * @param model: the ontology whose URI have to be relocated
+ * @param oldURI: the current URI prefix
+ * @param newURI: the new URI prefix
*/
public void renameOntology( OntModel model, String oldURI, String newURI ) {
Ontology onto = model.getOntology( oldURI );
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
index d4f2c1490bc4d4e758895fc72a74200ff2decebf..385685a09adcdce46095e4a507a1e07acaa3c3f3 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
@@ -115,6 +115,12 @@ public class BasicAlignment implements Alignment, Extensible {
* which will then replaced the one that was there at creation time
* or a "concrete" ontology which will be inserted in the fr.inrialpes.exmo.ontowrap.Ontology
* object.
+ *
+ * @param onto1 and
+ * @param onto2: the two aligned ontologies
+ * @param relType: the type of relations to use
+ * @param confType: the type of confidence measures to use
+ * @throws AlignmentException when something goes wrong
*/
public void init( Object onto1, Object onto2, Class<? extends Relation> relType, Class<?> confType ) throws AlignmentException {
relationType = relType;
@@ -159,7 +165,7 @@ public class BasicAlignment implements Alignment, Extensible {
return sum;
}
- /** A few statistical primitives, undocumented **/
+ /* A few statistical primitives, undocumented */
public double maxConfidence() {
double result = 0.;
for ( Cell c : this ) {
@@ -193,7 +199,7 @@ public class BasicAlignment implements Alignment, Extensible {
}
// For standard deviation, take the square root of variance
- /** Alignment methods * */
+ /* Alignment methods */
public Object getOntology1() {
return onto1.getOntology();
};
@@ -334,7 +340,7 @@ public class BasicAlignment implements Alignment, Extensible {
hash2 = new Hashtable<Object,Set<Cell>>();
}
- /** Cell methods **/
+ /* Cell methods */
// Could use a relationType.getIdRelation() / confidenceType.getTop() -- But kept this way
public Cell addAlignCell( Object ob1, Object ob2 ) throws AlignmentException {
return addAlignCell( (String)null, ob1, ob2, "=", BasicConfidence.getTopConfidence() );
@@ -350,6 +356,10 @@ public class BasicAlignment implements Alignment, Extensible {
/**
* The constructor to use
+ *
+ * @param rel: the string representing the relation
+ * @throws AlignmentException when something goes wrong
+ * @return a relation of the relevant type corresponding to the given string
*/
public Relation createRelation( String rel ) throws AlignmentException {
// Any of them... call the local createRelation()...
@@ -570,6 +580,9 @@ public class BasicAlignment implements Alignment, Extensible {
/***************************************************************************
* The cut function suppresses from an alignment all the cell over a
* particular threshold
+ *
+ * @param threshold: the threshold under which to cut
+ * @throws AlignmentException when something goes wrong (unlikely)
**************************************************************************/
public void cut2(double threshold) throws AlignmentException {
for ( Cell c : this ) {
@@ -580,6 +593,9 @@ public class BasicAlignment implements Alignment, Extensible {
/***************************************************************************
* Default cut implementation
* For compatibility with API until version 1.1
+ *
+ * @param threshold: the threshold under which to cut
+ * @throws AlignmentException when something goes wrong (unlikely)
**************************************************************************/
public void cut( double threshold ) throws AlignmentException {
cut( "hard", threshold );
@@ -587,6 +603,10 @@ public class BasicAlignment implements Alignment, Extensible {
/***************************************************************************
* Cut refinement :
+ * Rule:
+ * threshold is betweew 1 and 0
+ *
+ * @param method: the cut method to be used described as:
* - getting those cells with strength above n (hard)
* - getting the n best cells (best)
* - getting those cells with strength at worse n under the best (span)
@@ -594,8 +614,8 @@ public class BasicAlignment implements Alignment, Extensible {
* - getting those cells with strength at worse n% of the best (prop)
* - getting all cells until a gap of n (hardgap)
* - getting all cells until a gap of n% of the last (propgap)
- * Rule:
- * threshold is betweew 1 and 0
+ * @param threshold: the threshold under which to cut
+ * @throws AlignmentException when something goes wrong (unlikely)
**************************************************************************/
public void cut( String method, double threshold ) throws AlignmentException
{
@@ -646,6 +666,9 @@ public class BasicAlignment implements Alignment, Extensible {
/**
* The harden function acts like threshold but put all weights to 1.
+ *
+ * @param threshold: the threshold above which to harden
+ * @throws AlignmentException when something goes wrong (unlikely)
*/
public void harden(double threshold) throws AlignmentException {
for ( Cell c : this ) {
@@ -664,9 +687,16 @@ public class BasicAlignment implements Alignment, Extensible {
* - check compatibility and setup for type and level
* - conserve extensions if necessary
*/
- /*
+ /**
* This method is used by the algebraic operators
* It has to be overriden by implementations.
+ *
+ * @param onto1 and
+ * @param onto2: the two aligned ontologies
+ * @param relType: the type of relations to use
+ * @param confType: the type of confidence measures to use
+ * @throws AlignmentException when something goes wrong
+ * @return a newly created alignment
*/
public BasicAlignment createNewAlignment( Object onto1, Object onto2, Class<? extends Relation> relType, Class<?> confType ) throws AlignmentException {
BasicAlignment align = new BasicAlignment();
@@ -680,6 +710,10 @@ public class BasicAlignment implements Alignment, Extensible {
* alignment will contain:
* ( o, o', diff(n,n'), r)
* any pair which is only in the first alignment is preserved.
+ *
+ * @param align: the alignment which is substracted
+ * @throws AlignmentException when something goes wrong
+ * @return the difference between the current alignment and align
*/
public Alignment diff( Alignment align ) throws AlignmentException {
// Could also test: onto1 == getOntologyObject1();
@@ -722,6 +756,9 @@ public class BasicAlignment implements Alignment, Extensible {
/**
* Each cell of @align is contained in this alignment
* no semantics (a semantic predicate would be entails).
+ *
+ * @param align: the alignment for testing containment
+ * @return true is align is contained
*/
public boolean contains( Alignment align ) {
try {
@@ -752,6 +789,11 @@ public class BasicAlignment implements Alignment, Extensible {
* any pair which is in only one alignment is preserved.
*
* This does not pay any attention to the relations used: it returns a random relation!
+ *
+ * @param modality: the aggregation modality
+ * @param aligns: the alignments to be aggregated
+ * @throws AlignmentException when something goes wrong
+ * @return the aggregated alignment
*/
public static Alignment aggregate( String modality, Set<BasicAlignment> aligns ) throws AlignmentException {
// Could also test: onto1 == getOntologyObject1();
@@ -822,6 +864,8 @@ public class BasicAlignment implements Alignment, Extensible {
/**
* Generates a sorted iterator for the alignment
* WARNING: this is quite expensive since it allocates and sort a structure each time
+ *
+ * @return the set of cells in a sorted structure
*/
public TreeSet<Cell> getSortedIterator() {
TreeSet<Cell> result = new TreeSet<Cell>();
@@ -849,6 +893,8 @@ public class BasicAlignment implements Alignment, Extensible {
* alignment will contain:
* ( e, e', meet(n,n'), r)
* any pair which is in only one alignment is discarded.
+ *
+ * @param align:
*/
public Alignment meet( Alignment align ) throws AlignmentException {
// Could also test: onto1 == getOntologyObject1();
@@ -935,6 +981,10 @@ public class BasicAlignment implements Alignment, Extensible {
* any pair (o, o', n, r) in O and (o',o", n', r') in O' the resulting
* alignment will contain:
* ( o, o", join(n,n'), compose(r, r')) iff compose(r,r') exists.
+ *
+ * @param align: the alignment to compose with this one
+ * @return the composed alignments
+ * @throws AlignmentException when something goes wrong (e.g., the two alignments are not connected)
*/
public Alignment compose( Alignment align ) throws AlignmentException {
if ( !onto2.getURI().equals( align.getOntology1URI() ) )
@@ -1028,6 +1078,9 @@ public class BasicAlignment implements Alignment, Extensible {
* is applied, then the ingested alignmment will be modified as well.
* JE: May be a "force" boolean for really ingesting or copying may be
* useful
+ *
+ * @param alignment: the alignment to be included in the current alignment
+ * @throws AlignmentException when something goes wrong
*/
public void ingest( Alignment alignment ) throws AlignmentException {
if ( alignment != null )
@@ -1038,6 +1091,8 @@ public class BasicAlignment implements Alignment, Extensible {
/**
* Generate a copy of this alignment object
* It has the same content but a different id (no id indeed)
+ *
+ * @return a clone of this alignment
*/
public Object clone() {
BasicAlignment align;
@@ -1064,6 +1119,8 @@ public class BasicAlignment implements Alignment, Extensible {
/**
* Returns default exception for conversion to URIAlignments
*
+ * @return a URI alignment corresponding to this alignment
+ * @throws AlignmentException when something goes wrong (the alignment cannot be converted)
*/
public URIAlignment toURIAlignment() throws AlignmentException {
throw new AlignmentException("[BasicAlignment].toURIAlignment() cannot process");
@@ -1073,6 +1130,9 @@ public class BasicAlignment implements Alignment, Extensible {
* This should be rewritten in order to generate the axiom ontology instead
* of printing it! And then use ontology serialization for getting it
* printed.
+ *
+ * @param renderer: the renderer with which to render the alignment
+ * @throws AlignmentException when something goes wrong
*/
public void render( AlignmentVisitor renderer ) throws AlignmentException {
accept(renderer);
@@ -1085,8 +1145,6 @@ public class BasicAlignment implements Alignment, Extensible {
public void cleanUp() {}
/**
- * @param aQuery -- query to be re-written
- * @return -- rewritten query:
* - replaces all entity IRI by their counterpart in the ontology
*
* Caveats:
@@ -1094,6 +1152,9 @@ public class BasicAlignment implements Alignment, Extensible {
* - This does not care for the *:x status of alignments
* - This does work from ontology1 to ontology2, not the other way around
* (use invert() in this case).
+ * @param aQuery -- query to be re-written
+ * @return -- rewritten query:
+ * @throws AlignmentException when something goes wrong
*/
public String rewriteQuery( String aQuery ) throws AlignmentException {
return rewriteSPARQLQuery( aQuery );
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicCell.java b/src/fr/inrialpes/exmo/align/impl/BasicCell.java
index 1d9b96b4232ef5d3df3a801294a4edd91ced1a53..89dd2c3179c1ff049df21d57c05f09dc504e431d 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicCell.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicCell.java
@@ -59,7 +59,15 @@ public class BasicCell implements Cell, Comparable<Cell>, Extensible {
protected double strength = 0;
protected Extensions extensions = null;
- /** Creation **/
+ /** Creation
+ * Creates a correspondence
+ * @param id: the identifier of the correspondence
+ * @param ob1 and
+ * @param ob2 the related objects
+ * @param rel the relation
+ * @param m the confidence measure
+ * @throws AlignmentException when something goes wrong (an object is null, confidence is out of bound...)
+ **/
public BasicCell( String id, Object ob1, Object ob2, Relation rel, double m ) throws AlignmentException {
if ( ob1 == null ) throw new AlignmentException( "object1 cannot be null" );
if ( ob2 == null ) throw new AlignmentException( "object2 cannot be null" );
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicConfidence.java b/src/fr/inrialpes/exmo/align/impl/BasicConfidence.java
index 2315dd59ea4433ebc9ba68d9ed8d1d544ec67525..e822753a35074eb70a92bf81474505e7448ec3ed 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicConfidence.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicConfidence.java
@@ -41,7 +41,7 @@ import org.slf4j.LoggerFactory;
public class BasicConfidence {
final static Logger logger = LoggerFactory.getLogger( BasicConfidence.class );
- /** will never be used
+ /* will never be used
public void accept( TypeCheckingVisitor visitor ) throws AlignmentException {
visitor.visit(this);
}
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicEvaluator.java b/src/fr/inrialpes/exmo/align/impl/BasicEvaluator.java
index 13a84723a10ab1be8f320f3baa429564cb7bc722..42784e46abd1aa7f9366d8e29f2ab49297df392a 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicEvaluator.java
@@ -41,7 +41,13 @@ public abstract class BasicEvaluator implements Evaluator {
protected Alignment align1;
protected Alignment align2;
- /** Creation **/
+ /** Creation
+ * Creates an evaluator
+ *
+ * @param align1 and
+ * @param align2: the two alignments to be evaluated
+ * @throws AlignmentException when something goes wrong (never in this case)
+ **/
public BasicEvaluator( Alignment align1, Alignment align2 ) throws AlignmentException {
this.align1 = align1;
this.align2 = align2;
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java b/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java
index fbcd2758b5c690b36cabe91f1631da46dce068a3..cdf225d4a11a1287787dad66ae1381e39390f5e6 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java
@@ -223,6 +223,8 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
/**
* Clone does some deeper cloning
* It has the same content but a different id (no id indeed)
+ *
+ * @return a new network with the same set of ontologies
*/
public BasicOntologyNetwork copyOnto() {
//public Object clone() {
@@ -235,6 +237,8 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
* Invert all alignments in a network of ontologies
* In fact, this is closing by invert!
* Modifies the network
+ *
+ * @throws AlignmentException when something goes wrong (unlikely)
*/
public void invert() throws AlignmentException {
Vector<Alignment> newal = new Vector<Alignment>();
@@ -245,6 +249,8 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
/**
* Denormalizes an ontology network: suppress all empty alignments
* Modifies the network
+ *
+ * @throws AlignmentException when something goes wrong (unlikely)
*/
public void denormalize() throws AlignmentException {
Vector<Alignment> toremove = new Vector<Alignment>();
@@ -257,6 +263,8 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
/**
* Normalizes an ontology network for it to have exactly one alignment between each pair of ontologies.
* Modifies the network
+ *
+ * @throws AlignmentException when something goes wrong (unlikely)
*/
public void normalize() throws AlignmentException {
for ( OntologyTriple ot1 : ontologies.values() ) {
@@ -281,6 +289,11 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
/**
* This only works on normalised networks (and returns a normalised network)
* Combine all alignments into one (add an alignment to those existing merging everything)
+ *
+ * @param ot1 and
+ * @param ot2: two ontology triples
+ * @param newal: a new alignment to integrate with the alignment between these ontologies
+ * @throws AlignmentException when something goes wrong (unlikely)
*/
protected void mergeAlignments( OntologyTriple ot1, OntologyTriple ot2, Alignment newal ) throws AlignmentException {
Alignment al = getAlignments( ot1, ot2 ).iterator().next();
@@ -299,6 +312,12 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
* Because it depends on (a) the type of alignment and (b) the ontology language
* The code below is OK, but no alignment type is available...
* generateIdAlignment should be a static method of an alignment type depending on the ontology type
+ *
+ * @param reflexive: if the reflexive closure must be performed (non implements)
+ * @param symmetric: if the symmetric closure must be performed
+ * @param transitive: if the transitive closure must be performed
+ * @param params: parameters to pass to closure (currently unused)
+ * @throws AlignmentException when something goes wrong
*/
public void close( boolean reflexive, boolean symmetric, boolean transitive, Properties params ) throws AlignmentException {
normalize();
@@ -334,6 +353,10 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
* & al(o2,o1)-1 o al(o2,o3)
* & ...
* But this assumes symetric closure as well...
+ *
+ * @param params: parameters to pass to closure (currently unused)
+ * @throws AlignmentException when something goes wrong
+ * @return true if the composition has generated new correspondences
*/
protected boolean applyComposition( Properties params ) throws AlignmentException {
boolean change = false;
@@ -365,6 +388,12 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
/**
* Merge all alignments between the same ontology as one (conjunction)
* Create a new alignment...
+ *
+ * @param als: a set of alignments
+ * @param onto1 and
+ * @param onto2: the two ontologies between which these alignments are
+ * @throws AlignmentException when something goes wrong
+ * @return a new alignment equivalent to als, but normalised
*/
protected static Alignment normalizeAlignmentSet( Set<Alignment> als, Ontology<Object> onto1, Ontology<Object> onto2 ) throws AlignmentException {
Alignment result = null;
@@ -392,6 +421,12 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
* What is missing is the transitive closure...
*
* JE: beware: will bug if not provided with BasicOntologyNetworks
+ *
+ * @param on: a network of ontologies
+ * @param onto1 and
+ * @param onto2: the URI of two ontologies between which the alignments will be normalised
+ * @throws AlignmentException when something goes wrong
+ * @return a single new alignment between onto1 and onto2 equivalence to those of the network
*/
public static Alignment getQuasiNormalizedAlignment( OntologyNetwork on, URI onto1, URI onto2 ) throws AlignmentException {
// getAlignments returns a non mutable structure so it has to be copied
@@ -433,6 +468,12 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
* TODO
* Alternative definition!
* {@literal public void match( Class<? extends AlignmentProcess> method, boolean reflexive ) throws AlignmentException}
+ *
+ * @param method: the ontology matching method to use to match
+ * @param reflexive: if alignments have to be found between the same ontology
+ * @param symmetric: if alignments must be computed symmetrically
+ * @param params: parameters passed to the matching method
+ * @throws AlignmentException when something goes wrong
*/
public void match( String method, boolean reflexive, boolean symmetric, Properties params ) throws AlignmentException {
for ( OntologyTriple ot1 : ontologies.values() ) {
@@ -475,6 +516,10 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
/**
* Applies a threshold to all alignments in a network
* Modifies the network
+ *
+ * @param method: the trimming method
+ * @param threshold: the trimming threshold
+ * @throws AlignmentException when something goes wrong
*/
public void trim( String method, double threshold ) throws AlignmentException {
for ( Alignment al : alignments ) {
@@ -489,6 +534,11 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
* So the homomorphism is trivial
*
* TODO: add extensions? i.e., partial clone as BasicAlignment (same in diff and join)
+ *
+ * @param on1 and
+ * @param on2: the two networks to be met
+ * @throws AlignmentException when something goes wrong
+ * @return the result of the meet operation
*/
public static BasicOntologyNetwork meet( OntologyNetwork on1, OntologyNetwork on2 ) throws AlignmentException {
BasicOntologyNetwork result = new BasicOntologyNetwork();
@@ -521,6 +571,11 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
*
* The semantics used is the reduced semantics in which ontologies identified by their URIs can only be matched to themselves
* So the homomorphism is trivial
+ *
+ * @param on1 and
+ * @param on2: the two networks to be substracted
+ * @throws AlignmentException when something goes wrong
+ * @return the result of the diff operation
*/
public static BasicOntologyNetwork diff( OntologyNetwork on1, OntologyNetwork on2 ) throws AlignmentException {
BasicOntologyNetwork result = new BasicOntologyNetwork();
@@ -556,6 +611,11 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
*
* The semantics used is the reduced semantics in which ontologies identified by their URIs can only be matched to themselves
* So the homomorphism is trivial
+ *
+ * @param on1 and
+ * @param on2: the two networks to be joined
+ * @throws AlignmentException when something goes wrong
+ * @return the result of the join operation
*/
public static BasicOntologyNetwork join( OntologyNetwork on1, OntologyNetwork on2 ) throws AlignmentException {
BasicOntologyNetwork result = new BasicOntologyNetwork();
@@ -667,6 +727,10 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
/**
* Parsing
* here we use Jena
+ *
+ * @param uri: the URL of an RDF graph describing a network
+ * @throws AlignmentException when something goes wrong (I/O usually)
+ * @return the network of ontologies that has been read
*/
// Certainly not only URIs for testing reasons
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicParameters.java b/src/fr/inrialpes/exmo/align/impl/BasicParameters.java
index 04a4d02f18b48868686ccff5c924e451b1a136af..c1a26a634e7445f72e2743c5f9e98ac78a5704ab 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicParameters.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicParameters.java
@@ -108,7 +108,7 @@ public class BasicParameters extends Properties implements Parameters, Cloneable
* and p.loadFromXML( new FileInputStream( filename ) )
* which are natural implementers for this.
