diff --git a/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/AlignView.java b/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/AlignView.java
index ebfcd2e5e263b28cd8078e4f42a326065f6ca6f4..b0f023e55666463599e6b8ece74d16527fe3b0ff 100755
--- a/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/AlignView.java
+++ b/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/AlignView.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2007-2010, 2014
+ * Copyright (C) INRIA, 2007-2010, 2014-2015
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -75,18 +75,11 @@ import org.osgi.framework.Bundle;
import org.eclipse.core.runtime.Path;
import org.eclipse.core.runtime.FileLocator;
-//import org.eclipse.jface.dialogs.MessageDialog;
-//import org.semanticweb.kaon2.api.OntologyManager;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentVisitor;
-//import com.ontoprise.config.IConfig;
import org.neontoolkit.core.NeOnCorePlugin;
-//import org.neontoolkit.datamodel.DatamodelPlugin;
-//import org.neontoolkit.core.DatamodelTypes;
-//import com.ontoprise.ontostudio.datamodel.exception.ControlException;
-
import org.neontoolkit.core.command.project.CreateProject;
import org.neontoolkit.core.project.IOntologyProject;
import org.neontoolkit.core.project.OntologyProjectManager;
@@ -117,12 +110,8 @@ public class AlignView extends ViewPart implements SelectionListener, Listener {
localImportButton, serverImportButton, uploadButton,
localTrimButton, serverTrimButton, connButton, goButton, offlineButton, onlineButton;
private Button storeButton, matchButton, findButton, findAllButton;// fetchButton;
- //private String selectedProject = null;
- //private Section ontoSelectSection;
- //private Section alignViewSection;
private String selectedOnto1, selectedOnto2, selectedLocalAlign, selectedServerAlign;
- //private String[] ontoList = new String[0];
private String[] methodList = new String[0];
private HashMap<String,String> ontoByProj = new HashMap<String,String>(0);
@@ -158,7 +147,6 @@ public class AlignView extends ViewPart implements SelectionListener, Listener {
@Override
public void createPartControl(final Composite parent) {
- //FormToolkit formToolkit = new FormToolkit(Display.getCurrent());
formToolkit = new FormToolkit(Display.getCurrent());
ScrolledForm scrolledForm = formToolkit.createScrolledForm(parent);
Composite body = scrolledForm.getBody();
@@ -175,7 +163,6 @@ public class AlignView extends ViewPart implements SelectionListener, Listener {
IPath location = root.getLocation();
String path = location.toOSString();
- //ontoFolder = new File(path + IPath.SEPARATOR + "onto");
ontoFolder = new File(path + IPath.SEPARATOR + "align");
if (!ontoFolder.exists()) ontoFolder.mkdir();
@@ -207,7 +194,6 @@ public class AlignView extends ViewPart implements SelectionListener, Listener {
onlineButton.addSelectionListener(this);
// JE-RR for current version of the Alignment plug in
onlineButton.setEnabled( true );
- //onlineButton.setEnabled( false );
offlineButton = new Button(client, SWT.PUSH);
offlineButton.setText("Offline");
@@ -218,7 +204,6 @@ public class AlignView extends ViewPart implements SelectionListener, Listener {
Label dummy1 = new Label(client, SWT.NONE);
Label dummy2 = new Label(client, SWT.NONE);
Label dummy3 = new Label(client, SWT.NONE);
- //Label dummy4 = new Label(client, SWT.NONE);
// Choose ontology 1
Label onto1 = new Label(client, SWT.NONE);
@@ -235,7 +220,6 @@ public class AlignView extends ViewPart implements SelectionListener, Listener {
onto1Refresh.setEnabled(true);
Label dummy5 = new Label(client, SWT.NONE);
Label dummy6 = new Label(client, SWT.NONE);
- //Label dummy7 = new Label(client, SWT.NONE);
//Choose ontology 2
Label onto2 = new Label(client, SWT.NONE);
@@ -245,11 +229,6 @@ public class AlignView extends ViewPart implements SelectionListener, Listener {
ontoBox2.setLayoutData(gd);
ontoBox2.setEnabled(true);
ontoBox2.addSelectionListener(this);
- //onto2Refresh = new Button(client, SWT.PUSH);
- //onto2Refresh.setText("Refresh");
- //onto2Refresh.setSize(buttonWidth, buttonHeight);
- //onto2Refresh.addSelectionListener(this);
- //onto2Refresh.setEnabled(true);
Label dummy8 = new Label(client, SWT.NONE);
Label dummy9 = new Label(client, SWT.NONE);
// replaces the useless refresh
@@ -272,7 +251,6 @@ public class AlignView extends ViewPart implements SelectionListener, Listener {
Label dummy11 = new Label(client, SWT.NONE);
Label dummy12 = new Label(client, SWT.NONE);
- //Label dummy13 = new Label(client, SWT.NONE);
//server alignment list
Label serverAlignLabel = new Label(client, SWT.NONE );
@@ -342,14 +320,11 @@ public class AlignView extends ViewPart implements SelectionListener, Listener {
uploadButton.addSelectionListener(this);
uploadButton.setEnabled(false);
- //Label dummy14 = new Label(client, SWT.NONE);
-
Label dummy15 = new Label(client, SWT.NONE);
Label dummy16 = new Label(client, SWT.NONE);
Label dummy17 = new Label(client, SWT.NONE);
Label dummy18 = new Label(client, SWT.NONE);
Label dummy19 = new Label(client, SWT.NONE);
- //Label dummy20 = new Label(client, SWT.NONE);
Label dummy21 = new Label(client, SWT.NONE);
@@ -363,7 +338,6 @@ public class AlignView extends ViewPart implements SelectionListener, Listener {
Label dummy22 = new Label(client, SWT.NONE);
Label dummy23 = new Label(client, SWT.NONE);
Label dummy24 = new Label(client, SWT.NONE);
- //Label dummy25 = new Label(client, SWT.NONE);
Label dummy26 = new Label(client, SWT.NONE);
//find all
@@ -396,7 +370,7 @@ public class AlignView extends ViewPart implements SelectionListener, Listener {
//System.out.println(" html with alignKey="+alignKey);
htmlBrowser.setText("");
formToolkit.paintBordersFor(htmlClient);
- //I do not know why it no longer works if URI casting is put here!!!