*/
- public void write(){
+ public void write() {
System.out.println("<?xml version='1.0' ?>");
System.out.println("<Parameters>");
for ( Entry<Object,Object> e : entrySet() ) {
@@ -119,6 +119,8 @@ public class BasicParameters extends Properties implements Parameters, Cloneable
/**
* displays the current parameters (debugging)
+ *
+ * @param stream: the stream in which to display the parameters
*/
public void displayParameters( PrintStream stream ){
stream.println("Parameters:");
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicRelation.java b/src/fr/inrialpes/exmo/align/impl/BasicRelation.java
index ec677cfbfaa1678e3f870fc110c5f3d5d8174e9f..2aae271ffc2e24d9b2f0f5bbe7f0fb7f86c97f27 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicRelation.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicRelation.java
@@ -126,6 +126,8 @@ public class BasicRelation implements Relation {
/**
* The name to use if no other information is available
+ *
+ * @return the name of the relation class
*/
public String getClassName() {
return getClass().toString();
@@ -141,6 +143,10 @@ public class BasicRelation implements Relation {
/**
* The constructor to use
+ *
+ * @param rel: the string representation of the relation
+ * @return the corresponding relation object
+ * @throws AlignmentException if something goes wrong (e.g., rel cannot be interpreted)
*/
public static BasicRelation createRelation( String rel ) throws AlignmentException {
Class<?> relationClass = getClass( rel );
@@ -162,17 +168,31 @@ public class BasicRelation implements Relation {
}
}
- /** By default the inverse is the relation itself **/
+ /**
+ * By default the inverse is the relation itself
+ *
+ * @return the inverse of the relation
+ **/
public Relation inverse() {
return this;
}
- /** By default... no composition possible **/
+ /**
+ * By default... no composition possible
+ *
+ * @param r: a relation with which to compose
+ * @return this relation composed with r
+ **/
public Relation compose( Relation r ) {
return null;
}
- /** By default... meet if equals **/
+ /**
+ * By default... meet if equals
+ *
+ * @param rels: a set of relations to meet with this one
+ * @return the relation which is the result of the meet
+ **/
public BasicRelation meet( Relation... rels ) {
for( Relation r : rels ) {
if ( !this.equals( r ) ) return null;
@@ -180,7 +200,13 @@ public class BasicRelation implements Relation {
return this;
}
- /** By default... we are not in disjunctive relations... then returns null **/
+ /**
+ * By default... we are not in disjunctive relations... then returns null
+ *
+ *
+ * @param rels: a set of relations to join with this one
+ * @return the relation which is the result of the join
+ **/
public BasicRelation join( Relation... rels ) {
for( Relation r : rels ) {
if ( !this.equals( r ) ) return null;
@@ -188,10 +214,19 @@ public class BasicRelation implements Relation {
return this;
}
- /** Housekeeping **/
+ /**
+ * Housekeeping
+ *
+ * @param h: the content handler in which to dump the relation
+ **/
public void dump( ContentHandler h ){};
- /** This is kept for displayig more correctly the result **/
+ /**
+ * This is kept for displayig more correctly the result
+ *
+ *
+ * @param writer: the writer where to print the result
+ **/
public void write( PrintWriter writer ) {
if ( relation != null ) {
writer.print( relation );
@@ -202,7 +237,12 @@ public class BasicRelation implements Relation {
}
}
- /** Are the two relations equal **/
+ /**
+ * Are the two relations equal
+ *
+ * @param o: an object with which to compare this one
+ * @return true is o is equal to this object
+ **/
public boolean equals( Object o ) {
if ( o == this ) return true;
if ( o == null ) return false;
diff --git a/src/fr/inrialpes/exmo/align/impl/BitSetAlgebraRelation.java b/src/fr/inrialpes/exmo/align/impl/BitSetAlgebraRelation.java
index 64aa3fb5aa55d708f1ebb26f1b0d589c9935adb2..3589258b79db4320628239cdbafa4e77cf53cb52 100644
--- a/src/fr/inrialpes/exmo/align/impl/BitSetAlgebraRelation.java
+++ b/src/fr/inrialpes/exmo/align/impl/BitSetAlgebraRelation.java
@@ -50,6 +50,9 @@ public abstract class BitSetAlgebraRelation<T extends BaseRelation> extends BitS
/**
* composition
+ *
+ * @param dr: a bitset relation to compose with this one
+ * @return the bitset corresponding to the composed relation
*/
public BitSet protocompose( BitSetAlgebraRelation<T> dr ) {
BitSet bs = createSet();
@@ -67,7 +70,11 @@ public abstract class BitSetAlgebraRelation<T extends BaseRelation> extends BitS
protected abstract BitSet compose( T r1, T r2 );
- /** inverse, could potentially go to Disjunctive */
+ /**
+ * inverse, could potentially go to Disjunctive
+ *
+ * @return the bitset corresponding to the relation inverse to this one
+ */
protected BitSet protoinverse() {
BitSet bs = createSet();
for( T r : this ) {
diff --git a/src/fr/inrialpes/exmo/align/impl/BitSetDisjunctiveRelation.java b/src/fr/inrialpes/exmo/align/impl/BitSetDisjunctiveRelation.java
index a436d927392cc8f2794336ffc6bf4cc2236f80aa..a3850ccb64233665531fd49209b01bfb018c9d03 100644
--- a/src/fr/inrialpes/exmo/align/impl/BitSetDisjunctiveRelation.java
+++ b/src/fr/inrialpes/exmo/align/impl/BitSetDisjunctiveRelation.java
@@ -84,7 +84,12 @@ public abstract class BitSetDisjunctiveRelation<T extends BaseRelation> extends
return new RelationIterator<T>();
}
- /** intersection */
+ /**
+ * intersection
+ *
+ * @param drs: a set of bitset disjunctive relations to be intersected
+ * @return the bitset corresponding to the intersected relation
+ */
@SafeVarargs protected final BitSet protojoin( BitSetDisjunctiveRelation<T>... drs ) {
BitSet bs = (BitSet)relset.clone();
for( BitSetDisjunctiveRelation<T> dr : drs ) {
@@ -97,7 +102,12 @@ public abstract class BitSetDisjunctiveRelation<T extends BaseRelation> extends
throw new AlignmentException( "Cannot join relations from heterogeneous algebras" );
}
- /** union */
+ /**
+ * union
+ *
+ * @param drs: a set of bitset disjunctive relations to be met
+ * @return the bitset corresponding to the met relations
+ */
@SafeVarargs protected final BitSet protomeet( BitSetDisjunctiveRelation<T>... drs ) {
BitSet bs = (BitSet)relset.clone();
for( BitSetDisjunctiveRelation<T> dr : drs ) {
@@ -110,7 +120,12 @@ public abstract class BitSetDisjunctiveRelation<T extends BaseRelation> extends
throw new AlignmentException( "Cannot meet relations from heterogeneous algebras" );
}
- /** complement */
+ /**
+ * complement
+ *
+ * @param dr: a set of bitset disjunctive relations to be complemented
+ * @return the bitset corresponding to the complemented relation
+ */
protected BitSet protocompl( BitSetDisjunctiveRelation<T> dr ) {
BitSet bs = (BitSet)relset.clone();
//for( int i=0; i < size; i++ ) bs.flip( i );
diff --git a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java b/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
index e0733f15027f0bbe1b27fd925da97f72c31ec55f..95bd6004f30123357dc86a59ad9630d638e0a8f8 100644
--- a/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/DistanceAlignment.java
@@ -85,6 +85,8 @@ public abstract class DistanceAlignment extends ObjectAlignment implements Align
/**
* Prints the distance matrix
+ *
+ * @param params: the parameters of the distance
*/
public void printDistanceMatrix( Properties params ){
String algName = params.getProperty("algName");
@@ -120,6 +122,8 @@ public abstract class DistanceAlignment extends ObjectAlignment implements Align
/**
* Extract the alignment form the Similarity
+ *
+ * @param type: the type of alignment to extract:
* There are theoretically 16 types of extractors composing the
* characteristics
* [q]estion mark = ?, one or zero relation
@@ -131,6 +135,9 @@ public abstract class DistanceAlignment extends ObjectAlignment implements Align
* ** (covering ++, *+ and +*)
* ?* (covering 1*, 1+ and ?+)
* *? (covering +?, *1 and +1)
+ * @param params: the parameter of the measure
+ * @throws AlignmentException when something goes wrong
+ * @return the extracted alignment
*/
public Alignment extract(String type, Properties params) throws AlignmentException {
double threshold = 0.;
@@ -153,6 +160,10 @@ public abstract class DistanceAlignment extends ObjectAlignment implements Align
* Extract the alignment of a ?* type
* Non symmetric: for each entity of onto1, take the highest if superior to threshold
* Complexity: O(n^2)
+ *
+ * @param threshold: the threshold to apply to extracted correspondences
+ * @param params: the parameter of the measure
+ * @return the extracted alignment
*/
// JE: Yes, could only be implemented by copying the code...
public Alignment extractsq( double threshold, Properties params) {
@@ -228,6 +239,10 @@ public abstract class DistanceAlignment extends ObjectAlignment implements Align
* Extract the alignment of a ** type
* Symmetric: return all elements above threshold
* Complexity: O(n^2)
+ *
+ * @param threshold: the threshold to apply to extracted correspondences
+ * @param params: the parameter of the measure
+ * @return the extracted alignment
*/
@SuppressWarnings({"unchecked","rawTypes"}) //ConcatenatedIterator
public Alignment extractss( double threshold, Properties params) {
@@ -285,6 +300,10 @@ public abstract class DistanceAlignment extends ObjectAlignment implements Align
* raise problems:
* - It invert column and rows when nbrows > nbcol (Hungarian loops)
* - It prevents to generate alignments when one category has no elements.
+ *
+ * @param threshold: the threshold to apply to extracted correspondences
+ * @param params: the parameter of the measure
+ * @return the extracted alignment
*/
@SuppressWarnings({"unchecked","rawTypes"}) //ConcatenatedIterator
public Alignment extractqq( double threshold, Properties params) {
@@ -462,6 +481,10 @@ public abstract class DistanceAlignment extends ObjectAlignment implements Align
* This algorithm will select the first and last correspondances of
* overall similarity 1.1, while the optimum is the second solution
* with overall of 1.8.
+ *
+ * @param threshold: the threshold to apply to extracted correspondences
+ * @param params: the parameter of the measure
+ * @return the extracted alignment
*/
@SuppressWarnings({"unchecked","rawTypes"}) //ConcatenatedIterator
public Alignment extractqqgreedy( double threshold, Properties params) {
diff --git a/src/fr/inrialpes/exmo/align/impl/Extensible.java b/src/fr/inrialpes/exmo/align/impl/Extensible.java
index d125f5c24c752296ff973239f35b5fc13b01ef57..18afccd6fa6745f7337b9bf14e80f233a0fe6160 100644
--- a/src/fr/inrialpes/exmo/align/impl/Extensible.java
+++ b/src/fr/inrialpes/exmo/align/impl/Extensible.java
@@ -37,6 +37,8 @@ public interface Extensible {
* to the alignment structure itself.
* getExtensions returns a set of tripes: uri*label*value
* all three being String
+ *
+ * @return a collection of tripes: uri*label*value implemented as String[]
*/
public Collection<String[]> getExtensions();
diff --git a/src/fr/inrialpes/exmo/align/impl/InstanceBasedMatrixMeasure.java b/src/fr/inrialpes/exmo/align/impl/InstanceBasedMatrixMeasure.java
index ab50e6515739ca6149638d556a103c412b9c7623..dde23e644c45b640a8c008d7c65145446016d553 100644
--- a/src/fr/inrialpes/exmo/align/impl/InstanceBasedMatrixMeasure.java
+++ b/src/fr/inrialpes/exmo/align/impl/InstanceBasedMatrixMeasure.java
@@ -111,6 +111,8 @@ public abstract class InstanceBasedMatrixMeasure extends MatrixMeasure {
* This is the empty method of this abstract class
* it must compute the instance distance
* and fill the adequate indmatrix with these distances.
+ *
+ * @param params: the parameters of the distance (e.g., cmeasure)
*/
public abstract void computeInstanceDistance( Properties params );
diff --git a/src/fr/inrialpes/exmo/align/impl/ObjectCell.java b/src/fr/inrialpes/exmo/align/impl/ObjectCell.java
index 27bc7730f62f8a72d69d3621e53a7fb2cb136cd1..49be6998f4f942c8fcd50e4915095b963478c16d 100644
--- a/src/fr/inrialpes/exmo/align/impl/ObjectCell.java
+++ b/src/fr/inrialpes/exmo/align/impl/ObjectCell.java
@@ -50,7 +50,16 @@ public class ObjectCell extends BasicCell {
// visitor.visit( this );
//}
- /** Creation **/
+ /**
+ * Creation
+ *
+ * @param id: the identifier of the correspondence (may be null)
+ * @param ob1 and
+ * @param ob2: the two objects related by the correspondence
+ * @param rel: the relation between the objects
+ * @param m: the confidence measure in the correspondence
+ * @throws AlignmentException when something goes wrong (e.g., confidence out of bounds)
+ **/
public ObjectCell( String id, Object ob1, Object ob2, Relation rel, double m ) throws AlignmentException {
super( id, ob1, ob2, rel, m );
};
diff --git a/src/fr/inrialpes/exmo/align/impl/Similarity.java b/src/fr/inrialpes/exmo/align/impl/Similarity.java
index c2e26ebb92fd906102e684b686153f29101f6c9f..5c388eb2dc14b6d460aea47154d7bd251e6ad423 100644
--- a/src/fr/inrialpes/exmo/align/impl/Similarity.java
+++ b/src/fr/inrialpes/exmo/align/impl/Similarity.java
@@ -39,23 +39,34 @@ public interface Similarity
// ontology1 and ontology2
/**
* Is it a similarity or a distance?
+ *
+ * @return true if the object represent a similarity (otherwise, it is a distance)
*/
public boolean getSimilarity();
// JE: OntoRewr: This should not be in init
/**
* Initialize the similarity value with various useful structures
+ *
+ * @param onto1 and
+ * @param onto2: the two ontologies which are matched
*/
public void initialize( LoadedOntology<Object> onto1, LoadedOntology<Object> onto2 );
public void initialize( LoadedOntology<Object> onto1, LoadedOntology<Object> onto2, Alignment align );
/**
* actually computes the similarity and store it in the adequate structures
+ *
+ * @param p: the parameters of the measure to compute
*/
public void compute( Properties p );
/**
* Accessors to the stored similarity values
+ *
+ * @param c1 and
+ * @param c2: the two objects for which computing the similarity
+ * @return the measure value
*/
public double getClassSimilarity( Object c1, Object c2 );
public double getPropertySimilarity( Object p1, Object p2);
@@ -63,6 +74,8 @@ public interface Similarity
/**
* Printers of the obtained similarity values
+ *
+ * @param type: the type of layout of the printout
*/
public void printClassSimilarityMatrix( String type );
public void printPropertySimilarityMatrix( String type );
diff --git a/src/fr/inrialpes/exmo/align/impl/URICell.java b/src/fr/inrialpes/exmo/align/impl/URICell.java
index 8a3146e6a97a5d3a739521d48ecb21627750ba55..33215c7f3a9b423a6069b30e30c04fb3974b5205 100644
--- a/src/fr/inrialpes/exmo/align/impl/URICell.java
+++ b/src/fr/inrialpes/exmo/align/impl/URICell.java
@@ -50,11 +50,19 @@ public class URICell extends BasicCell {
visitor.visit( this );
}
- /** Creation **/
+ /**
+ * Creation
+ *
+ * @param id: the identifier of the correspondence (may be null)
+ * @param ob1 and
+ * @param ob2: the URI of the two objects related by the correspondence
+ * @param rel: the relation between the objects
+ * @param m: the confidence measure in the correspondence
+ * @throws AlignmentException when something goes wrong (e.g., confidence out of bounds)
+ **/
// public URICell( Object ob1, Object ob2 ) throws AlignmentException {
// super( ob1, ob2 );
// };
-
public URICell( String id, URI ob1, URI ob2, Relation rel, double m ) throws AlignmentException {
super( id, ob1, ob2, rel, m );
}
diff --git a/src/fr/inrialpes/exmo/align/impl/aggr/BasicAggregator.java b/src/fr/inrialpes/exmo/align/impl/aggr/BasicAggregator.java
index 8ebaa717797675747ba5bd90b1dd8af77abf9a1d..a0183dfd8e756a3d122518b051ab33ecb768ab06 100644
--- a/src/fr/inrialpes/exmo/align/impl/aggr/BasicAggregator.java
+++ b/src/fr/inrialpes/exmo/align/impl/aggr/BasicAggregator.java
@@ -77,6 +77,9 @@ public abstract class BasicAggregator extends BasicAlignment {
/**
* Record the content of alignments.
+ *
+ * @param al: an alignment to intergrate
+ * @throws AlignmentException when something goes wrong (e.g., ontologies are different)
*/
public void ingest( BasicAlignment al ) throws AlignmentException {
Ontology<? extends Object> onto1 = getOntologyObject1();
@@ -106,6 +109,8 @@ public abstract class BasicAggregator extends BasicAlignment {
/**
* Extract the alignment from consensus
* This has to be implemented in concrete classes
+ *
+ * @throws AlignmentException when something goes wrong
*/
public abstract void extract() throws AlignmentException;
@@ -115,6 +120,9 @@ public abstract class BasicAggregator extends BasicAlignment {
* NOTE: It may be worth to consider that the relations do not have to
* be equal but could be more specific or general than one another.
* This could typically be made with algebras of relations.
+ *
+ * @param c: a cell to test the presence in the current aggregation
+ * @return the cell corresponding to c if it exists, null otherwise
*/
public Cell isAlreadyThere( Cell c ){
try {
diff --git a/src/fr/inrialpes/exmo/align/impl/edoal/ClassId.java b/src/fr/inrialpes/exmo/align/impl/edoal/ClassId.java
index fc65b0e98069d281e1dc1971f0b1cfe19b928a2d..09b1f86c14db5f903832d6beed11006a7f9712c3 100644
--- a/src/fr/inrialpes/exmo/align/impl/edoal/ClassId.java
+++ b/src/fr/inrialpes/exmo/align/impl/edoal/ClassId.java
@@ -88,14 +88,11 @@ public class ClassId extends ClassExpression implements Id {
}
/**
- * <p>
- * Returns a simple description of this object. <b>The format of the
+ * @return a simple description of this object.
+ * <b>The format of the
* returned String is undocumented and subject to change.</b>
- * <p>
- * <p>
* An expamle return String could be:
* <code>classId: http://my/super/class</code>
- * </p>
*/
public String toString() {
return "classId: " + id;
diff --git a/src/fr/inrialpes/exmo/align/impl/edoal/EDOALAlignment.java b/src/fr/inrialpes/exmo/align/impl/edoal/EDOALAlignment.java
index bb470c6deea72171aa9d96a7799a6a2b2dc62f37..99be16db4be9c555fc2e6f1be88457eceb8d0a5d 100644
--- a/src/fr/inrialpes/exmo/align/impl/edoal/EDOALAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/edoal/EDOALAlignment.java
@@ -265,6 +265,10 @@ public class EDOALAlignment extends BasicAlignment {
/**
* convert an URI alignment into a corresponding EDOALAlignment
* The same could be implemented for ObjectAlignent if necessary
+ *
+ * @param onto: the URI of the ontology to load
+ * @return the loaded ontology
+ * @throws AlignmentException when something goes wrong (ontology not loadable)
*/
// This works for any BasicAlignment but will return an empty
// alignment if they do not have proper URI dereferencing.
@@ -319,7 +323,10 @@ public class EDOALAlignment extends BasicAlignment {
}
/**
* The EDOALAlignment has LoadedOntologies as ontologies
- */
+ *
+ * @param al: an alignment to convert as an EDOALAlignement
+ * @throws AlignmentException when something goes wrong (typically cannot access the aligned ontologies)
+ */
public void convertToEDOAL( BasicAlignment al ) throws AlignmentException {
setType( al.getType() );
setExtensions( al.getExtensionsObject().convertExtension( "toEDOAL", "fr.inrialpes.exmo.align.edoal.EDOALAlignment#toEDOAL" ) );
@@ -362,6 +369,8 @@ public class EDOALAlignment extends BasicAlignment {
/**
* Generate a copy of this alignment object
+ *
+ * @return a clone of this alignment
*/
// JE: this is a mere copy of the method in BasicAlignement
// It has two difficulties
diff --git a/src/fr/inrialpes/exmo/align/impl/edoal/EDOALCell.java b/src/fr/inrialpes/exmo/align/impl/edoal/EDOALCell.java
index 83074c1429bba79aa201069438e6c4b23bb396a0..edac79b339a782d69b59991d1c09a6112a129336 100644
--- a/src/fr/inrialpes/exmo/align/impl/edoal/EDOALCell.java
+++ b/src/fr/inrialpes/exmo/align/impl/edoal/EDOALCell.java
@@ -55,7 +55,16 @@ public class EDOALCell extends BasicCell {
visitor.visit( this );
}
- /** Creation **/
+ /**
+ * Creation
+ *
+ * @param id: the identifier of the correspondence (may be null)
+ * @param ob1 and
+ * @param ob2: the two EDOAL expressions related by the correspondence
+ * @param rel: the relation between the objects
+ * @param m: the confidence measure in the correspondence
+ * @throws AlignmentException when something goes wrong (e.g., confidence out of bounds)
+ **/
public EDOALCell( String id, Expression ob1, Expression ob2, Relation rel, double m ) throws AlignmentException {
super( id, (Object)ob1, (Object)ob2, rel, m );
};
@@ -84,6 +93,8 @@ public class EDOALCell extends BasicCell {
/**
* May be null
+ *
+ * @return the set of transformations attached to this correspondence
*/
public Set<Transformation> transformations() {
return transformations;
@@ -95,6 +106,11 @@ public class EDOALCell extends BasicCell {
}
linkkeys.add( linkkey );
}
+ /**
+ * May be null
+ *
+ * @return the set of link keys attached to this correspondence
+ */
public Set<Linkkey> linkkeys() {
return linkkeys;
}
diff --git a/src/fr/inrialpes/exmo/align/impl/edoal/InstanceId.java b/src/fr/inrialpes/exmo/align/impl/edoal/InstanceId.java
index 57771bab0a1ff19282299e04d8c39dc041beef92..7eedb6374c4b410f5d352386d238fbc35be3f0c2 100644
--- a/src/fr/inrialpes/exmo/align/impl/edoal/InstanceId.java
+++ b/src/fr/inrialpes/exmo/align/impl/edoal/InstanceId.java
@@ -85,14 +85,11 @@ public class InstanceId extends InstanceExpression implements Id {
/**
- * <p>
- * Returns a simple description of this object. <b>The format of the
+ * @return a simple description of this object.
+ * <b>The format of the
* returned String is undocumented and subject to change.</b>
- * <p>
- * <p>
* An expamle return String could be:
- * <code>instanceId: http://my/super/instance</code>
- * </p>
+ * <code>InstanceId: http://my/super/instance</code>
*/
public String toString() {
return "instanceId: " + uri;
diff --git a/src/fr/inrialpes/exmo/align/impl/edoal/PropertyId.java b/src/fr/inrialpes/exmo/align/impl/edoal/PropertyId.java
index 3ab1c6aa50664af21d58a9ad5d0a0093d3b832e4..18ef1f732ce6d95666938a461dba6d59378f330c 100644
--- a/src/fr/inrialpes/exmo/align/impl/edoal/PropertyId.java
+++ b/src/fr/inrialpes/exmo/align/impl/edoal/PropertyId.java
@@ -72,14 +72,11 @@ public class PropertyId extends PropertyExpression implements Id {
}
/**
- * <p>
- * Returns a simple description of this object. <b>The format of the
+ * @return a simple description of this object.
+ * <b>The format of the
* returned String is undocumented and subject to change.</b>
- * <p>
- * <p>
- * An expamle return String could be:
- * <code>attributeId: http://my/super/attribute</code>
- * </p>
+ * An example return String could be:
+ * <code>PropertyId: http://my/super/property</code>
*/
public String toString() {
return "PropertyId: " + id;
diff --git a/src/fr/inrialpes/exmo/align/impl/edoal/RelationId.java b/src/fr/inrialpes/exmo/align/impl/edoal/RelationId.java
index 11767bc4714adca78d62f5febaab552379ae7dc6..e28bc422dd50d8406e0451adbfb0fb26c990f1ae 100644
--- a/src/fr/inrialpes/exmo/align/impl/edoal/RelationId.java
+++ b/src/fr/inrialpes/exmo/align/impl/edoal/RelationId.java
@@ -84,14 +84,11 @@ public class RelationId extends RelationExpression implements Id {
}
/**
- * <p>
- * Returns a simple description of this object. <b>The format of the
+ * @return a simple description of this object.
+ * <b>The format of the
* returned String is undocumented and subject to change.</b>
- * <p>
- * <p>
- * An expamle return String could be:
- * <code>RelationId: http://my/super/class</code>
- * </p>
+ * An example return String could be:
+ * <code>RelationId: http://my/super/relation</code>
*/
public String toString() {
return "RelationId: " + id;
diff --git a/src/fr/inrialpes/exmo/align/impl/edoal/Transformation.java b/src/fr/inrialpes/exmo/align/impl/edoal/Transformation.java
index 83c72c30fc774633d5a12cc30b71898bac1ce5df..7510394d07a5f2677dffd85b5f32eae88eb4f993 100644
--- a/src/fr/inrialpes/exmo/align/impl/edoal/Transformation.java
+++ b/src/fr/inrialpes/exmo/align/impl/edoal/Transformation.java
@@ -47,7 +47,14 @@ public class Transformation {
return visitor.visit(this);
}
- /** Creation **/
+ /**
+ * Creation
+ *
+ * @param type: the direction of the transformation
+ * @param ob1 and
+ * @param ob2: the two components of the transformation
+ * @throws AlignmentException when something goes wrong (unlikely)
+ **/
public Transformation( String type, ValueExpression ob1, ValueExpression ob2 ) throws AlignmentException {
this.type = type;
expr1 = ob1;
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/AveragePRGraphEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/AveragePRGraphEvaluator.java
index 97cd78c3a2bf800eba61a6945a7743860caa2c35..ad7800b20c7fd610adb8c95ef3d6ad77e6f02a34 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/AveragePRGraphEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/AveragePRGraphEvaluator.java
@@ -33,6 +33,8 @@ import java.util.SortedSet;
import java.util.Comparator;
import java.util.Vector;
import java.io.PrintWriter;
+import java.io.IOException;
+
import java.net.URI;
import org.slf4j.Logger;
@@ -190,8 +192,11 @@ public class AveragePRGraphEvaluator extends GraphEvaluator {
/**
* This output the result
+ *
+ * @param writer: the writer where to print the result
+ * @throws IOException when something goes wrong
*/
- public void write(PrintWriter writer) throws java.io.IOException {
+ public void write(PrintWriter writer) throws IOException {
writer.println("<?xml version='1.0' encoding='utf-8' standalone='yes'?>");
writer.println("<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'>");
writer.println(" <output rdf:about=''>");
@@ -206,9 +211,12 @@ public class AveragePRGraphEvaluator extends GraphEvaluator {
writer.print(" </output>\n</rdf:RDF>\n");
}
- /* Write out the final interpolated recall/precision graph data.
+ /**
+ * Write out the final interpolated recall/precision graph data.
* One line for each recall/precision point in the form: 'R-value P-value'.
* This is the format needed for GNUPLOT.
+ *
+ * @param writer: the writer where to print the result
*/
public void writePlot( PrintWriter writer ) {
for(int i = 0; i < STEP+1; i++){
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/DiffEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/DiffEvaluator.java
index 799a72dc066198401042bfae607e51875e8dc932..a6f4d6f6a52465ad83a9286d1d25963326a66889 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/DiffEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/DiffEvaluator.java
@@ -67,6 +67,7 @@ public class DiffEvaluator extends BasicEvaluator implements Evaluator {
* @param align2 : the alignment to evaluate
* The two parameters are transformed into URIAlignment before being processed
* Hence, if one of them is modified after initialisation, this will not be taken into account.
+ * @throws AlignmentException when something goes wrong
**/
public DiffEvaluator(Alignment align1, Alignment align2) throws AlignmentException {
super(((BasicAlignment)align1).toURIAlignment(), ((BasicAlignment)align2).toURIAlignment());
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/ExtPREvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/ExtPREvaluator.java
index 9fd989754f6fb26aaab7cda05bd02c3f11d2c10e..07b045faa229d50a49d4d048a39e78c920b48ba2 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/ExtPREvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/ExtPREvaluator.java
@@ -37,7 +37,9 @@ import fr.inrialpes.exmo.ontowrap.OntowrapException;
import java.util.Properties;
import java.util.HashSet;
import java.util.Set;
+
import java.io.PrintWriter;
+import java.io.IOException;
import java.net.URI;
@@ -106,7 +108,14 @@ public class ExtPREvaluator extends BasicEvaluator implements Evaluator {
private boolean withConfidence = true;
private boolean relsensitive = false;
- /** Creation **/
+ /**
+ * Creation
+ *
+ * @param align1 and
+ * @param align2: two alignments on which extended precision and recall will be computed
+ * @throws AlignmentException when something goes wrong
+ *
+ **/
public ExtPREvaluator(Alignment align1, Alignment align2) throws AlignmentException {
super(align1, align2);
convertToObjectAlignments( align1, align2 );
@@ -210,6 +219,10 @@ public class ExtPREvaluator extends BasicEvaluator implements Evaluator {
* the similarity is symALPHA^(val1+val2), symALPHA being lower than 1.
* valx is the length of the subclass chain.
* Table 1 (and 2) of [Ehrig and Euzenat 2005]
+ *
+ * @param c1: the cell whose similarity is measured
+ * @param s2: alignment against which similarity is computed
+ * @return the symmetric similarity
*/
protected double computeSymSimilarity( Cell c1, Alignment s2 ){
double sim = 0; // the similarity between the pair of elements
@@ -254,6 +267,10 @@ public class ExtPREvaluator extends BasicEvaluator implements Evaluator {
* Effort-based relaxed precision and recal similarity
* Note: it will be better if the parameters were replaced by the actual sibling (choice)
* Table 3 of [Ehrig2005]
+ *
+ * @param c1: the cell whose similarity is measured
+ * @param s2: alignment against which similarity is computed
+ * @return the effort-based similarity
*/
protected double computeEffSimilarity( Cell c1, Alignment s2 ){
double sim = 0; // the similarity between the pair of elements
@@ -300,6 +317,10 @@ public class ExtPREvaluator extends BasicEvaluator implements Evaluator {
/**
* Oriented relaxed precision and recal similarity
* Table 4 (and 5) of [Ehrig and Euzenat 2005]
+ *
+ * @param c1: the cell whose similarity is measured
+ * @param s2: alignment against which similarity is computed
+ * @return the precision-oriented similarity
*/
protected double computePrecisionOrientedSimilarity( Cell c1, Alignment s2 ){
double sim = 0; // the similarity between the pair of elements
@@ -353,6 +374,10 @@ public class ExtPREvaluator extends BasicEvaluator implements Evaluator {
/**
* Oriented relaxed precision and recal similarity
* Table 6 (and 7) of [Ehrig and Euzenat 2005]
+ *
+ * @param c1: the cell whose similarity is measured
+ * @param s2: alignment against which similarity is computed
+ * @return the recall-oriented similarity
*/
protected double computeRecallOrientedSimilarity( Cell c1, Alignment s2 ){
double sim = 0; // the similarity between the pair of elements
@@ -404,10 +429,16 @@ public class ExtPREvaluator extends BasicEvaluator implements Evaluator {
}
/**
- * Returns the relative position of two entities:
+ * Returns the relative position of two entities in an ontology
+ *
+ * @param o1 and
+ * @param o2: two objects the position of which is computed
+ * @param onto: the ontology to which the objects belong
+ * @return the relative position:
* 0: unrelated
* n: o1 is a n-step sub-entity of o2
* -n: o2 is a n-step sub-entity of o1
+ * @throws AlignmentException when something goes wrong (typically objects do not belong to the ontology)
*/
protected int relativePosition( Object o1, Object o2, HeavyLoadedOntology<Object> onto ) throws AlignmentException {
try {
@@ -436,6 +467,12 @@ public class ExtPREvaluator extends BasicEvaluator implements Evaluator {
*
* This would require computing the transitive reduction of the superClass
* relation which is currently returned by HeavyLoadedOntology.
+ *
+ * @param class1 and
+ * @param class2: two classes superclass relationship is tested
+ * @param ontology: the ontology to which the classes belong
+ * @return the relation between these classes
+ * @throws AlignmentException when something goes wrong
*/
@SuppressWarnings({"unchecked"})
public int isSuperClass( Object class1, Object class2, HeavyLoadedOntology<Object> ontology ) throws AlignmentException {
@@ -505,8 +542,11 @@ public class ExtPREvaluator extends BasicEvaluator implements Evaluator {
/**
* This now output the results in Lockheed format.
+ *
+ * @param writer: the writer where to print the result
+ * @throws IOException when something goes wrong
*/
- public void write(PrintWriter writer) throws java.io.IOException {
+ public void write(PrintWriter writer) throws IOException {
writer.println("<?xml version='1.0' encoding='utf-8' standalone='yes'?>");
writer.println("<"+SyntaxElement.RDF.print()+" xmlns:"+Namespace.RDF.shortCut+"='"+Namespace.RDF.prefix+"'\n xmlns:"+Namespace.ATLMAP.shortCut+"='"+Namespace.ATLMAP.prefix+"'>");
writer.println(" <"+Namespace.ATLMAP.shortCut+":output "+SyntaxElement.RDF_ABOUT.print()+"=''>");
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/GraphEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/GraphEvaluator.java
index d257af41d0608ee6dc703d33286b004ea8b3b73f..35391b846a03db0f6811065778f6c44f01590dbb 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/GraphEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/GraphEvaluator.java
@@ -34,6 +34,7 @@ import java.util.Vector;
import java.util.SortedSet;
import java.util.Comparator;
import java.io.PrintWriter;
+import java.io.IOException;
import java.net.URI;
import org.slf4j.Logger;
@@ -73,15 +74,20 @@ public abstract class GraphEvaluator {
public boolean invalid = true;
/**
- * Returns the points to display in a graph
+ * @return the points to display in a graph
+ * @throws AlignmentException when something goes wrong
*/
public abstract Vector<Pair> eval() throws AlignmentException;
/**
- * Returns the points to display in a graph
+ * @param params: display parameters
+ * @return the points to display in a graph
+ * @throws AlignmentException when something goes wrong
*/
public abstract Vector<Pair> eval( Properties params ) throws AlignmentException;
/**
* Retuns a simple global evaluation measure if any
+ *
+ * @return a global value assessing the result
*/
public abstract double getGlobalResult();
@@ -146,9 +152,11 @@ public abstract class GraphEvaluator {
}
}
- /*
- * Tells if the cell is found in the reference alignment
- * (without relation consideration)
+ /**
+ * Integrate the cells of the alignment to evaluate in cellSet if the cell is found in the reference alignment
+ *
+ * @param al: the alignment to evaluate
+ * @param ref: the reference alignment
*/
public void ingest( Alignment al, Alignment ref ){
nbexpected += ref.nbCells();
@@ -167,9 +175,13 @@ public abstract class GraphEvaluator {
else return cellSet.size();
}
- /*
+ /**
* Tells if the cell is found in the reference alignment
* (without relation consideration)
+ *
+ * @param c: the cell to consider
+ * @param ref: the reference alignment
+ * @return true if the cell is correct
*/
public boolean isCorrect( Cell c, Alignment ref ) {
try {
@@ -190,8 +202,11 @@ public abstract class GraphEvaluator {
/**
* This output the resulting plot in XML
+ *
+ * @param writer: the writer where to print the result
+ * @throws IOException when something goes wrong
*/
- public void writeXMLMap( PrintWriter writer) throws java.io.IOException {
+ public void writeXMLMap( PrintWriter writer) throws IOException {
for( Pair precrec: points ) {
writer.print(" <step>\n <x>");
writer.print( precrec.getX() );
@@ -201,9 +216,12 @@ public abstract class GraphEvaluator {
}
}
- /* Write out the final interpolated recall/precision graph data.
+ /**
+ * Write out the final interpolated recall/precision graph data.
* One line for each recall/precision point in the form: 'R-value P-value'.
* This is the format needed for GNUPLOT.
+ *
+ * @param writer: the writer where to print the result
*/
public void writePlot( PrintWriter writer ) {
for( Pair p : points ){
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java
index c74e7163d6c59cfa0eed4d2c6256662600721508..3716c891ec490a4d351fa6024213ff7cc11e9134 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/PRGraphEvaluator.java
@@ -34,7 +34,10 @@ import java.util.Set;
import java.util.SortedSet;
import java.util.Comparator;
import java.util.Vector;
+
import java.io.PrintWriter;
+import java.io.IOException;
+
import java.net.URI;
import org.slf4j.Logger;
@@ -79,6 +82,8 @@ public class PRGraphEvaluator extends GraphEvaluator {
/**
* Compute precision and recall graphs.
+ *
+ * @return the points to display in a graph
*/
public Vector<Pair> eval() { // throws AlignmentException
return eval( (Properties)null );
@@ -86,6 +91,9 @@ public class PRGraphEvaluator extends GraphEvaluator {
/**
* Compute precision and recall graphs.
+ *
+ * @param params: display parameters
+ * @return the points to display in a graph
*/
public Vector<Pair> eval( Properties params ) { // throws AlignmentException
points = new Vector<Pair>(STEP+1);
@@ -100,6 +108,8 @@ public class PRGraphEvaluator extends GraphEvaluator {
/**
* Returns a list of Precision at recall points (Pairs)
* From an ordered vector of cells with their correctness status
+ *
+ * @return the points to display in a graph
*/
public Vector<Pair> evalOpenEnded() {
// Determine what the increment is
@@ -141,6 +151,8 @@ public class PRGraphEvaluator extends GraphEvaluator {
/**
* Returns a list of Precision at recall points (Pairs)
* From an ordered vector of cells with their correctness status
+ *
+ * @return the points to display in a graph
*/
public Vector<Pair> evalOldStyle() {
double[] precisions = new double[STEP+1];
@@ -213,8 +225,11 @@ public class PRGraphEvaluator extends GraphEvaluator {
/**
* This output the result
+ *
+ * @param writer: the writer where to print the result
+ * @throws IOException when something goes wrong
*/
- public void write(PrintWriter writer) throws java.io.IOException {
+ public void write(PrintWriter writer) throws IOException {
writer.println("<?xml version='1.0' encoding='utf-8' standalone='yes'?>");
writer.println("<"+SyntaxElement.RDF.print()+" xmlns:"+Namespace.RDF.shortCut+"='"+Namespace.RDF.prefix+"'>");
writer.println(" <output "+SyntaxElement.RDF_ABOUT.print()+"=''>");
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
index cd8be2a36d78636f02badb44a09d21a3e1f87bc0..d403b105ade26286891164b60698be355b9d2a2b 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/PRecEvaluator.java
@@ -77,7 +77,9 @@ public class PRecEvaluator extends BasicEvaluator implements Evaluator {
* @param align2 : the alignment to evaluate
* The two parameters are transformed into URIAlignment before being processed
* Hence, if one of them is modified after initialisation, this will not be taken into account.
- **/
+ *
+ * @throws AlignmentException when something goes wrong
+ */
public PRecEvaluator( Alignment align1, Alignment align2 ) throws AlignmentException {
super(((BasicAlignment)align1).toURIAlignment(), ((BasicAlignment)align2).toURIAlignment());
}
@@ -96,6 +98,7 @@ public class PRecEvaluator extends BasicEvaluator implements Evaluator {
}
/**
+ * Computes the evaluation measure (the results are stored in the object)
*
* The formulas are standard:
* given a reference alignment A
@@ -108,6 +111,10 @@ public class PRecEvaluator extends BasicEvaluator implements Evaluator {
* with inter = set intersection and |.| cardinal.
*
* In the implementation |B|=nbfound, |A|=nbexpected and |A inter B|=nbcorrect.
+ *
+ * @param params: the evaluation parameters
+ * @return the semantic F-measure of the alignment
+ * @throws AlignmentException when something goes wrong
*/
public double eval( Properties params ) throws AlignmentException {
init();
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/ROCCurveEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/ROCCurveEvaluator.java
index 0fd2cfb0361fa58a2f5bf5ec978bb4436533afc1..97c103f56521925b83b5e21e0f26532dfa35e2e7 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/ROCCurveEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/ROCCurveEvaluator.java
@@ -34,7 +34,10 @@ import java.util.Set;
import java.util.SortedSet;
import java.util.Comparator;
import java.util.Vector;
+
import java.io.PrintWriter;
+import java.io.IOException;
+
import java.net.URI;
/**
@@ -84,6 +87,9 @@ public class ROCCurveEvaluator extends GraphEvaluator {
/**
* Compute ROCCurve points
* From an ordered vector of cells with their correctness status
+ *
+ * @param param: parameters of the evaluation
+ * @return the curve as a set of points
*/
public Vector<Pair> eval( Properties param ) {
// Local variables
@@ -150,6 +156,8 @@ public class ROCCurveEvaluator extends GraphEvaluator {
/**
* For the moment
+ * *
+ * @return the points to display in a graph
*/
public Vector<Pair> eval() {
return eval( (Properties)null );
@@ -157,8 +165,11 @@ public class ROCCurveEvaluator extends GraphEvaluator {
/**
* This output the result
+ *
+ * @param writer: the writer where to print the result
+ * @throws IOException when something goes wrong
*/
- public void write(PrintWriter writer) throws java.io.IOException {
+ public void write(PrintWriter writer) throws IOException {
writer.println("<?xml version='1.0' encoding='utf-8' standalone='yes'?>");
writer.println("<"+SyntaxElement.RDF.print()+" xmlns:"+Namespace.RDF.shortCut+"='"+Namespace.RDF.prefix+"'>");
writer.println(" <output rdf:about=''>");
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/SemPRecEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/SemPRecEvaluator.java
index 47e847f2662256b9a0e7ab22ae2f0a5f85b1774d..821b58d2724cc3da0a1da42e45d84e9f03c4a5a7 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/SemPRecEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/SemPRecEvaluator.java
@@ -111,6 +111,7 @@ public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
* Initiate Evaluator for precision and recall
* @param al1 : the reference alignment
* @param al2 : the alignment to evaluate
+ * @throws AlignmentException when something goes wrong
**/
public SemPRecEvaluator( Alignment al1, Alignment al2 ) throws AlignmentException {
super( al1, al2 );
@@ -133,20 +134,16 @@ public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
}
/**
+ * Computes the evaluation measure (the results are stored in the object)
*
- * The formulas are standard:
- * given a reference alignment A
- * given an obtained alignment B
- * which are sets of cells (linking one entity of ontology O to another of ontolohy O').
- *
- * P = |A inter B| / |B|
- * R = |A inter B| / |A|
- * F = 2PR/(P+R)
- * with inter = set intersection and |.| cardinal.
- *
- * In the implementation |B|=nbfound, |A|=nbexpected and |A inter B|=nbcorrect.
+ * The formulas are standard (see PREvaluation) except that they use
+ * the entailment of a correspondence by an alignment instead of set-membership
*
* This takes semantics as a parameter which should be a litteral of fr.paris8.iut.info.iddl.conf.Semantics
+ *
+ * @param params: the evaluation parameters
+ * @return the semantic F-measure of the alignment
+ * @throws AlignmentException when something goes wrong
*/
public double eval( Properties params ) throws AlignmentException {
init( params );
@@ -222,7 +219,9 @@ public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
/**
* Even simpler if they are loaded: just merge them on the spot
- *
+ *
+ * @param align: the alignment to load
+ * @throws AlignmentException when something goes wrong (typically IO and syntax problem)
*/
public void loadAlignedOntologies( ObjectAlignment align ) throws AlignmentException {
// Get the two ontologies
@@ -262,8 +261,11 @@ public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
}
- /*
+ /**
* Loads the Aligned ontologies without intermediate file
+ *
+ * @param align: the alignment to load
+ * @throws AlignmentException when something goes wrong (typically IO and syntax problem)
*/
public void loadPipedAlignedOntologies( final ObjectAlignment align ) throws AlignmentException {
PipedInputStream in = new PipedInputStream();
@@ -322,8 +324,11 @@ public class SemPRecEvaluator extends PRecEvaluator implements Evaluator {
}
}
- /*
+ /**
* Loads the Aligned ontologies through an intermediate file
+ *
+ * @param align: the alignment to load
+ * @throws AlignmentException when something goes wrong (typically IO and syntax problem)
*/
public void loadFileAlignedOntologies( ObjectAlignment align ) throws AlignmentException {
// Render the alignment
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/SymMeanEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/SymMeanEvaluator.java
index 2ec66d4bc63b93bd4a3b8c7bbef293d9bfbc1743..fd79db2028c4805dee1f658387c71a2b8dca952b 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/SymMeanEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/SymMeanEvaluator.java
@@ -57,7 +57,13 @@ public class SymMeanEvaluator extends BasicEvaluator implements Evaluator {
private double propScore = 0.;
private double indScore = 0.;
- /** Creation **/
+ /**
+ * Creation
+ *
+ * @param align1 and
+ * @param align2: the two alignments to compare
+ * @throws AlignmentException when something goes wrong
+ **/
public SymMeanEvaluator( Alignment align1, Alignment align2 ) throws AlignmentException {
super(align1,align2);
convertToObjectAlignments( align1, align2 );
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/ThresholdGraphEvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/ThresholdGraphEvaluator.java
index 55fdeaef2b036e24b1db1f440326c9e0427d02b8..d5775fa75a0cd11792b19e47ec681f908805c0a9 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/ThresholdGraphEvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/ThresholdGraphEvaluator.java
@@ -34,7 +34,10 @@ import java.util.Set;
import java.util.SortedSet;
import java.util.Comparator;
import java.util.Vector;
+
import java.io.PrintWriter;
+import java.io.IOException;
+
import java.net.URI;
import org.slf4j.Logger;
@@ -61,6 +64,8 @@ public class ThresholdGraphEvaluator extends GraphEvaluator {
/**
* Compute threshold graph
+ *
+ * @return the curve as a set of points
*/
public Vector<Pair> eval() { // throws AlignmentException
return eval( (Properties)null );
@@ -75,6 +80,8 @@ public class ThresholdGraphEvaluator extends GraphEvaluator {
* But it is better to: take the cells in reverse order
* Compute the measures on the fly
*
+ * @param params: parameters of the evaluation
+ * @return the curve as a set of points
*/
public Vector<Pair> eval( Properties params ) { // throws AlignmentException
points = new Vector<Pair>(STEP+1);
@@ -140,8 +147,11 @@ public class ThresholdGraphEvaluator extends GraphEvaluator {
/**
* This output the result
+ *
+ * @param writer: the writer where to print the result
+ * @throws IOException when something goes wrong
*/
- public void write(PrintWriter writer) throws java.io.IOException {
+ public void write(PrintWriter writer) throws IOException {
writer.println("<?xml version='1.0' encoding='utf-8' standalone='yes'?>");
writer.println("<"+SyntaxElement.RDF.print()+" xmlns:"+Namespace.RDF.shortCut+"='"+Namespace.RDF.prefix+"'>");
writer.println(" <output "+SyntaxElement.RDF_ABOUT.print()+"=''>");
diff --git a/src/fr/inrialpes/exmo/align/impl/eval/WeightedPREvaluator.java b/src/fr/inrialpes/exmo/align/impl/eval/WeightedPREvaluator.java
index ec62c43bf137bf51d3dd7985a8f7fc16c604e654..5e2eb4552c5296d77f58452ba4e0e71776bdb23e 100644
--- a/src/fr/inrialpes/exmo/align/impl/eval/WeightedPREvaluator.java
+++ b/src/fr/inrialpes/exmo/align/impl/eval/WeightedPREvaluator.java
@@ -33,7 +33,10 @@ import fr.inrialpes.exmo.align.impl.Annotations;
import java.util.Properties;
import java.util.Set;
+
import java.io.PrintWriter;
+import java.io.IOException;
+
import java.net.URI;
import org.slf4j.Logger;
@@ -79,6 +82,8 @@ public class WeightedPREvaluator extends BasicEvaluator implements Evaluator {
* @param align2 : the alignment to evaluate
* The two parameters are transformed into URIAlignment before being processed
* Hence, if one of them is modified after initialisation, this will not be taken into account.
+ *
+ * @throws AlignmentException when something goes wrong
**/
public WeightedPREvaluator(Alignment align1, Alignment align2) throws AlignmentException {
super(((BasicAlignment)align1).toURIAlignment(), ((BasicAlignment)align2).toURIAlignment());
@@ -99,18 +104,14 @@ public class WeightedPREvaluator extends BasicEvaluator implements Evaluator {
}
/**
+ * Computes the evaluation measure (the results are stored in the object)
*
- * The formulas are standard:
- * given a reference alignment A
- * given an obtained alignment B
- * which are sets of cells (linking one entity of ontology O to another of ontolohy O').
+ * The formulas are standard (see PREvaluation) except that they use
+ * the difference between confidences instead of booleans
*
- * P = |A inter B| / |B|
- * R = |A inter B| / |A|
- * F = 2PR/(P+R)
- * with inter = set intersection and |.| cardinal.
- *
- * In the implementation |B|=nbfound, |A|=nbexpected and |A inter B|=nbcorrect.
+ * @param params: the evaluation parameters
+ * @return the weighted F-measure of the alignment
+ * @throws AlignmentException when something goes wrong
*/
public double eval( Properties params ) throws AlignmentException {
init();
@@ -219,8 +220,11 @@ return result;
/**
* This now output the results in Lockheed format.
+ *
+ * @param writer: the writer in which to write the result
+ * @throws IOException when something goes wrong
*/
- public void write(PrintWriter writer) throws java.io.IOException {
+ public void write(PrintWriter writer) throws IOException {
writer.println("<?xml version='1.0' encoding='utf-8' standalone='yes'?>");
writer.println("<"+SyntaxElement.RDF.print()+" xmlns:"+Namespace.RDF.shortCut+"='"+Namespace.RDF.prefix+"'\n xmlns:"+Namespace.ATLMAP.shortCut+"='"+Namespace.ATLMAP.prefix+"'>");
writer.println(" <"+Namespace.ATLMAP.shortCut+":output "+SyntaxElement.RDF_ABOUT.print()+"=''>");
diff --git a/src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java
index 9c91fb022032381902fc0936bd7a2a2e5cc55f62..733b3fce61a54b452c9c4ecd923253e83bd2b978 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/ClassStructAlignment.java
@@ -73,6 +73,11 @@ public class ClassStructAlignment extends DistanceAlignment implements Alignment
/**
* Initialisation
* The class requires HeavyLoadedOntologies
+ *
+ * @param o1 and
+ * @param o2: the two ontoogies to match
+ * @param ontologies: an ontology cache
+ * @throws AlignmentException when something goes wrong
*/
public void init(Object o1, Object o2, Object ontologies) throws AlignmentException {
super.init( o1, o2, ontologies );
@@ -81,7 +86,13 @@ public class ClassStructAlignment extends DistanceAlignment implements Alignment
throw new AlignmentException( "ClassStructAlignment requires HeavyLoadedOntology ontology loader" );
}
- /** Processing **/
+ /**
+ * Processing
+ *
+ * @param alignment: an initial alignment
+ * @param params: the parameters of the matching process
+ * @throws AlignmentException when something goes wrong
+ */
// Could better use similarity
public void align( Alignment alignment, Properties params ) throws AlignmentException {
loadInit( alignment );
diff --git a/src/fr/inrialpes/exmo/align/impl/method/NameAndPropertyAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/NameAndPropertyAlignment.java
index c7abb0bcac97ad62166567d89dc1984cfe73c814..cbc1499ce6160c273b4b4f2d4603b8b6e0e6b553 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/NameAndPropertyAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/NameAndPropertyAlignment.java
@@ -71,6 +71,11 @@ public class NameAndPropertyAlignment extends DistanceAlignment implements Align
/**
* Initialisation
* The class requires HeavyLoadedOntologies
+ *
+ * @param o1 and
+ * @param o2: the two ontoogies to match
+ * @param ontologies: an ontology cache
+ * @throws AlignmentException when something goes wrong
*/
public void init(Object o1, Object o2, Object ontologies) throws AlignmentException {
super.init( o1, o2, ontologies );
@@ -79,7 +84,13 @@ public class NameAndPropertyAlignment extends DistanceAlignment implements Align
throw new AlignmentException( "NameAndPropertyAlignment requires HeavyLoadedOntology ontology loader" );
}
- /** Processing **/
+ /**
+ * Processing
+ *
+ * @param alignment: an initial alignment
+ * @param params: the parameters of the matching process
+ * @throws AlignmentException when something goes wrong
+ */
// Could better use similarity
public void align( Alignment alignment, Properties params ) throws AlignmentException {
loadInit( alignment );
@@ -250,6 +261,9 @@ public class NameAndPropertyAlignment extends DistanceAlignment implements Align
/**
* Make a local alignement
+ *
+ * @param prop1 and
+ * @param prop2: the two set of properties for a single class to match
* @return an average of all the property alignement
*/
private double alignLocal( Set<? extends Object> prop1, Set<? extends Object> prop2) {
diff --git a/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java
index 20bff41a7987ba18ce0226dfc6ca2452cfbb2005..fd24055fa5f13b7e552ba2f871147750f43cd283 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java
@@ -98,7 +98,13 @@ public class StringDistAlignment extends DistanceAlignment implements AlignmentP
//setType("**");
}
- /* Processing */
+ /**
+ * Processing
+ *
+ * @param alignment: an initial alignment
+ * @param params: the parameters of the matching process
+ * @throws AlignmentException when something goes wrong
+ */
public void align( Alignment alignment, Properties params ) throws AlignmentException {
// Get function from params
String f = params.getProperty("stringFunction");
diff --git a/src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java
index 7c529114976284a917cca2594f44927926540174..64bb9f99c6f23c82099028a6ec816f380791c282 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/StrucSubsDistAlignment.java
@@ -71,6 +71,11 @@ public class StrucSubsDistAlignment extends DistanceAlignment implements Alignme
/**
* Initialisation
* The class requires HeavyLoadedOntologies
+ *
+ * @param o1 and
+ * @param o2: the two ontoogies to match
+ * @param ontologies: an ontology cache
+ * @throws AlignmentException when something goes wrong
*/
public void init(Object o1, Object o2, Object ontologies) throws AlignmentException {
super.init( o1, o2, ontologies );
@@ -79,7 +84,13 @@ public class StrucSubsDistAlignment extends DistanceAlignment implements Alignme
throw new AlignmentException( "StrucSubsDistAlignment requires HeavyLoadedOntology ontology loader" );
}
- /** Processing **/
+ /**
+ * Processing
+ *
+ * @param alignment: an initial alignment
+ * @param params: the parameters of the matching process
+ * @throws AlignmentException when something goes wrong
+ */
// Could better use similarity
public void align( Alignment alignment, Properties params ) throws AlignmentException {
loadInit( alignment );
diff --git a/src/fr/inrialpes/exmo/align/impl/rel/A16AlgebraRelation.java b/src/fr/inrialpes/exmo/align/impl/rel/A16AlgebraRelation.java
index c760827049f99cd0f6841db23989180767049e9a..f75a0e2c077bb4719648e148209927bfaa4106ce 100644
--- a/src/fr/inrialpes/exmo/align/impl/rel/A16AlgebraRelation.java
+++ b/src/fr/inrialpes/exmo/align/impl/rel/A16AlgebraRelation.java
@@ -309,6 +309,8 @@ public class A16AlgebraRelation extends BitSetAlgebraRelation<A16BaseRelation> {
/**
* This is private because it refers to the implementation as BitSet
+ *
+ * @param rels: the internal representation of the relation
*/
private A16AlgebraRelation( BitSet rels ) {
super( rels );
diff --git a/src/fr/inrialpes/exmo/align/impl/rel/A2AlgebraRelation.java b/src/fr/inrialpes/exmo/align/impl/rel/A2AlgebraRelation.java
index 9717328e48de7dcb3c8481a4decef69006bb4855..4667d1c8c726a431487f2fb2cfe579e901a91893 100644
--- a/src/fr/inrialpes/exmo/align/impl/rel/A2AlgebraRelation.java
+++ b/src/fr/inrialpes/exmo/align/impl/rel/A2AlgebraRelation.java
@@ -92,6 +92,8 @@ public class A2AlgebraRelation extends BitSetAlgebraRelation<A2BaseRelation> {
/**
* This is private because it refers to the implementation as BitSet
+ *
+ * @param rels: the internal representation of the relation
*/
private A2AlgebraRelation( BitSet rels ) {
super( rels );
diff --git a/src/fr/inrialpes/exmo/align/impl/rel/A5AlgebraRelation.java b/src/fr/inrialpes/exmo/align/impl/rel/A5AlgebraRelation.java
index 8fed7c12c4d5329f6a4fe4558fe92f34cb9ba3ea..28474377e2f2f030eb589e5e963bafd6058bfa08 100644
--- a/src/fr/inrialpes/exmo/align/impl/rel/A5AlgebraRelation.java
+++ b/src/fr/inrialpes/exmo/align/impl/rel/A5AlgebraRelation.java
@@ -141,6 +141,8 @@ public class A5AlgebraRelation extends BitSetAlgebraRelation<A5BaseRelation> {
/**
* This is private because it refers to the implementation as BitSet
+ *
+ * @param rels: the internal representation of the relation
*/
private A5AlgebraRelation( BitSet rels ) {
super( rels );
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/GenericReflectiveVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/GenericReflectiveVisitor.java
index 1f8389197c6d09272a0e8113e8feae08b10ce77d..0ab8e484ce0e679c89e2043ea4956a1aa37f64d0 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/GenericReflectiveVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/GenericReflectiveVisitor.java
@@ -44,6 +44,10 @@ public class GenericReflectiveVisitor {
* Look-up for X in the superclass of c (up to root, otherwise it loops)
* If not found, look it up in the implemented interface
* (there may be such a method for interfaces)
+ *
+ * @param c: the class in which the method should apply
+ * @param root: the topmost class above c
+ * @return the relevant method
*/
protected Method getMethod( Class<?> c, Class<?> root ) {
Class<?> newc = c;
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/GraphPatternRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/GraphPatternRendererVisitor.java
index b52a3562a1912c219f404f1da8fc32e53d9c2d99..6bb70767f7c2e9960399ad2620eac844ee037abe 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/GraphPatternRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/GraphPatternRendererVisitor.java
@@ -164,6 +164,8 @@ public abstract class GraphPatternRendererVisitor extends IndentedRendererVisito
* Generates anew variable. This is always an object because we know
* the subjects (named by outside).
* It may be necessary to generate blanks.
+ *
+ * @return the new variable
*/
protected String createVarName() {
if ( blanks ) {
@@ -272,8 +274,8 @@ public abstract class GraphPatternRendererVisitor extends IndentedRendererVisito
/**
* Produce Query only for local call.
*
- * @param referer
- * @return
+ * @param referer: the reference to a query (corresponding to a correspondence)
+ * @return the query
*/
public String getQuery( Object referer ) {
return queries.get( referer );
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java
index b503399c2fa0007fdc251ddb2ee0ddb2a1e1e8af..72919a149dc6fe43203b4dc97811a2a5007418d7 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java
@@ -308,6 +308,10 @@ public class OWLAxiomsRendererVisitor extends IndentedRendererVisitor implements
/**
* For EDOAL relation name depends on type of expressions
+ *
+ * @param rel: the relation to render
+ * @param ob: an object on which this relation applies
+ * @return the rendered relation
*/
public String getRelationName( Relation rel, Object ob ) {
if ( RelationTransformer.isEquivalence( rel ) ) {
@@ -350,8 +354,12 @@ public class OWLAxiomsRendererVisitor extends IndentedRendererVisitor implements
/**
* Regular: relation name depends on loaded ontology
+ *
+ * @param onto: the ontology in which belongs ob
+ * @param rel: a relation to render
+ * @param ob: an object affected by this relation
+ * @return the rendered relation
*/
-
public String getRelationName( LoadedOntology<? extends Object> onto, Relation rel, Object ob ) {
try {
if ( RelationTransformer.isEquivalence( rel ) ) {
@@ -585,6 +593,9 @@ public class OWLAxiomsRendererVisitor extends IndentedRendererVisitor implements
* OWL, and in particular OWL 2, does not allow for more Relation (ObjectProperty)
* and Property (DataProperty) constructor than owl:inverseOf
* It is thus imposible to transcribe our and, or and not constructors.
+ *
+ * @param e: a compound property to render
+ * @throws AlignmentException when something goes wrong
*/
public void visit( final PropertyConstruction e ) throws AlignmentException {
Relation toProcessNext = toProcess;
@@ -731,6 +742,9 @@ public class OWLAxiomsRendererVisitor extends IndentedRendererVisitor implements
* defining a property subsumed by this closure through an axiom.
* It is also possible to rewrite the reflexive closures as axioms as well.
* But the transitive closure can only be obtained through subsumption.
+ *
+ * @param e: a compound relation to render
+ * @throws AlignmentException when something goes wrong
*/
public void visit( final RelationConstruction e ) throws AlignmentException {
Relation toProcessNext = toProcess;
@@ -843,6 +857,8 @@ public class OWLAxiomsRendererVisitor extends IndentedRendererVisitor implements
*
* OWL offers further possiblities, such as additional owl:withRestriction
* clauses
+ *
+ * @param e: a datatype to render
*/
public void visit( final Datatype e ) {
indentedOutput("<owl:Datatype><owl:onDataType rdf:resource=\""+e.getType()+"\"/></owl:Datatype>");
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/SILKRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/SILKRendererVisitor.java
index 7826b835124fb829fa2529cb5507e0c1023858e6..c944eb30545015a624adc5fb1ead90cbbaf09c9e 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/SILKRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/SILKRendererVisitor.java
@@ -56,6 +56,10 @@ import fr.inrialpes.exmo.align.impl.edoal.LinkkeyEquals;
import fr.inrialpes.exmo.align.impl.edoal.LinkkeyIntersects;
import fr.inrialpes.exmo.align.parser.SyntaxElement.Constructor;
+/**
+ * This renders only a skeleton for the SILK script.
+ * In particular, it is impossible to know where to fetch the data from (this could eventually be injected)
+ */
public class SILKRendererVisitor extends GraphPatternRendererVisitor implements AlignmentVisitor {
final static Logger logger = LoggerFactory.getLogger(SILKRendererVisitor.class);
@@ -322,6 +326,11 @@ public class SILKRendererVisitor extends GraphPatternRendererVisitor implements
/**
* This is incomplete as SILK is able to deal with reverse (\) and constraints ([])
+ *
+ * @param var: the starting point of the path (a variable)
+ * @param pex: the path expression to render
+ * @return the rendering of the path expression
+ * @throws AlignmentException when something goes wrong
*/
private String generateSILKPath( String var, PathExpression pex ) throws AlignmentException {
String path = var;
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/SPARQLSelectRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/SPARQLSelectRendererVisitor.java
index 5dd6f845cf8c2f0912c0e51a05527b3de073a336..5402de75aecf938743f75c101e5b0e38b4a290bb 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/SPARQLSelectRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/SPARQLSelectRendererVisitor.java
@@ -167,6 +167,9 @@ public class SPARQLSelectRendererVisitor extends GraphPatternRendererVisitor imp
/**
* Linkkeys are irrelevant to SELECT queries
+ *
+ * @param linkkeyEquals: the link key to render
+ * @throws AlignmentException when something goes wrong
*/
public void visit(final LinkkeyEquals linkkeyEquals) throws AlignmentException {
return;
@@ -174,12 +177,15 @@ public class SPARQLSelectRendererVisitor extends GraphPatternRendererVisitor imp
/**
* Linkkeys are irrelevant to SELECT queries
+ *
+ * @param linkkeyIntersects: the link key to render
+ * @throws AlignmentException when something goes wrong
*/
public void visit(final LinkkeyIntersects linkkeyIntersects) throws AlignmentException {
return;
}
- /*** JE: shouldn't it be in Graph ***/
+ /* JE: shouldn't it be in Graph ***/
protected void beginNamedGraph(String namedGraph) {
if (namedGraph != null) {
addToGP("GRAPH <" + namedGraph + "> {" + NL);
diff --git a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
index f145730283efdd1cf30313b3e68327f8c7f9df3d..fe8a019651968a09494719a3e10ae9f1c67a3021 100644
--- a/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
+++ b/src/fr/inrialpes/exmo/align/parser/AlignmentParser.java
@@ -105,8 +105,11 @@ public class AlignmentParser {
* Parses the document corresponding to the URI given in parameter
* If the current process has links (import or include) to others documents then they are
* parsed.
- * @param uri URI of the document to parse
- * @param loaded (cached ontologies)
+ *
+ * @param uri: URI of the document to parse
+ * @param loaded: (cached ontologies)
+ * @return the parsed alignment
+ * @throws AlignmentException when something goes wrong
* @deprecated use parse( URI ) instead
*/
@Deprecated
@@ -118,8 +121,10 @@ public class AlignmentParser {
* Parses the document given in parameter
* If the current process has links (import or include) to others documents then they are
* parsed.
- * @param o
- * A URI, InputStream, String or Reader
+ *
+ * @param o: a URI, InputStream, String or Reader containing the alignment
+ * @return the parsed alignment
+ * @throws AlignmentException when something goes wrong
*/
private Alignment callParser( Object o ) throws AlignmentException {
try {
@@ -151,6 +156,11 @@ public class AlignmentParser {
/**
* This dispatch is ridiculous, but that's life
+ *
+ * @param p: a parser
+ * @param o: a URI, InputStream, String or Reader containing the alignment
+ * @return the parsed alignment
+ * @throws AlignmentException when something goes wrong
*/
private Alignment callParser( XMLParser p, Object o ) throws AlignmentException {
if ( o instanceof URI ) return p.parse( ((URI)o).toString() );
@@ -170,7 +180,10 @@ public class AlignmentParser {
/**
* Parses the content of a string
- * @param s String the string to parse
+ *
+ * @param s: a string containing an alignment
+ * @return the parsed alignment
+ * @throws AlignmentException when something goes wrong
*/
public Alignment parseString( String s ) throws AlignmentException {
// The problem here is that InputStream are consumed by parsers
@@ -181,7 +194,10 @@ public class AlignmentParser {
/**
* Parses a the content of a reader
+ *
* @param r the reader to parse
+ * @return the parsed alignment
+ * @throws AlignmentException when something goes wrong
*/
public Alignment parse( Reader r ) throws AlignmentException {
callParser( r );
@@ -190,7 +206,10 @@ public class AlignmentParser {
/**
* Parses a URI expressed as a String
+ *
* @param uri the URI as a String
+ * @return the parsed alignment
+ * @throws AlignmentException when something goes wrong
* This is only here for compatibility purposes
*/
public Alignment parse( String uri ) throws AlignmentException {
@@ -204,7 +223,10 @@ public class AlignmentParser {
/**
* Parses a URI
+ *
* @param uri the URI
+ * @return the parsed alignment
+ * @throws AlignmentException when something goes wrong
*/
public Alignment parse( URI uri ) throws AlignmentException {
callParser( uri );
@@ -213,7 +235,10 @@ public class AlignmentParser {
/**
* Parses an inputStream
+ *
* @param s the Stream to parse
+ * @return the parsed alignment
+ * @throws AlignmentException when something goes wrong
*/
public Alignment parse( InputStream s ) throws AlignmentException {
callParser( s );
diff --git a/src/fr/inrialpes/exmo/align/parser/RDFParser.java b/src/fr/inrialpes/exmo/align/parser/RDFParser.java
index fffcd25be689aac3e8d64d53e7946ec88639571c..85cb5023ff96e5f54f1ae7e4f06d1c1d02d1ef24 100644
--- a/src/fr/inrialpes/exmo/align/parser/RDFParser.java
+++ b/src/fr/inrialpes/exmo/align/parser/RDFParser.java
@@ -134,7 +134,7 @@ public class RDFParser {
/**
* Creates an RDF Parser.
*
- * @param debugMode The value of the debug mode (DEPRECATED)
+ * @param debugMode: The value of the debug mode (DEPRECATED)
*/
public RDFParser(int debugMode) {
}
@@ -161,9 +161,9 @@ public class RDFParser {
* Parse the input model. The model shall include one statement that include
* (?,RDF.type,Alignment)
*
- * @param rdfmodel the rdfmodel containing the RDF representation of the
+ * @param rdfmodel: the rdfmodel containing the RDF representation of the
* parsed alignment
- * @return the result EDOALAlignment
+ * @return the parsed EDOALAlignment
* @throws AlignmentException if there is any exception, throw
* AlignmentException that include describe infomation and a caused
* exception.
@@ -230,7 +230,7 @@ public class RDFParser {
*
* @param node the alignment resource
* @return the parsed mapping document
- * @throws AlignmentException
+ * @throws AlignmentException when something goes wrong
*/
public EDOALAlignment parseAlignment(final Resource node) throws AlignmentException {
if (node == null) {
@@ -368,6 +368,7 @@ public class RDFParser {
* @param node the ontology node
* @return the Ontology object
* @throws NullPointerException if the node is null
+ * @throws AlignmentException when something goes wrong
*/
protected Ontology<Object> parseOntology(final Resource node) throws AlignmentException {
if (node == null) {
@@ -395,9 +396,9 @@ public class RDFParser {
* Parses a mapping rule. The parsed node must be a Cell resource including
* the mandatory Statement. <code><Cell></code> tag.
*
- * @param node the <code><Cell></code> tag
- * @return the parsed rule
- * @exception AlignmentException
+ * @param node: a node of type Cell
+ * @return the parsed correspondence
+ * @exception AlignmentException when something goes wrong
*/
protected EDOALCell parseCell( final Resource node ) throws AlignmentException {
if (node == null) {
@@ -529,9 +530,9 @@ public class RDFParser {
/**
*
- * @param node
- * @return
- * @throws AlignmentException
+ * @param node: a node corresponding to a link key binding
+ * @return the parsed binding
+ * @throws AlignmentException when something goes wrong
*/
protected LinkkeyBinding parseLinkkeyBinding(final Resource node) throws AlignmentException {
if (node == null) {
diff --git a/src/fr/inrialpes/exmo/align/parser/SyntaxElement.java b/src/fr/inrialpes/exmo/align/parser/SyntaxElement.java
index 6b05f47c29ddb9909684002db8da3121141adf56..84a2845add297c063e8238933c4356050327e924 100644
--- a/src/fr/inrialpes/exmo/align/parser/SyntaxElement.java
+++ b/src/fr/inrialpes/exmo/align/parser/SyntaxElement.java
@@ -267,7 +267,9 @@ public enum SyntaxElement {
}
/**
+ * @param name: the name of the element to retrieve
* @return the resource of the element.
+ * @throws AlignmentException when the syntactic resources have not been initialised (use init())
*/
public static Object getResource(String name) throws AlignmentException {
if (register == null) {
@@ -313,9 +315,9 @@ public enum SyntaxElement {
* namespace of the element, the formated string will not be prefixed bye
* the namespace and ':'.
*
- * @param namespace the namespace for which not to prefix the resulting
+ * @param namespace: the namespace for which not to prefix the resulting
* string
- * @return teh formated string
+ * @return the formated string
* @see #print()
*/
public String print(final Namespace namespace) {
diff --git a/src/fr/inrialpes/exmo/align/parser/XMLParser.java b/src/fr/inrialpes/exmo/align/parser/XMLParser.java
index c46ba7a4735c348d8a57ab6cd8f25a8b7eeeeb3f..230f95e1d8aa5b228d37a22b947ace4ff0ca3756 100644
--- a/src/fr/inrialpes/exmo/align/parser/XMLParser.java
+++ b/src/fr/inrialpes/exmo/align/parser/XMLParser.java
@@ -176,6 +176,8 @@ public class XMLParser extends DefaultHandler {
/**
* Creates an XML Parser.
+ * @throws SAXException when syntax errors are encountered
+ * @throws ParserConfigurationException when the parser cannot be configured
*/
public XMLParser() throws ParserConfigurationException, SAXException {
this(false);
@@ -183,8 +185,10 @@ public class XMLParser extends DefaultHandler {
/**
* Creates an XML Parser.
- * @param validate 0 if non validating, more otherwise
+ * @param validate: 0 if non validating, more otherwise
* This should become a boolean
+ * @throws SAXException when syntax errors are encountered
+ * @throws ParserConfigurationException when the parser cannot be configured
*/
public XMLParser( int validate ) throws ParserConfigurationException, SAXException {
this( (validate > 0) );
@@ -209,6 +213,9 @@ public class XMLParser extends DefaultHandler {
* @param uri URI of the document to parse
* Note: SAXParser has a parse( String uri ) method but it does not do content negotiation
* Hence we have to reimplement it (2014)
+ *
+ * @return the parsed alignment
+ * @throws AlignmentException when something goes wrong
*/
public Alignment parse( String uri ) throws AlignmentException {
try {
@@ -227,7 +234,10 @@ public class XMLParser extends DefaultHandler {
/**
* Parses a reader, used for reading from a string
+ *
* @param r the reader from which to parse
+ * @return the parsed alignment
+ * @throws AlignmentException when something goes wrong
*/
public Alignment parse( Reader r ) throws AlignmentException {
try {
@@ -242,7 +252,10 @@ public class XMLParser extends DefaultHandler {
/**
* Parses a string instead of a URI
+ *
* @param s String the string to parse
+ * @return the parsed alignment
+ * @throws AlignmentException when something goes wrong
*/
public Alignment parse( InputStream s ) throws AlignmentException {
try {
@@ -269,15 +282,16 @@ public class XMLParser extends DefaultHandler {
cellids = new HashSet<String>();
}
- /**
- * Called by the XML parser at the begining of an element.
- * The corresponing graph component is create for each element.
- *
- * @param namespaceURI The namespace of the current element
- * @param pName The local name of the current element
- * @param qname The name of the current element
- * @param atts The attributes name of the current element
- */
+ /**
+ * Called by the XML parser at the begining of an element.
+ * The corresponing graph component is create for each element.
+ *
+ * @param namespaceURI: The namespace of the current element
+ * @param pName: The local name of the current element
+ * @param qname: The name of the current element
+ * @param atts: The attributes name of the current element
+ * @throws SAXException when something goes wrong
+ */
public void startElement( String namespaceURI, String pName, String qname, Attributes atts ) throws SAXException {
logger.trace( "startElement XMLParser : {}", pName );
parseLevel++;
@@ -386,11 +400,16 @@ public class XMLParser extends DefaultHandler {
throw new SAXException("[XMLParser] bad URI syntax : "+name);}
}
- /* From a patch proposed by Sabine Massmann
+ /**
+ * From a patch proposed by Sabine Massmann
* Get around some nasty double parsing bug. Sometimes it parses
* 6.925955630686735E-4 as
* content XMLParser : 6.925955630686735
* content XMLParser : E-4
+ *
+ * @param ch: an array of chars from the string part of XML
+ * @param start: the beging of the string to extract
+ * @param length: the length of the string to extract
*/
public void characters( char ch[], int start, int length ) {
String newContent = new String( ch, start, length );
@@ -407,9 +426,10 @@ public class XMLParser extends DefaultHandler {
/**
* Called by the XML parser at the end of an element.
*
- * @param namespaceURI The namespace of the current element
- * @param pName The local name of the current element
- * @param qName The name of the current element
+ * @param namespaceURI: The namespace of the current element
+ * @param pName: The local name of the current element
+ * @param qName: The name of the current element
+ * @throws SAXException when something goes wrong
*/
public void endElement( String namespaceURI, String pName, String qName ) throws SAXException {
logger.trace( "endElement XMLParser : {}", pName );
diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index 8f35625df3454841dc7c1bab13d6e427aed96e15..212f8aff5b815d2d83aa54aff31467440843bea2 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -151,6 +151,11 @@ public class AServProtocolManager implements Service {
* Initialization and constructor
*********************************************************************/
+ /**
+ * Creation
+ *
+ * @param dir: a hash-table of all directories by which the service will be registred
+ */
public AServProtocolManager ( Hashtable<String,Directory> dir ) {
directories = dir;
}
@@ -337,6 +342,9 @@ public class AServProtocolManager implements Service {
/**
* returns null if alignment not retrieved
* Otherwise returns AlignmentId or an ErrorMsg
+ *
+ * @param params: the parameters of the query
+ * @return a message containing the query result
*/
private Message retrieveAlignment( Properties params ){
String method = params.getProperty("method");
@@ -614,9 +622,12 @@ public class AServProtocolManager implements Service {
}
}
- /*
+ /**
* Returns only the metadata of an alignment and returns it in
* parameters
+ *
+ * @param params: the parameters of the query
+ * @return a message containing the query result
*/
public Message metadata( Properties params ){
// Retrieve the alignment
@@ -647,6 +658,12 @@ public class AServProtocolManager implements Service {
* There is no way an alignment server could modify an alignment
*********************************************************************/
+ /**
+ * Trim an alignment
+ *
+ * @param params: the parameters of the query
+ * @return a message containing the query result
+ */
public Message trim( Properties params ) {
// Retrieve the alignment
String id = params.getProperty("id");
@@ -788,6 +805,9 @@ public class AServProtocolManager implements Service {
/**
* Store evaluation result from its URI
+ *
+ * @param params: the parameters of the query
+ * @return a message containing the query result
*/
public Message storeEval( Properties params ){
return new ErrorMsg( params, newId(), serverId,"Not yet implemented" );
@@ -795,6 +815,9 @@ public class AServProtocolManager implements Service {
/**
* Evaluate a track: a set of results
+ *
+ * @param params: the parameters of the query
+ * @return a message containing the query result
*/
// It is also possible to try a groupeval ~> with a zipfile containing results
// ~~> But it is more difficult to know where is the reference (non public)
@@ -808,6 +831,9 @@ public class AServProtocolManager implements Service {
/**
* Store the result
+ *
+ * @param params: the parameters of the query
+ * @return a message containing the query result
*/
public Message storeGroupEval( Properties params ){
return new ErrorMsg( params, newId(), serverId,"Not yet implemented" );
@@ -815,6 +841,9 @@ public class AServProtocolManager implements Service {
/**
* Retrieve the results (all registered result) of a particular test
+ *
+ * @param params: the parameters of the query
+ * @return a message containing the query result
*/
public Message getResults( Properties params ){
return new ErrorMsg( params, newId(), serverId,"Not yet implemented" );
@@ -847,6 +876,12 @@ public class AServProtocolManager implements Service {
* Ontology Networks
*/
+ /**
+ * Load a network of ontologies from its description
+ *
+ * @param params: the parameters of the query
+ * @return a message containing the query result
+ */
public Message loadOntologyNetwork( Properties params ) {
// load the ontology network
String name = params.getProperty("url");
@@ -1256,6 +1291,11 @@ public class AServProtocolManager implements Service {
* requires to store the node that can be
*/
+ /**
+ *
+ * @param params: the parameters of the query
+ * @return a message containing the query result
+ */
// Implements: reply-with
public Message replywith(Properties params){
@@ -1292,6 +1332,12 @@ public class AServProtocolManager implements Service {
* Utilities: reaching and loading ontologies
*********************************************************************/
+ /**
+ * Load an ontology
+ *
+ * @param uri: the URI (URL) of the ontology
+ * @return the loaded ontology
+ */
public LoadedOntology<? extends Object> reachable( URI uri ){
try {
OntologyFactory factory = OntologyFactory.getFactory();
@@ -1312,7 +1358,9 @@ public class AServProtocolManager implements Service {
/**
* Display all the classes inheriting or implementing a given
* interface in the currently loaded packages.
- * @param toclass the interface to implement
+ *
+ * @param toclass: the interface to implement
+ * @return the set of strings corresponding to the implementation of the class
*/
public Set<String> implementations( Class<?> toclass ) {
return implementations( toclass, new HashSet<String>() );
diff --git a/src/fr/inrialpes/exmo/align/service/AlignmentServiceProfile.java b/src/fr/inrialpes/exmo/align/service/AlignmentServiceProfile.java
index 14cff0ebf11f66078cd60066912c408200c381cd..aea3bd91a39c545e37a9b33513e32978c52cb0c9 100644
--- a/src/fr/inrialpes/exmo/align/service/AlignmentServiceProfile.java
+++ b/src/fr/inrialpes/exmo/align/service/AlignmentServiceProfile.java
@@ -26,22 +26,38 @@ public interface AlignmentServiceProfile {
/**
* Creates the Service object and declares it after any
- * required registery
+ * required registry
+ *
+ * @param p: the parameters of the service
+ * @param m: the protocol manager that the service will call
+ * @throws AServException when something goes wrong
*/
public void init( Properties p, AServProtocolManager m ) throws AServException;
/**
* Tells if it accept requests with this prefix
+ *
+ * @param prefix: the prefix of the URI of an incoming query
+ * @return true when the URI prefix is an accepted query
*/
public boolean accept( String prefix );
/**
* Process a particular request
+ *
+ * @param uri: the URI of the query
+ * @param prefix: its prefix
+ * @param perf: its performative (the action to be processed)
+ * @param header: the HTTP header
+ * @param params: the parameters of the query
+ * @return true when the URI prefix is an accepted query
*/
public String process( String uri, String prefix, String perf, Properties header, Properties params );
/**
* Shutdown the Service and undeclare it from any registery
+ *
+ * @throws AServException when something goes wrong
*/
public void close() throws AServException;
}
diff --git a/src/fr/inrialpes/exmo/align/service/Cache.java b/src/fr/inrialpes/exmo/align/service/Cache.java
index c3bf06cb8091fe13bedef224f5e608eba204da05..abcb5626f49e4de31d20e53677e440679086c52c 100644
--- a/src/fr/inrialpes/exmo/align/service/Cache.java
+++ b/src/fr/inrialpes/exmo/align/service/Cache.java
@@ -39,6 +39,10 @@ public interface Cache {
/**
* loads the alignment descriptions from the database and put them in the
* alignmentTable hashtable
+ *
+ * @param p: the initialisation parameters
+ * @param prefix: the URI prefix of the current server
+ * @throws AlignmentException when something goes wrong (cannot access database, but format)
*/
public void init( Properties p, String prefix ) throws AlignmentException;
@@ -68,22 +72,38 @@ public interface Cache {
* retrieve alignment metadata from id
* This is more difficult because we return the alignment we have
* disreagarding if it is complete o only metadata
+ *
+ * @param uri: the URI of the alignment whose metadata to retrieve
+ * @return the retrieved alignment filled only with its metadata
+ * @throws AlignmentException when something goes wrong (cannot resolve URI)
*/
public Alignment getMetadata( String uri ) throws AlignmentException;
/**
* retrieve full alignment from id (and cache it)
+ *
+ * @param uri: the URI of the alignment to retrieve
+ * @return the retrieved alignment
+ * @throws AlignmentException when something goes wrong (cannot resolve URI)
*/
public Alignment getAlignment( String uri ) throws AlignmentException;
/**
* retrieve full alignment from URI or description
+ *
+ * @param uri: the URI of the alignments to retrieve
+ * @return the set of retrieved alignments
+ * @throws AlignmentException when something goes wrong (cannot resolve URI)
*/
public Set<Alignment> getAlignmentByURI( String uri ) throws AlignmentException;
public Set<Alignment> getAlignmentsByDescription( String desc ) throws AlignmentException;
/**
* retrieve network of ontologies from id
+ *
+ * @param uri: the URI of the network to retrieve
+ * @return the retrieved network of ontologies
+ * @throws AlignmentException when something goes wrong (cannot resolve URI)
*/
public OntologyNetwork getOntologyNetwork( String uri ) throws AlignmentException;
@@ -92,6 +112,10 @@ public interface Cache {
/**
* returns the alignments between two ontologies
* if one of the ontologies is null, then return them all
+ *
+ * @param uri1 and
+ * @param uri2: the URIs two ontologies from which retrieving alignments
+ * @return the retrieved alignments
*/
public Set<Alignment> getAlignments( URI uri1, URI uri2 );
@@ -107,21 +131,41 @@ public interface Cache {
/**
* records newly created alignment and returns its idenfifier
+ *
+ * @param alignment: the alignment to record
+ * @param force: true if the alignment is too be recorded even if it was recorded
+ * @return the URI of the recorded alignment
*/
public String recordNewAlignment( Alignment alignment, boolean force );
/**
* records alignment identified by id and returns its idenfifier
+ *
+ * @param uri: the URI of the alignment to record
+ * @param al: the alignment to record
+ * @param force: true if the alignment is too be recorded even if it was recorded
+ * @return the URI of the recorded alignment
+ * @throws AlignmentException when something goes wrong (cannot resolve URI)
*/
public String recordNewAlignment( String uri, Alignment al, boolean force ) throws AlignmentException;
/**
* records newly created network and returns its idenfifier
+ *
+ * @param network: the network of ontologies to record
+ * @param force: true if the network is too be recorded even if it was recorded
+ * @return the URI of the recorded network
*/
public String recordNewNetwork( OntologyNetwork network, boolean force );
/**
* records network identified by id and returns its idenfifier
+ *
+ * @param uri: the URI of the network to record
+ * @param network: the network of ontologies to record
+ * @param force: true if the network is too be recorded even if it was recorded
+ * @return the URI of the recorded network
+ * @throws AlignmentException when something goes wrong (cannot resolve URI)
*/
public String recordNewNetwork( String uri, OntologyNetwork network, boolean force ) throws AlignmentException;
@@ -134,6 +178,10 @@ public interface Cache {
/**
* Non publicised class
+ *
+ * @param uri: the URI of the alignment to erase
+ * @param eraseFromDB: true if the alignment is erased from the database cache
+ * @throws AlignmentException when something goes wrong (cannot resolve URI)
*/
public void eraseAlignment( String uri, boolean eraseFromDB ) throws AlignmentException;
diff --git a/src/fr/inrialpes/exmo/align/service/Directory.java b/src/fr/inrialpes/exmo/align/service/Directory.java
index f5cc91e3c118d85f474dfa33519f0988fcf1186a..75c05c00a3db15f6b4c5eb8249bd7618a81f0096 100644
--- a/src/fr/inrialpes/exmo/align/service/Directory.java
+++ b/src/fr/inrialpes/exmo/align/service/Directory.java
@@ -31,21 +31,32 @@ public interface Directory {
* Parameters can contain, e.g.:
* - the directory address
* - the declaration of the current service
+ *
+ * @param p: the properties of the connection to open
+ * @throws AServException when something goes wrong
*/
public void open( Properties p ) throws AServException;
/**
* Register an alignment to the directory (if necessary)
+ *
+ * @param al: the alignment to register
+ * @throws AServException when something goes wrong
*/
public void register( Alignment al ) throws AServException;
/**
* Unregister an alignment to the directory (if necessary)
+ *
+ * @param al: the alignment to unregister
+ * @throws AServException when something goes wrong
*/
public void unregister( Alignment al ) throws AServException;
/**
* Shutdown the connection and/or registration to the directory
+ *
+ * @throws AServException when something goes wrong
*/
public void close() throws AServException;
}
diff --git a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
index 25e3bb8d945ffda8312c90ad82940e19044b9abf..e56ff205a0884ce104716df6c001520d522d522b 100644
--- a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
+++ b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
@@ -129,7 +129,14 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
/**
* HTTP administration interface
+ * Handles administrative specific requests
* Allows some limited administration of the server through HTTP
+ *
+ * @param uri: the URL comming from the HTTP server
+ * @param perf: its performative (the action to be processed)
+ * @param header: the HTTP header
+ * @param params: the parameters of the query
+ * @return the HTML output to be displayed
*/
public String adminAnswer( String uri, String perf, Properties header, Properties params ) {
//logger.trace( "ADMIN[{}]", perf);
@@ -203,7 +210,14 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
/**
* HTTP ontology networks interface
+ * Handles network of ontologies specific requests
* Allows the ontology networks management through HTTP
+ *
+ * @param uri: the URL comming from the HTTP server
+ * @param perf: its performative (the action to be processed)
+ * @param header: the HTTP header
+ * @param params: the parameters of the query
+ * @return the HTML output to be displayed
*/
public String ontologyNetworkAnswer( String uri, String perf, Properties header, Properties params ) {
logger.trace( "ONTONET[{}]", perf);
@@ -418,6 +432,13 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
/**
* User friendly HTTP interface
* uses the protocol but offers user-targeted interaction
+ * Handles alignment specific requests
+ *
+ * @param uri: the URL comming from the HTTP server
+ * @param perf: its performative (the action to be processed)
+ * @param header: the HTTP header
+ * @param params: the parameters of the query
+ * @return the HTML output to be displayed
*/
public String htmlAnswer( String uri, String perf, Properties header, Properties params ) {
logger.trace("HTML[{}]", perf );
diff --git a/src/fr/inrialpes/exmo/align/service/HTTPResponse.java b/src/fr/inrialpes/exmo/align/service/HTTPResponse.java
index dee4374b50468cf2e08cd18109b9a857079801d7..7d31815761518d4318690d16047a7915dd39b2d3 100644
--- a/src/fr/inrialpes/exmo/align/service/HTTPResponse.java
+++ b/src/fr/inrialpes/exmo/align/service/HTTPResponse.java
@@ -62,6 +62,10 @@ public class HTTPResponse {
/**
* Basic constructor.
+ *
+ * @param status: the HTTP status value (OK, ERR...)
+ * @param mimeType: the MIME type of the answer
+ * @param data: the content of the answer
*/
public HTTPResponse( String status, String mimeType, InputStream data ) {
this.status = status;
@@ -72,6 +76,10 @@ public class HTTPResponse {
/**
* Convenience method that makes an InputStream out of
* given text.
+ *
+ * @param status: the HTTP status value (OK, ERR...)
+ * @param mimeType: the MIME type of the answer
+ * @param txt: the text of the answer (to be encoded)
*/
public HTTPResponse( String status, String mimeType, String txt ) {
this.status = status;
@@ -83,6 +91,9 @@ public class HTTPResponse {
/**
* Adds given line to the header.
+ *
+ * @param name: name of the property to add to the HTTP header
+ * @param value: value of the property
*/
public void addHeader( String name, String value ) {
header.put( name, value );
diff --git a/src/fr/inrialpes/exmo/align/service/HTTPTransport.java b/src/fr/inrialpes/exmo/align/service/HTTPTransport.java
index 01702616b4b8374efd4c73b6c4190207523adf03..fc4afc115aab44449fda521fda360a73427fad0b 100644
--- a/src/fr/inrialpes/exmo/align/service/HTTPTransport.java
+++ b/src/fr/inrialpes/exmo/align/service/HTTPTransport.java
@@ -83,8 +83,12 @@ public class HTTPTransport {
// ==================================================
/**
- * Starts a HTTP server to given port.<p>
- * Throws an exception if the socket is already in use
+ * Starts a HTTP server to given port.
+ *
+ * @param params: the parameters of the connection, including HTTP port and host
+ * @param manager: the manager which will deal with connections
+ * @param serv: the set of services to be listening on this connection
+ * @throws AServException when something goes wrong (e.g., socket already in use)
*/
public void init( Properties params, AServProtocolManager manager, Vector<AlignmentServiceProfile> serv ) throws AServException {
this.manager = manager;
@@ -243,15 +247,15 @@ public class HTTPTransport {
// ==================================================
/**
- * Override this to customize the server.<p>
+ * Override this to customize the server.
*
* (By default, this delegates to serveFile() and allows directory listing.)
*
- * @param uri Percent-decoded URI without parameters, for example "/index.cgi"
- * @param method "GET", "POST" etc.
- * @param parms Parsed, percent decoded parameters from URI and, in case of POST, data.
- * @param header Header entries, percent decoded
- * @return HTTP response, see class Response for details
+ * @param uri: Percent-decoded URI without parameters, for example "/index.cgi"
+ * @param method: "GET", "POST" etc.
+ * @param parms: Parsed, percent decoded parameters from URI and, in case of POST, data.
+ * @param header: Header entries, percent decoded
+ * @return an HTTP response made of these elements (see @class Response for details)
*/
public HTTPResponse serve( String uri, String method, Properties header, Properties parms ) {
logger.debug( "{} '{}'", method, uri );
@@ -345,6 +349,10 @@ public class HTTPTransport {
/**
* Returns the alignment in negociated format
+ *
+ * @param uri: the URI of an alignment
+ * @param mimeType: the MIME type in which the alignment is requested
+ * @return an HTTP response corresponding to the alignment in the requested MIME type
*/
public HTTPResponse returnAlignment( String uri, String mimeType ) {
Properties params = new Properties();
@@ -367,6 +375,10 @@ public class HTTPTransport {
/**
* Returns the network in HTML or RDF
+ *
+ * @param uri: the URI of a network of ontologies
+ * @param mimeType: the MIME type in which the network of ontologies is requested
+ * @return an HTTP response corresponding to the network of ontologies in the requested MIME type
*/
public HTTPResponse returnNetwork( String uri, String mimeType ) {
Properties params = new Properties();
diff --git a/src/fr/inrialpes/exmo/align/service/SQLCache.java b/src/fr/inrialpes/exmo/align/service/SQLCache.java
index f20e5baa697f898e3169c15794f3b949a0877202..831dee336e11f9e19ec945b32fc13fd1d48cbdd0 100644
--- a/src/fr/inrialpes/exmo/align/service/SQLCache.java
+++ b/src/fr/inrialpes/exmo/align/service/SQLCache.java
@@ -136,6 +136,10 @@ public class SQLCache extends VolatilCache implements Cache {
/**
* loads the alignment descriptions from the database and put them in the
* alignmentTable hashtable
+ *
+ * @param p: the initialisation parameters
+ * @param prefix: the URI prefix of the current server
+ * @throws AlignmentException when something goes wrong (cannot access database, but format)
*/
public void init( Properties p, String prefix ) throws AlignmentException {
super.init( p, prefix );
@@ -198,6 +202,9 @@ public class SQLCache extends VolatilCache implements Cache {
/**
* loads the alignment descriptions and networks of ontologies from the
* database and put them in the indexes
+ *
+ * @param force: true if data is downloaded from the database
+ * @throws SQLException when something goes wrong (e.g., no database access)
*/
private void load( boolean force ) throws SQLException {
logger.debug( "Loading alignments and networks..." );
@@ -206,7 +213,6 @@ public class SQLCache extends VolatilCache implements Cache {
OntologyNetwork noo = null;
Vector<String> idInfo = new Vector<String>();
-
if (force) {
// Retrieve the alignment ids
try ( Statement st = conn.createStatement() ) {
@@ -249,6 +255,9 @@ public class SQLCache extends VolatilCache implements Cache {
/**
* loads the description of alignments from the database and set them
* in an alignment object
+ *
+ * @param id: the id of an alignment
+ * @return the loaded alignment
*/
protected Alignment retrieveDescription( String id ) {
ResultSet rs;
@@ -330,7 +339,13 @@ public class SQLCache extends VolatilCache implements Cache {
* should be invoked when:
* ( result.getExtension(CACHED) == ""
* AND result.getExtension(STORED) != "") {
-
+ *
+ * @param uri: the uri of an alignment
+ * @param alignment: the alignment structure containing its metadata
+ * @return the retrieved alignment
+ * @throws SQLException when the database is not accessible
+ * @throws URISyntaxException when the URI is invalid
+ * @throws AlignmentException when something else goes wrong (no corresponding alignment)
*/
protected Alignment retrieveAlignment( String uri, Alignment alignment ) throws SQLException, AlignmentException, URISyntaxException {
String id = stripAlignmentUri( uri );
@@ -438,6 +453,11 @@ public class SQLCache extends VolatilCache implements Cache {
/**
* retrieve full alignment from id (and cache it)
+ *
+ * @param uri: the URI of an alignment
+ * @param result: its alignment structure
+ * @return the fetched alignment
+ * @throws AlignmentException when something goes wrong
*/
protected Alignment fetchAlignment( String uri, Alignment result ) throws AlignmentException {
try {
@@ -446,7 +466,7 @@ public class SQLCache extends VolatilCache implements Cache {
logger.trace( "Cache: cannot read from DB", sqlex );
throw new AlignmentException( "getAlignment: SQL exception", sqlex );
} catch ( URISyntaxException urisex ) {
- logger.trace( "Cache: cannot read from DB", urisex );
+ logger.trace( "Cache: Incorrect URI", urisex );
throw new AlignmentException( "getAlignment: Cannot find alignment", urisex );
}
}
@@ -456,11 +476,14 @@ public class SQLCache extends VolatilCache implements Cache {
/**
* quote:
* Prepare a string to be used in SQL queries by preceeding occurences of
- * "'", """, and "\" by a "\".
+ * "'", """, and "\'" by a "\"".
* This should be implemented at a lower level within Java itself
* (or the sql package).
* This function is used here for protecting everything to be entered in
* the database
+ *
+ * @param s: a string to be passed to SQL
+ * @return the string with quotes protected
*/
public static String quote( String s ) {
if ( s == null ) return "NULL";
@@ -481,6 +504,9 @@ public class SQLCache extends VolatilCache implements Cache {
/**
* Non publicised class
+ *
+ * @param uri: the URI of the alignment to suppress from the store
+ * @throws AlignmentException when something goes wrong (cannot resolve URI)
*/
public void unstoreAlignment( String uri ) throws AlignmentException {
Alignment alignment = getAlignment( uri );
diff --git a/src/fr/inrialpes/exmo/align/service/VolatilCache.java b/src/fr/inrialpes/exmo/align/service/VolatilCache.java
index e41eb00c09a66457858f595a838bf7cc3b7b93af..d9305ee04de1b4c2456e5b6eb1099a69f7a1d5ed 100644
--- a/src/fr/inrialpes/exmo/align/service/VolatilCache.java
+++ b/src/fr/inrialpes/exmo/align/service/VolatilCache.java
@@ -96,6 +96,10 @@ public class VolatilCache implements Cache {
/**
* loads the alignment descriptions from the database and put them in the
* alignmentTable hashtable
+ *
+ * @param p: the initialisation parameters
+ * @param prefix: the URI prefix of the current server
+ * @throws AlignmentException when something goes wrong (cannot access database, but format)
*/
public void init( Properties p, String prefix ) throws AlignmentException {
logger.debug( "Initializing Database cache" );
@@ -130,6 +134,9 @@ public class VolatilCache implements Cache {
/**
* Find alignments by URI
+ *
+ * @param uri: the URI of the alignment to retrieve
+ * @return the set of retrieved alignments
*/
public Set<Alignment> getAlignmentByURI( String uri ) {
Set<Alignment> result = null;
@@ -144,7 +151,10 @@ public class VolatilCache implements Cache {
/**
* Find alignments by pretty
- * NOT IMPLEMENTED YET
+ * TODO: NOT IMPLEMENTED YET
+ *
+ * @param desc: a string describing the sought alignment
+ * @return the set of retrieved alignments
*/
public Set<Alignment> getAlignmentsByDescription( String desc ) {
return null;
@@ -152,6 +162,9 @@ public class VolatilCache implements Cache {
/**
* Find alignments by ontology URIs
+ *
+ * @param uri: the URI of one ontology
+ * @return the set of retrieved alignments
*/
public Set<Alignment> getAlignments( URI uri ) {
return ontologyTable.get( uri );
@@ -160,6 +173,10 @@ public class VolatilCache implements Cache {
/**
* returns the alignments between two ontologies
* if one of the ontologies is null, then return them all
+ *
+ * @param uri1 and
+ * @param uri2: the URIs two ontologies from which retrieving alignments
+ * @return the set of retrieved alignments
*/
public Set<Alignment> getAlignments( URI uri1, URI uri2 ) {
Set<Alignment> result;
@@ -302,6 +319,10 @@ public class VolatilCache implements Cache {
* retrieve alignment metadata from id
* This is more difficult because we return the alignment we have
* disreagarding if it is complete o only metadata
+ *
+ * @param uri: the URI of the alignment whose metadata to retrieve
+ * @return the retrieved alignment filled only with its metadata
+ * @throws AlignmentException when something goes wrong (cannot resolve URI)
*/
public Alignment getMetadata( String uri ) throws AlignmentException {
Alignment result = alignmentTable.get( uri );
@@ -312,6 +333,10 @@ public class VolatilCache implements Cache {
/**
* retrieve full alignment from id (and cache it)
+ *
+ * @param uri: the URI of the alignment to retrieve
+ * @return the retrieved alignment
+ * @throws AlignmentException when something goes wrong (cannot resolve URI)
*/
public Alignment getAlignment( String uri ) throws AlignmentException {
Alignment result = null;
@@ -342,6 +367,10 @@ public class VolatilCache implements Cache {
/**
* retrieve network of ontologies from id
+ *
+ * @param uri: the URI of the network to retrieve
+ * @return the retrieved network of ontologies
+ * @throws AlignmentException when something goes wrong (cannot resolve URI)
*/
public OntologyNetwork getOntologyNetwork( String uri ) throws AlignmentException {
try {
@@ -370,6 +399,8 @@ public class VolatilCache implements Cache {
* should be invoked when:
* ( result.getExtension(CACHED) != ""
* AND obviously result.getExtension(STORED) != ""
+ *
+ * @param alignment: the alignment to unload
*/
protected void flushAlignment( Alignment alignment ) {// throws AlignmentException
//alignment.removeAllCells();
@@ -382,6 +413,10 @@ public class VolatilCache implements Cache {
/**
* records newly created alignment
+ *
+ * @param alignment: the alignment to record
+ * @param force: true if the alignment is too be recorded even if it was recorded
+ * @return the URI of the recorded alignment
*/
public String recordNewAlignment( Alignment alignment, boolean force ) {
try { return recordNewAlignment( generateAlignmentUri(), alignment, force );
@@ -390,6 +425,12 @@ public class VolatilCache implements Cache {
/**
* records alignment identified by id
+ *
+ * @param uri: the URI of the alignment to record
+ * @param al: the alignment to record
+ * @param force: true if the alignment is too be recorded even if it was recorded
+ * @return the URI of the recorded alignment
+ * @throws AlignmentException when something goes wrong (cannot resolve URI)
*/
public String recordNewAlignment( String uri, Alignment al, boolean force ) throws AlignmentException {
al.setExtension(SVCNS, OURI1, al.getOntology1URI().toString());
@@ -406,6 +447,11 @@ public class VolatilCache implements Cache {
/**
* records alignment identified by id
* force will register the new alignment even if it is already registered
+ *
+ * @param uri: the URI of the alignment to record
+ * @param alignment: the alignment to record
+ * @param force: true if the alignment is too be recorded even if it was recorded
+ * @return the URI of the recorded alignment
*/
public String recordAlignment( String uri, Alignment alignment, boolean force ) {
// URIINdex: if this guy already has a URI, record in table
@@ -451,6 +497,8 @@ public class VolatilCache implements Cache {
/**
* suppresses the record for an alignment
+ *
+ * @param alignment: the alignment to unrecord
*/
public void unRecordAlignment( Alignment alignment ) {
String id = alignment.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
@@ -476,6 +524,10 @@ public class VolatilCache implements Cache {
/**
* records a newly created network
+ *
+ * @param network: the network of ontologies to record
+ * @param force: true if the network is too be recorded even if it was recorded
+ * @return the URI of the recorded network
*/
public String recordNewNetwork( OntologyNetwork network, boolean force ) {
try {
@@ -488,6 +540,12 @@ public class VolatilCache implements Cache {
/**
* records alignment identified by id
+ *
+ * @param uri: the URI of the network to record
+ * @param network: the network of ontologies to record
+ * @param force: true if the network is too be recorded even if it was recorded
+ * @return the URI of the recorded network
+ * @throws AlignmentException when something goes wrong (cannot resolve URI)
*/
public String recordNewNetwork( String uri, OntologyNetwork network, boolean force ) throws AlignmentException {
logger.debug( "Recording network with URI {}", uri );
@@ -502,6 +560,11 @@ public class VolatilCache implements Cache {
/**
* records a network identified by id
+ *
+ * @param uri: the URI of the network to record
+ * @param network: the network of ontologies to record
+ * @param force: true if the network is too be recorded even if it was recorded
+ * @return the URI of the recorded network
*/
public String recordNetwork( String uri, OntologyNetwork network, boolean force ) {
// record the network at the corresponding Uri in tables!
@@ -521,6 +584,8 @@ public class VolatilCache implements Cache {
/**
* suppresses the record for a network of ontologies
+ *
+ * @param network: the network of ontologies to record
*/
public void unRecordNetwork( OntologyNetwork network ) {
String id = ((BasicOntologyNetwork)network).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
@@ -542,6 +607,10 @@ public class VolatilCache implements Cache {
/**
* Non publicised class
+ *
+ * @param uri: the URI of the alignment to erase
+ * @param eraseFromDB: true if the alignment is erased from the database cache
+ * @throws AlignmentException when something goes wrong (cannot resolve URI)
*/
public void eraseAlignment( String uri, boolean eraseFromDB ) throws AlignmentException {
Alignment alignment = getAlignment( uri );
diff --git a/src/fr/inrialpes/exmo/align/service/WSAServProfile.java b/src/fr/inrialpes/exmo/align/service/WSAServProfile.java
index 3fbecc2e9fdb45dac6218a6e1d7798e01b026517..8356b1d3c68a26f4b1c2fb3ab0cbce306aa16aa2 100644
--- a/src/fr/inrialpes/exmo/align/service/WSAServProfile.java
+++ b/src/fr/inrialpes/exmo/align/service/WSAServProfile.java
@@ -224,6 +224,12 @@ public class WSAServProfile implements AlignmentServiceProfile {
* and the answer is through the resulting page (RDF? SOAP? HTTP? JSON?)
* Not implemented yet
* but reserved if appears useful
+ *
+ * @param uri: the URI of the request
+ * @param perf: its performative (the action to be processed)
+ * @param header: the HTTP header
+ * @param param: the parameters of the request
+ * @return the answer to the request as a string
*/
public String protocolAnswer( String uri, String perf, Properties header, Properties param ) {
String method = null;
@@ -645,6 +651,9 @@ public class WSAServProfile implements AlignmentServiceProfile {
/**
* Extract parameters from a DOM document resulting from parsing a SOAP messgae
+ *
+ * @param doc: a DOM document resulting from parsing a SOAP messgae
+ * @return the content of the SOAP message as a property set
*/
private Properties getParameters( Document doc ) {
Properties params = new Properties();
diff --git a/src/fr/inrialpes/exmo/align/service/msg/Message.java b/src/fr/inrialpes/exmo/align/service/msg/Message.java
index 5d8691227a67888075ba30c990f43157cbf7b7db..4fc3e834f48fc0eb8cf7b41e689d0f9f9d28094f 100644
--- a/src/fr/inrialpes/exmo/align/service/msg/Message.java
+++ b/src/fr/inrialpes/exmo/align/service/msg/Message.java
@@ -60,6 +60,8 @@ public class Message {
/**
* This must return an XML object, typically an attribute.
+ *
+ * @return a string containing the message as XML
*/
public String RESTString(){
return "<Message>"+getXMLContent()+"</Message>";
@@ -67,6 +69,8 @@ public class Message {
/**
* For HTML interface calling the REST interface
+ *
+ * @return a string containing the message as HTML
*/
public String HTMLRESTString(){
return "<Message/>";
@@ -78,6 +82,8 @@ public class Message {
/**
* This must return a JSON object, that will typically be an attribute value.
+ *
+ * @return a string containing the message as JSON
*/
public String JSONString(){
return "\""+getJSONContent()+"\"";
diff --git a/src/fr/inrialpes/exmo/align/service/osgi/Service.java b/src/fr/inrialpes/exmo/align/service/osgi/Service.java
index fd771ef5a6618aa304e16da84cecbd2bfa964d37..63b6f84bf3540193d7f19a71c0f1f6bed96310fd 100644
--- a/src/fr/inrialpes/exmo/align/service/osgi/Service.java
+++ b/src/fr/inrialpes/exmo/align/service/osgi/Service.java
@@ -65,6 +65,12 @@ public interface Service {
* Basic protocol primitives
*********************************************************************/
+ /**
+ * load an alignment
+ *
+ * @param mess: the parameters of the request
+ * @return the message corresponding to the answer of the request
+ */
public Message load( Properties mess );
public Message align( Properties mess );
@@ -83,6 +89,12 @@ public interface Service {
* Extended protocol primitives
*********************************************************************/
+ /**
+ * store an alignment
+ *
+ * @param mess: the parameters of the request
+ * @return the message corresponding to the answer of the request
+ */
public Message store( Properties mess );
//public Message erase( Properties mess );
@@ -96,6 +108,12 @@ public interface Service {
* There is no way an alignment server could modify an alignment
*********************************************************************/
+ /**
+ * trim an alignment
+ *
+ * @param mess: the parameters of the request
+ * @return the message corresponding to the answer of the request
+ */
public Message trim( Properties mess );
public Message harden( Properties mess );
@@ -116,6 +134,12 @@ public interface Service {
* Network of alignment server implementation
*********************************************************************/
+ /**
+ * load a network of ontologies
+ *
+ * @param params: the parameters of the request
+ * @return the message corresponding to the answer of the request
+ */
public Message loadOntologyNetwork( Properties params );
public Message renderOntologyNetwork( Properties params );
@@ -142,6 +166,12 @@ public interface Service {
* Utilities: reaching and loading ontologies
*********************************************************************/
+ /**
+ * store an alignment
+ *
+ * @param al: the alignment to store
+ * @return true if everything has worked properly
+ */
public boolean storedAlignment( Alignment al );
public boolean storedNetwork( OntologyNetwork on );
diff --git a/src/fr/inrialpes/exmo/ontowrap/LoadedOntology.java b/src/fr/inrialpes/exmo/ontowrap/LoadedOntology.java
index 72e2304b2a3706fb2646d74c8ec161343daebc60..a8233fca255b2013c5bf51b598a6af49a327de41 100644
--- a/src/fr/inrialpes/exmo/ontowrap/LoadedOntology.java
+++ b/src/fr/inrialpes/exmo/ontowrap/LoadedOntology.java
@@ -31,7 +31,8 @@ public interface LoadedOntology<O> extends Ontology<O> {
/**
* returns the entity corresponding to the given URI
* If no such entity exists, may return null or raise an exception
- * @param u an URI
+ *
+ * @param u: the URI of an entity
* @return the corresponding entity in the ontology or null
* @throws OntowrapException when an exception has been caught
*/
@@ -39,7 +40,8 @@ public interface LoadedOntology<O> extends Ontology<O> {
/**
* returns the URI of an entity in the ontology
- * @param o the entity
+ *
+ * @param o: the entity
* @return its URI if it exists or null
* @throws OntowrapException when an exception has been caught
*/
@@ -54,9 +56,10 @@ public interface LoadedOntology<O> extends Ontology<O> {
* last fragment (after the last "/" or just before) in this order.
* Because of its low definiteness, it is not advised to use this primitive
* and it is better to use other ones (getNames, getComments, getAnnotations).
- * @param o the entity
- * @return a label
- * @throws OntowrapException
+ *
+ * @param o: the entity
+ * @return the name of the entity
+ * @throws OntowrapException when something went wrong
*/
public String getEntityName( Object o ) throws OntowrapException;
@@ -68,43 +71,49 @@ public interface LoadedOntology<O> extends Ontology<O> {
* otherwise returns the default name (getEntityName)
* Because of its low definiteness, it is not advised to use this primitive
* and it is better to use other ones (getNames, getComments, getAnnotations).
- * @param o the entity
- * @return a label
- * @throws OntowrapException
+ *
+ * @param o: the entity
+ * @param lang: the code of the language ("en", "fr", "es", etc.)
+ * @return a name of the entity
+ * @throws OntowrapException when something went wrong
*/
public String getEntityName( Object o, String lang ) throws OntowrapException;
/**
* returns all the names of an entity in a language if specified.
* otherwise, returns null
- * @param o the entity
- * @param lang the code of the language ("en", "fr", "es", etc.)
+ *
+ * @param o: the entity
+ * @param lang: the code of the language ("en", "fr", "es", etc.)
* @return the default name
- * @throws OntowrapException
+ * @throws OntowrapException when something went wrong
*/
public Set<String> getEntityNames( Object o, String lang ) throws OntowrapException;
/**
* Returns all the names a given entity (e.g., rdfs:labels in OWL/RDFS).
- * @param o the entity
+ *
+ * @param o: the entity
* @return the set of labels
- * @throws OntowrapException
+ * @throws OntowrapException when something went wrong
*/
public Set<String> getEntityNames( Object o ) throws OntowrapException;
/**
* Returns the values ofof textual properties (e.g., "rdfs:comment", rdfs:label in RDFS/OWL) for a given entity and for a given natural language (attribute xml:lang).
- * @param o the entity
- * @param lang the code of the language ("en", "fr", "es", etc.)
+ *
+ * @param o: the entity
+ * @param lang: the code of the language ("en", "fr", "es", etc.)
* @return the set of comments
- * @throws OntowrapException
+ * @throws OntowrapException when something went wrong
*/
public Set<String> getEntityComments( Object o , String lang ) throws OntowrapException;
/**
* Returns all the values of textual properties (e.g., "rdfs:comment", rdfs:label in RDFS/OWL) for a given entity
- * @param o the entity
+ *
+ * @param o: the entity
* @return the set of comments
- * @throws OntowrapException
+ * @throws OntowrapException when something went wrong
*/
public Set<String> getEntityComments( Object o ) throws OntowrapException;
@@ -112,9 +121,10 @@ public interface LoadedOntology<O> extends Ontology<O> {
* Returns all the values of the "owl:AnnotationProperty" property for a given entity.
* These annotations are those predefined in owl (owl:versionInfo, rdfs:label, rdfs:comment, rdfs:seeAlso and rdfs:isDefinedBy)
* but also all other defined annotation properties which are subClass of "owl:AnnotationProperty"
- * @param o the entity
+ *
+ * @param o: the entity
* @return the set of annotation values
- * @throws OntowrapException
+ * @throws OntowrapException when something went wrong
*/
public Set<String> getEntityAnnotations( Object o ) throws OntowrapException;
@@ -124,10 +134,11 @@ public interface LoadedOntology<O> extends Ontology<O> {
* Returns all the values of the "owl:AnnotationProperty" property for a given entity expressed in the required language.
* These annotations are those predefined in owl (owl:versionInfo, rdfs:label, rdfs:comment, rdfs:seeAlso and rdfs:isDefinedBy)
* but also all other defined annotation properties which are subClass of "owl:AnnotationProperty"
- * @param o the entity
- * @param lang the code of the language ("en", "fr", "es", etc.)
+ *
+ * @param o: the entity
+ * @param lang: the code of the language ("en", "fr", "es", etc.)
* @return the set of annotation values
- * @throws OntowrapException
+ * @throws OntowrapException when something went wrong
*/
public Set<String> getEntityAnnotations( Object o, String lang ) throws OntowrapException;
@@ -140,7 +151,9 @@ public interface LoadedOntology<O> extends Ontology<O> {
/**
* Returns all named entities having URI beginning with the ontology URI
+ *
* @return the set of entities
+ * @throws OntowrapException when something went wrong
*/
public Set<? extends Object> getEntities() throws OntowrapException;
public Set<? extends Object> getClasses() throws OntowrapException;
diff --git a/src/fr/inrialpes/exmo/ontowrap/OntologyFactory.java b/src/fr/inrialpes/exmo/ontowrap/OntologyFactory.java
index 84077c067aab75ed64ef50bfba6d0bacefe17f95..6369c296de5ea7f697ebb16a06500b33d948b658 100644
--- a/src/fr/inrialpes/exmo/ontowrap/OntologyFactory.java
+++ b/src/fr/inrialpes/exmo/ontowrap/OntologyFactory.java
@@ -141,12 +141,19 @@ public abstract class OntologyFactory {
/**
* All Ontologies must implement clearCache()
* which unload their ontologies if any cache is enabled.
+ *
+ * @throws OntowrapException when something goes wrong
*/
public abstract void clearCache() throws OntowrapException;
/**
* Encapsulate an ontology already in the environment
* These methods should rather be in a LoadableOntologyFactory
+ *
+ * @param onto: the ontology to be encapsulated
+ * @param onlyLocalEntities: true if only the entities in the namespace of the ontology have to be considered
+ * @return the LoadedOntology object
+ * @throws OntowrapException when something goes wrong
*/
public abstract LoadedOntology<? extends Object> newOntology( Object onto , boolean onlyLocalEntities ) throws OntowrapException;
@@ -157,14 +164,22 @@ public abstract class OntologyFactory {
/**
* Load an ontology, cache enabled
* These methods should rather be in a LoadableOntologyFactory
+ *
+ * @param uri: the URI (URL) of the ontology to load
+ * @return the loaded ontology
+ * @throws OntowrapException when something goes wrong
*/
public LoadedOntology<? extends Object> loadOntology( URI uri ) throws OntowrapException {
// logger.trace( "loading URI: {}", uri );
return loadOntology( uri, true );
}
- /*
+ /**
* Loads and ontology which is not loaded yet
+ *
+ * @param onto: the Ontology object corresponding to the ontology to load
+ * @return the corresponding LoadedOntology object
+ * @throws OntowrapException when something goes wrong
*/
public LoadedOntology<? extends Object> loadOntology( Ontology<? extends Object> onto ) throws OntowrapException {
// logger.trace( "loading Ontology: {}", onto );
@@ -182,6 +197,11 @@ public abstract class OntologyFactory {
/**
* Load an ontology, cache enabled
* These methods should rather be in a LoadableOntologyFactory
+ *
+ * @param uri: the URI (URL) of the ontology to load
+ * @param onlyLocalEntities: true if only the entities in the namespace of the ontology have to be considered
+ * @return the LoadedOntology object
+ * @throws OntowrapException when something goes wrong
*/
public abstract LoadedOntology<? extends Object> loadOntology( URI uri, boolean onlyLocalEntities ) throws OntowrapException;
diff --git a/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntology.java b/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntology.java
index afb47057a3e5ad39c75b220e0f7ef26d69c36b4b..935cea64fce011cd4a744f41dd5c8b765af0171d 100644
--- a/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntology.java
+++ b/src/fr/inrialpes/exmo/ontowrap/owlapi10/OWLAPIOntology.java
@@ -530,6 +530,9 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements HeavyL
/**
* returns emptyset in case of error (e.g., if p is a property)
+ *
+ * @param p: the class on which to find cardinality restrictions
+ * @return the set of cardinality restrictions
*/
public Set<Object> getCardinalityRestrictions( Object p ){
Set<Object> spcl = new HashSet<Object>();
@@ -545,6 +548,9 @@ public class OWLAPIOntology extends BasicOntology<OWLOntology> implements HeavyL
/**
* Inherits all properties of a class
+ *
+ * @param cl: the class on which to find cardinality restrictions
+ * @return the set of inherited properties of the class
*/
private Set<Object> getInheritedProperties( OWLClass cl ) {
Set<Object> resultSet = new HashSet<Object>();
diff --git a/src/fr/inrialpes/exmo/ontowrap/owlapi30/OWLAPI3Ontology.java b/src/fr/inrialpes/exmo/ontowrap/owlapi30/OWLAPI3Ontology.java
index 735329fa7f9f58092cbe6b4497abda8e8eb977c9..64c38d81ade2be75be196fc669888aa7d61ef2cb 100644
--- a/src/fr/inrialpes/exmo/ontowrap/owlapi30/OWLAPI3Ontology.java
+++ b/src/fr/inrialpes/exmo/ontowrap/owlapi30/OWLAPI3Ontology.java
@@ -120,6 +120,11 @@ public class OWLAPI3Ontology extends BasicOntology<OWLOntology> implements Heavy
/**
* type and lang can be null
+ *
+ * @param o: the OWL entity on which to find annotations
+ * @param type: the URI of the annotation type
+ * @param lang: the code of the language ("en", "fr", "es", etc.)
+ * @return the set of annotations on the entity expressed in the given language
*/
protected Set<String> getEntityAnnotations( Object o, URI type, String lang ) {
// We cannot retreive encapsulated annotations with this API
diff --git a/src/fr/inrialpes/exmo/ontowrap/skosapi/SKOSThesaurus.java b/src/fr/inrialpes/exmo/ontowrap/skosapi/SKOSThesaurus.java
index 8f8ab92103ec64df6aab96e1682054b2de3a3bb3..3b9ad94a74e7f046d53bc4e2d44c5e4549f35ae0 100644
--- a/src/fr/inrialpes/exmo/ontowrap/skosapi/SKOSThesaurus.java
+++ b/src/fr/inrialpes/exmo/ontowrap/skosapi/SKOSThesaurus.java
@@ -68,11 +68,11 @@ public class SKOSThesaurus extends BasicOntology<SKOSDataset> implements HeavyLo
* ontology (the S is for Simple).
*
* Translation from SKOS to OWL (by Antoine Isaac):
- * skos:Concept --> owl:Class
- * skos:broader --> rdfs:subClassOf
- * skos:prefLabel, skos:altLabel, skos:hiddenLabel --> rdfs:label
- * skos:notes, skos:definition, skos:scopeNote --> rdfs:comments
- * skos:related --> rdfs:seeAlso [ignored]
+ * skos:Concept --> owl:Class
+ * skos:broader -->, rdfs:subClassOf
+ * skos:prefLabel, skos:altLabel, skos:hiddenLabel --> rdfs:label
+ * skos:notes, skos:definition, skos:scopeNote --> rdfs:comments
+ * skos:related --> rdfs:seeAlso [ignored]
*
* OK So what is in the SKOS Data model, since this is the only one that we
* will take into account...
@@ -86,7 +86,7 @@ public class SKOSThesaurus extends BasicOntology<SKOSDataset> implements HeavyLo
*
**/
- /**
+ /*
onto.getSKOSDataRelationAssertions(concept)
assertion.getSKOSObject();
@@ -100,14 +100,20 @@ lang = untypedLiteral.getLang();
}}
*/
-
- public void getDataValues( SKOSConcept o, SKOSDataProperty p, Set<String> result ){
+ /**
+ * Returns one of the prefLabel property values for a given SKOS concept.
+ *
+ * @param o: the concept whose property value is sought
+ * @param p: the sought property
+ * @param result: a set of strings containing the result
+ */
+ private void getDataValues( SKOSConcept o, SKOSDataProperty p, Set<String> result ){
for ( SKOSLiteral lit : onto.getSKOSDataRelationByProperty( o, p ) ){
result.add( lit.getLiteral() );
}
}
- public void getDataValues( SKOSConcept o, SKOSDataProperty p, Set<String> result, String lang ){
+ private void getDataValues( SKOSConcept o, SKOSDataProperty p, Set<String> result, String lang ){
for ( SKOSLiteral lit : onto.getSKOSDataRelationByProperty( o, p ) ){
if ( !lit.isTyped() ) {
SKOSUntypedLiteral l = lit.getAsSKOSUntypedLiteral();
@@ -119,18 +125,19 @@ lang = untypedLiteral.getLang();
/**
We should document:
- name < names
+ name < names
annotations
- comments(lang) < comments
+ comments(lang) < comments
**/
// NEARLY DONE
/**
- * returns one of the prefLabel property values for a given SKOS concept.
- * @param o the entity
- * @return a label
- * @throws OntowrapException
- * JE// This is not satisfying because in case of several PrefLabels it will return the first one...
+ * Returns one of the prefLabel property values for a given SKOS concept.
+ *
+ * @param o: the entity whose name is sought
+ * @return the name of the entity
+ * @throws OntowrapException when something goes wrong
+ * JE: This is not satisfying because in case of several PrefLabels it will return the first one...
*/
public String getEntityName( Object o ) throws OntowrapException {
Set<String> result = new HashSet<String>();
@@ -141,12 +148,13 @@ lang = untypedLiteral.getLang();
// NEARLY DONE
/**
- * returns one of the prefLabel property values for a given SKOS concept in a given language.
- * @param o the entity
- * @param lang the code of the language ("en", "fr", "es", etc.)
- * @return a label
- * @throws OntowrapException
- * JE// This is not satisfying because in case of several PrefLabels it will return the first one...
+ * Returns one of the prefLabel property values for a given SKOS concept in a given language.
+ *
+ * @param o: the entity whose prefered label is sought
+ * @param lang: the code of the language ("en", "fr", "es", etc.)
+ * @return the preferred label in the given language if available
+ * @throws OntowrapException when something goes wrong
+ * JE: This is not satisfying because in case of several PrefLabels it will return the first one...
*/
public String getEntityName( Object o, String lang ) throws OntowrapException {
Set<String> result = new HashSet<String>();
@@ -157,10 +165,11 @@ lang = untypedLiteral.getLang();
/**
* Returns the values of the prefLabel, hiddenLabel and altLabel properties in a given language.
- * @param o the entity
- * @param lang the code of the language ("en", "fr", "es", etc.)
- * @return the set of labels
- * @throws OntowrapException
+ *
+ * @param o: the entity whose preferred labels are sought
+ * @param lang: the code of the language ("en", "fr", "es", etc.)
+ * @return the set of preferred label in the given language if available
+ * @throws OntowrapException when something goes wrong
*/
public Set<String> getEntityNames( Object o, String lang ) throws OntowrapException {
Set<String> result = new HashSet<String>();
@@ -172,9 +181,10 @@ lang = untypedLiteral.getLang();
/**
* Returns the values of the prefLabel, hiddenLabel and altLabel properties.
- * @param o the concept
- * @return the set of labels
- * @throws OntowrapException
+ *
+ * @param o: the concept
+ * @return the set of labels of the concept
+ * @throws OntowrapException when something goes wrong
*/
public Set<String> getEntityNames(Object o) throws OntowrapException {
Set<String> result = new HashSet<String>();
@@ -188,10 +198,11 @@ lang = untypedLiteral.getLang();
// TODO
/**
* Returns the values of the "rdfs:comment" property for a given entity and for a given natural language (attribute xml:lang).
- * @param o the entity
- * @param lang the code of the language ("en", "fr", "es", etc.)
- * @return the set of comments
- * @throws OntowrapException
+ *
+ * @param o: the concept the comments on which are sought
+ * @param lang: the code of the language ("en", "fr", "es", etc.)
+ * @return the set of comments in the given language
+ * @throws OntowrapException when something goes wrong
*/
public Set<String> getEntityComments(Object o, String lang) throws OntowrapException {
Set<String> comments = new HashSet<String>();
@@ -213,9 +224,10 @@ lang = untypedLiteral.getLang();
// TODO
/**
* Returns all the values of the "rdfs:comment" property for a given entity
- * @param o the entity
- * @return the set of comments
- * @throws OntowrapException
+ *
+ * @param o: the concept the comments on which are sought
+ * @return the set of comments on the concept
+ * @throws OntowrapException when something goes wrong
*/
public Set<String> getEntityComments( Object o ) throws OntowrapException {
return getEntityComments(o,null);
@@ -229,9 +241,10 @@ lang = untypedLiteral.getLang();
* skos:note, skos:changeNote, skos:definition, skos:editorialNote,
* skos:example, skos:historyNote and skos:scopeNote
* but also all other defined annotation properties which are subClass of "owl:AnnotationProperty"
- * @param o the entity
- * @return the set of annotation values
- * @throws OntowrapException
+ *
+ * @param o: the concept the annotations on which are sought
+ * @return the set of annotations on the concept
+ * @throws OntowrapException when something goes wrong
*/
public Set<String> getEntityAnnotations( Object o ) throws OntowrapException {
Set<String> annots = new HashSet<String>();
@@ -249,6 +262,11 @@ lang = untypedLiteral.getLang();
/**
* There is no languages on annotations in SKOS API
* Hence we return all of them
+ *
+ * @param o: the concept the annotations on which are sought
+ * @param lang: the code of the language ("en", "fr", "es", etc.)
+ * @return the set of annotations on the concept in the given language
+ * @throws OntowrapException when something goes wrong
*/
public Set<String> getEntityAnnotations( Object o, String lang ) throws OntowrapException {
return getEntityAnnotations( o );
diff --git a/src/fr/inrialpes/exmo/queryprocessor/QueryProcessor.java b/src/fr/inrialpes/exmo/queryprocessor/QueryProcessor.java
index 2527eaabc1bad7c9f93fd1d10cf7ffa9545f661c..d81a4afb7cb72c21b7ef49fbefd59787a8cf5fd0 100644
--- a/src/fr/inrialpes/exmo/queryprocessor/QueryProcessor.java
+++ b/src/fr/inrialpes/exmo/queryprocessor/QueryProcessor.java
@@ -35,27 +35,33 @@ public interface QueryProcessor {
/**
* @param query -- The query string
* @param type -- The query type, can be one of SELECT, ASK, CONSTRUCT, or DESCRIBE
- * @return Result, result form depends on type
+ * @return the query result as a Result object depending on type
*/
- public Result query(String query, Type type);
+ public Result query( String query, Type type );
/**
- *@param query -- The query string
+ * @param query -- The query string
+ * @return the query result as a Result object
*/
- public Result query(String query);
+ public Result query( String query );
/**
- *@param query -- The query string
- *@return query results as string
+ * @param query -- The query string
+ * @return the query results as a string
*/
- public String queryWithStringResults(String query);
+ public String queryWithStringResults( String query );
/**
- *@param query -- the query string
- *@return the type of the query
+ * @param query -- the query string
+ * @return the type of the query
*/
- public int getType(String query);
+ public int getType( String query );
- public void loadOntology(String uri);
+ /**
+ * Loads an ontology
+ *
+ * @param uri -- the URI of the ontology to load
+ */
+ public void loadOntology( String uri );
}
diff --git a/src/fr/inrialpes/exmo/queryprocessor/Result.java b/src/fr/inrialpes/exmo/queryprocessor/Result.java
index 9dcf06df07ad4932d018c8e059ab018d72ddd134..6eac6e947861067ae956d08ea79fe9b48a35afbd 100644
--- a/src/fr/inrialpes/exmo/queryprocessor/Result.java
+++ b/src/fr/inrialpes/exmo/queryprocessor/Result.java
@@ -28,24 +28,32 @@ import java.util.Vector;
* @author Arun Sharma
*/
public interface Result {
- /**@return the type of the result set
+ /**
+ * @return the type of the result set
*/
public int getType();
- /**@return the reslut for ASK type queries
+ /**
+ * @return the reslut for ASK type queries
+ * @throws QueryTypeMismatchException when the query cannot be evaluated
*/
public boolean getAskResult() throws QueryTypeMismatchException;
/**
- *@return the RDF graph for construct queries
+ * @return the RDF graph for construct queries
+ * @throws QueryTypeMismatchException when the query cannot be evaluated
*/
public RDFGraph getConstructResult() throws QueryTypeMismatchException;
- /**@return a collection set for SELECT queries
+ /**
+ * @return a collection set for SELECT queries
+ * @throws QueryTypeMismatchException when the query cannot be evaluated
*/
public Collection<Vector<Object>> getSelectResult() throws QueryTypeMismatchException;
- /**@return an XML string for the SELECT queries
+ /**
+ * @return an XML string for the SELECT queries
+ * @throws QueryTypeMismatchException when the query cannot be evaluated
*/
public String getSelectResultasXML() throws QueryTypeMismatchException;
diff --git a/src/org/semanticweb/owl/align/Alignment.java b/src/org/semanticweb/owl/align/Alignment.java
index c7a99901382fceafa2efc6ba0df2518eae64fe44..0e8e55c6b6a3a89278b015b00bfdea77edc97fcf 100644
--- a/src/org/semanticweb/owl/align/Alignment.java
+++ b/src/org/semanticweb/owl/align/Alignment.java
@@ -45,34 +45,55 @@ import org.xml.sax.ContentHandler;
public interface Alignment extends Cloneable, Iterable<Cell>, Visitable {
/** Initialize the alignement before using it
- * @param onto1, @param onto2: the two ontologies aligned
- * @throws AlignmentException
+ * @param onto1 and
+ * @param onto2: the two ontologies aligned
+ * @throws AlignmentException if cannot initialize
**/
public void init( Object onto1, Object onto2 ) throws AlignmentException;
/**
* Initialize the alignement before using it, with some ontology caching trick
* //@deprecated The OntologyCache is now internal, use init( onto1, onto2 ) instead
- * @param onto1, @param onto2: the two ontologies aligned
+ * @param onto1 and
+ * @param onto2: the two ontologies aligned
* @param cache: a cache where to find and store the ontologies
- * @throws AlignmentException
+ * @throws AlignmentException when cannot initialise
**/
//@Deprecated
public void init( Object onto1, Object onto2, Object cache ) throws AlignmentException;
- /** Alignment methods **/
+ /* Alignment methods */
+ /**
+ * @return the first ontology of the alignment
+ */
public Object getOntology1();
+
+ /**
+ * @return the second ontology of the alignment
+ */
public Object getOntology2();
+
+ /**
+ * @return the URI of the first ontology of the alignment
+ * @throws AlignmentException when no URI is found (unlikely)
+ */
public URI getOntology1URI() throws AlignmentException;
+
+ /**
+ * @return the URI of the second ontology of the alignment
+ * @throws AlignmentException when no URI is found (unlikely)
+ */
public URI getOntology2URI() throws AlignmentException;
public void setOntology1(Object ontology) throws AlignmentException;
public void setOntology2(Object ontology) throws AlignmentException;
/**
* Alignment type:
- * Currently defined a sa String.
+ * Currently defined as a String.
* This string is supposed to contain two characters: among ?, 1, *, +
* Can be implemented otherwise
+ *
+ * @param level the level of the alignment
*/
public void setLevel( String level );
public String getLevel();
@@ -81,18 +102,21 @@ public interface Alignment extends Cloneable, Iterable<Cell>, Visitable {
* Currently defined a sa String.
* This string is supposed to contain two characters: among ?, 1, *, +
* Can be implemented otherwise
+ *
+ * @param type the type of the alignment
*/
public void setType( String type );
public String getType();
/**
- * Alignment type:
- * Currently defined a sa String.
- * This string is supposed to contain two characters: among ?, 1, *, +
- * Can be implemented otherwise
+ * Set the ontology used by the alignment
+ * This URI is in fact a URL of where to fetch the ontology.
+ * It may be local.
+ *
+ * @param file: the URI of the first ontology
*/
- public void setFile1( URI type );
- public void setFile2( URI type );
+ public void setFile1( URI file );
+ public void setFile2( URI file );
public URI getFile1();
public URI getFile2();
@@ -109,11 +133,19 @@ public interface Alignment extends Cloneable, Iterable<Cell>, Visitable {
/**
* Cells are created and indexed at once
+ *
+ * @param ob1 the object of the first ontology in the correspondence
+ * @param ob2 the object of the second ontology in the correspondence
+ * @param relation the relation between these objects
+ * @param measure the confidence measure in the correspondence
+ * @return the corresponding cell
+ * @throws AlignmentException when something goes wrong (unknown objects, bad relation)
*/
- public Cell addAlignCell( Object ob1, Object ob, String relation, double measure) throws AlignmentException;
+ public Cell addAlignCell( Object ob1, Object ob2, String relation, double measure) throws AlignmentException;
public Cell addAlignCell( Object ob1, Object ob2) throws AlignmentException;
public void remCell( Cell c ) throws AlignmentException;
+
/**
* Cells are retrieved
* These primitives are deprecated. Use getAlignCells1 and getAlignCells2
@@ -121,15 +153,23 @@ public interface Alignment extends Cloneable, Iterable<Cell>, Visitable {
* Reason: this applies only for 1:1 alignments
* Some implementations might act cleverly (retrieving the best value).
* Basic implementations may raise the exception
+ *
+ * @param ob the object of the first ontology from which to retrieve the correspondence
+ * @return the corresponding cell
+ * @throws AlignmentException when something goes wrong
* //@deprecated There is more than one cell about one object
*/
//@Deprecated
public Cell getAlignCell1( Object ob ) throws AlignmentException;
/**
* //@deprecated There is more than one cell about one object
+ * @param ob the object of the second ontology from which to retrieve the correspondence
+ * @return the corresponding cell
+ * @throws AlignmentException when something goes wrong
*/
//@Deprecated
public Cell getAlignCell2( Object ob ) throws AlignmentException;
+
/**
* Each part of the cell can be queried independently.
* These primitives are deprecated. Use getAlignCells1 and getAlignCells2
@@ -137,6 +177,11 @@ public interface Alignment extends Cloneable, Iterable<Cell>, Visitable {
* Reason: this applies only for 1:1 alignments
* Some implementations might act cleverly (retrieving the best value).
* Basic implementations may raise the exception
+ *
+ * @param ob the object of the first ontology from which to retrieve the correspondence
+ * @return the corresponding object
+ * @throws AlignmentException when something goes wrong
+ * //@deprecated There is more than one cell about one object
*/
public Object getAlignedObject1( Object ob ) throws AlignmentException;
public Object getAlignedObject2( Object ob ) throws AlignmentException;
@@ -152,6 +197,10 @@ public interface Alignment extends Cloneable, Iterable<Cell>, Visitable {
* Reason: this applies only for 1:1 alignments
* Some implementations might act cleverly (retrieving the best value).
* Basic implementations may raise the exception
+ *
+ * @param ob the object of the first ontology from which to retrieve the correspondences
+ * @return the set of correspondences involving this object
+ * @throws AlignmentException when something goes wrong
*/
public Set<Cell> getAlignCells1( Object ob ) throws AlignmentException;
public Set<Cell> getAlignCells2( Object ob ) throws AlignmentException;
@@ -161,6 +210,8 @@ public interface Alignment extends Cloneable, Iterable<Cell>, Visitable {
* to the alignment structure itself.
* getExtensions returns a set of tripes: uri*label*value
* all three being String
+ *
+ * @return the collection of extensions of the alignment
*/
public Collection<String[]> getExtensions();
public String getExtension( String uri, String label );
@@ -175,7 +226,10 @@ public interface Alignment extends Cloneable, Iterable<Cell>, Visitable {
// HARD,
// ...
// }
- /*
+ /**
+ * Trim an alignment under a particular threshold
+ *
+ * @param method: a string indicating the cutting method
* - getting those cells with strength above n (hard)
* - getting the n best cells (best)
* - getting those cells with strength at worse n under the best (span)
@@ -183,14 +237,17 @@ public interface Alignment extends Cloneable, Iterable<Cell>, Visitable {
* - getting those cells with strength at worse n% of the best (prop)
* - getting all cells until a gap of n (hardgap)
* - getting all cells until a gap of n% of the last (propgap)
+ * @param threshold: the threshold
+ * @throws AlignmentException when something goes wrong (unknown method)
*/
-
public void cut( String method, double threshold ) throws AlignmentException;
public void cut( double threshold ) throws AlignmentException;
public void harden( double threshold ) throws AlignmentException;
/**
* Algebra of alignment manipulation operations: compose, join, meet.
+ * @return the inverse alignment from onto2 to onto1
+ * @throws AlignmentException when something goes wrong (unlikely)
*/
public Alignment inverse() throws AlignmentException;
public Alignment diff(Alignment align) throws AlignmentException;
@@ -205,20 +262,27 @@ public interface Alignment extends Cloneable, Iterable<Cell>, Visitable {
* methods in Cell and Relation.
*/
/**
+ * Dumps an alignment into a SAX handler
* Dump should be implemented as a method generating SAX events
* for a SAXHandler provided as input
+ *
+ * @param h: a SAX content handler
*/
public void dump(ContentHandler h);
// public void write( PrintStream writer ) throws IOException, AlignmentException;
//public void write( PrintWriter writer ) throws IOException, AlignmentException;
/** Exporting
- The alignments are exported for other purposes.
+ * The alignments are exported for other purposes.
+ *
+ * @param renderer an AlignmentVisitor object which determines how the alignment is rendered
+ * @throws AlignmentException when something goes wrong (cannot render in this format)
*/
public void render( AlignmentVisitor renderer ) throws AlignmentException;
/** Implementation of the clone method
- */
+ * @return a clone of the alignment
+ */
public Object clone();
}
diff --git a/src/org/semanticweb/owl/align/AlignmentProcess.java b/src/org/semanticweb/owl/align/AlignmentProcess.java
index 243fbbfd3b3c88a69bdeabf5a02282271a0d7a6a..6f5c92edfeaa56f996b6a1460f8af0d374e5c845 100644
--- a/src/org/semanticweb/owl/align/AlignmentProcess.java
+++ b/src/org/semanticweb/owl/align/AlignmentProcess.java
@@ -36,6 +36,10 @@ public interface AlignmentProcess extends Alignment
* The align method computes the alignment from the ontologies.
* It is hightly dependent on the implementation.
* It take an initial Alignment as input.
+ *
+ * @param alignment: an alignment taken as input to the matching operation (may be null)
+ * @param param: the parameter of the matching operation
+ * @throws AlignmentException when something goes wrong
*/
public void align( Alignment alignment, Properties param ) throws AlignmentException;
diff --git a/src/org/semanticweb/owl/align/AlignmentRepairer.java b/src/org/semanticweb/owl/align/AlignmentRepairer.java
index 94e8299f88f08508562d6a805c4e3ff42ef5015c..97713886307179ca39586b967ed0f28a956e68de 100644
--- a/src/org/semanticweb/owl/align/AlignmentRepairer.java
+++ b/src/org/semanticweb/owl/align/AlignmentRepairer.java
@@ -41,6 +41,9 @@ public interface AlignmentRepairer {
*
* Known parameters (for both alignments and networks):
* - reasoner (hermit|pellet|elk): which reasoner is used
+ *
+ * @param param: set of properties expressing the parameters for this repairer
+ * @throws AlignmentException when something goes wrong
*/
public void init( Properties param ) throws AlignmentException;
@@ -59,11 +62,21 @@ public interface AlignmentRepairer {
* - optimality (global|local|greedy|greedymin|globaliso): does the repairer look for particular optimum
* - entities (concepts|properties|conceptproperties): types of correspondences taken into account
* -
+ *
+ * @param alignment: the alignment to be repaired
+ * @param param: specific repairing parameters as properties
+ * @return the repaired alignment
+ * @throws AlignmentException when something goes wrong
*/
public Alignment repair( Alignment alignment, Properties param ) throws AlignmentException;
/**
* Perform repair on a whole network of ontologies.
+ *
+ * @param network: the network of ontologies to be repaired
+ * @param param: specific repairing parameters as properties
+ * @return the repaired network of ontologies
+ * @throws AlignmentException when something goes wrong
*/
public OntologyNetwork repair( OntologyNetwork network, Properties param ) throws AlignmentException;
diff --git a/src/org/semanticweb/owl/align/Cell.java b/src/org/semanticweb/owl/align/Cell.java
index 8b27e4180e0c75ac3e19d34b70dd72681fb88c94..9896229f5d522ed626a436f76d5a7bd4f3341c61 100644
--- a/src/org/semanticweb/owl/align/Cell.java
+++ b/src/org/semanticweb/owl/align/Cell.java
@@ -44,7 +44,9 @@ import org.xml.sax.SAXException;
public interface Cell extends Comparable<Cell>, Visitable {
/** Creation **/
-
+ /**
+ * @return the Id of the cell (null if there is no id)
+ */
public String getId();
public void setId( String id );
public String getSemantics();
@@ -52,11 +54,15 @@ public interface Cell extends Comparable<Cell>, Visitable {
public Object getObject1();
public Object getObject2();
/**
+ * @return the URI of the object of the first ontology
+ * @throws AlignmentException if something goes wrong (has no URI)
* //@deprecated use getObject1AsURI( null ) instead
*/
//@Deprecated
public URI getObject1AsURI() throws AlignmentException;
/**
+ * @return the URI of the object of the first ontology
+ * @throws AlignmentException if something goes wrong (has no URI)
* //@deprecated use getObject2AsURI( null ) instead
*/
//@Deprecated
@@ -77,6 +83,8 @@ public interface Cell extends Comparable<Cell>, Visitable {
* to the Cell structure itself.
* getExtensions returns a set of tripes: uri*label*value
* all three being String
+ *
+ * @return the collection of extensions of the alignment
*/
public Collection<String[]> getExtensions();
//public Parameters getExtensions();
@@ -88,7 +96,11 @@ public interface Cell extends Comparable<Cell>, Visitable {
// V5: This will have to be Set<Cell> compose...
public Cell compose( Cell c ) throws AlignmentException;
- /** Housekeeping **/
+ /**
+ * Dumps an alignment into a SAX handler
+ *
+ * @param h: a SAX content handler
+ */
public void dump(ContentHandler h);
// public void write( PrintStream writer ) throws IOException, AlignmentException;
// public void write( PrintWriter writer ) throws IOException, AlignmentException;
diff --git a/src/org/semanticweb/owl/align/Evaluator.java b/src/org/semanticweb/owl/align/Evaluator.java
index 6490a622fc6ee44e97ad117305f5be98a2028fe7..5870399dddfa797a9d1b3c5c3297d69d4da4a988 100644
--- a/src/org/semanticweb/owl/align/Evaluator.java
+++ b/src/org/semanticweb/owl/align/Evaluator.java
@@ -21,6 +21,8 @@
package org.semanticweb.owl.align;
import java.io.PrintWriter;
+import java.io.IOException;
+
import java.util.Properties;
/**
@@ -39,6 +41,10 @@ public interface Evaluator {
* Run the evaluation between the two ontologies.
* Returns a double (between 0 and 1) providing an idea of the
* proximity
+ *
+ * @param param: evaluation parameters
+ * @return the result of the evaluation as a single value
+ * @throws AlignmentException when something goes wrong
*/
public double eval( Properties param ) throws AlignmentException;
@@ -47,6 +53,11 @@ public interface Evaluator {
* Returns a double (between 0 and 1) providing an idea of the
* proximity
* The additional argument allows to cache the ontologies if necessary
+ *
+ * @param param: evaluation parameters
+ * @param cache: an ontology cache
+ * @return the result of the evaluation as a single value
+ * @throws AlignmentException when something goes wrong
* //@deprecated The OntologyCache is now internal, use eval( params ) instead
**/
//@Deprecated
@@ -56,12 +67,17 @@ public interface Evaluator {
/**
* Outputs (in XML/RDF) a full report on the proximity of the two
* ontologies.
+ *
+ * @param writer: the writer to use for outputing the evaluation
+ * @throws IOException when the output cannot be performed
*/
- public void write( PrintWriter writer ) throws java.io.IOException ;
+ public void write( PrintWriter writer ) throws IOException ;
/**
* Returns the results as a property list not further described but
* suitable for display.
+ *
+ * @return the results as a set of properties
*/
public Properties getResults();
}
diff --git a/src/org/semanticweb/owl/align/OntologyNetwork.java b/src/org/semanticweb/owl/align/OntologyNetwork.java
index 3675bdc3cf3688b178472c621f6b6d3902148a68..963fa9fa4d898e5b3d5b20b9ad820b2330c7b8d3 100644
--- a/src/org/semanticweb/owl/align/OntologyNetwork.java
+++ b/src/org/semanticweb/owl/align/OntologyNetwork.java
@@ -49,6 +49,8 @@ public interface OntologyNetwork extends Cloneable {
/**
* close reflexively the network.
* The network is modified.
+ *
+ * @throws AlignmentException if something goes wrong
*/
public void invert() throws AlignmentException;
}
diff --git a/src/org/semanticweb/owl/align/Relation.java b/src/org/semanticweb/owl/align/Relation.java
index 7e9b2ea7a9533095fda2996f5733f65bf081519f..0b1e546581311979952b7693f08e40ac79c04a32 100644
--- a/src/org/semanticweb/owl/align/Relation.java
+++ b/src/org/semanticweb/owl/align/Relation.java
@@ -32,7 +32,7 @@ import org.xml.sax.ContentHandler;
public interface Relation extends Visitable {
- /** Creation **/
+
public String getRelation();
// V5: this, especially compose should be allowed to throw errors
@@ -43,7 +43,9 @@ public interface Relation extends Visitable {
// It should be deprecated in version 5 of the API!
public boolean equals( Relation r );
- /** Housekeeping **/
+ /** Housekeeping
+ * @param h: a SAX content handler
+ **/
public void dump( ContentHandler h );
public void write( PrintWriter writer );