+ // I do not know why it no longer works if URI casting is put here!!!
Alignment align = AlignView.alignmentTable.get(alignKey);
StringWriter htmlMessage = null;
@@ -433,7 +407,6 @@ public class AlignView extends ViewPart implements SelectionListener, Listener {
alignKey = alignFolder.getAbsolutePath() + File.separator + getNewAlignId();
- //System.out.println("alignKey="+alignKey);
String rdfPath = alignKey + ".rdf";
try {
@@ -450,11 +423,8 @@ public class AlignView extends ViewPart implements SelectionListener, Listener {
ap.setEmbedded( true );
//System.out.println(" parsing string ... ");
- //align = ap.parseString( rdfalignStr );
align = ap.parse( file.toURI().toString() );
- //if(align==null) System.out.println("align null" ); else System.out.println("align non null" );
-
AlignView.alignmentTable.put( alignKey, align );
idMap.put(id, alignKey);
localAlignBox.setEnabled(true);
@@ -613,33 +583,17 @@ public class AlignView extends ViewPart implements SelectionListener, Listener {
viewHTMLAlign(alignKey);
}
} else { //offline
- /*
-MessageDialog.openError(this.getSite().getShell(), "Error message",
- "method: "+selectedMethod);
-MessageDialog.openError(this.getSite().getShell(), "Error message",
- "onto1: "+selectedOnto1);
-MessageDialog.openError(this.getSite().getShell(), "Error message",
- "onto2: "+selectedOnto2);
-MessageDialog.openError(this.getSite().getShell(), "Error message",
- "onto2: "+selectedOnto2);
- */
try {
selectedLocalAlign = offlineAlign.matchAndExportAlign( selectedMethod, ontoByProj.get(selectedOnto1), selectedOnto1, ontoByProj.get(selectedOnto2), selectedOnto2);
} catch ( Exception ex ) {
MessageDialog.openError(this.getSite().getShell(), "Error message", ex.getMessage() );
return;
}
- /*
-MessageDialog.openError(this.getSite().getShell(), "Error message",
- "returned: "+selectedLocalAlign);
- */ localAlignBox.setEnabled( true );
localAlignBox.add( selectedLocalAlign, 0 );
localImportButton.setEnabled( true );
localTrimButton.setEnabled( true );
localAlignBox.select(0);
localAlignBox.redraw();
- //if( AlignView.alignmentTable.get( selectedLocalAlign ) != null) System.out.println("Offline match OK");
- //else System.out.println("Offline match Non ");
viewHTMLAlign( selectedLocalAlign );
} //offline
//processing alignment fetching
@@ -757,7 +711,6 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
String[] projects = OntologyProjectManager.getDefault().getOntologyProjects();
- //String[] projects = DatamodelPlugin.getDefault().getOntologyProjects();
if(projects!=null) {
boolean found = false;
@@ -770,12 +723,7 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
if(!found) {
- //Properties proper = new Properties();
- //proper.put(IConfig.ONTOLOGY_LANGUAGE.toString(), IConfig.OntologyLanguage.OWL.toString());
-
new CreateProject( inputName, OWLManchesterProjectFactory.FACTORY_ID, new Properties()).run();
-
- //new CreateProject( inputName, DatamodelTypes.RAM, proper ).run();
}
}
@@ -790,24 +738,9 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
out.flush();
out.close();
- //ImportExportUtils ieControl = new ImportExportUtils();
-
URI uris[] = new URI[1];
uris[0] = new File(owlPath).toURI();
new OntologyFileSystemImport(inputName, new String[] {uris[0].toString()}).run();
- //String[] importedUri = new String[1];
- //importedUri[0] = ImportExportUtils.copyOntologyFileToProject(uris[0].toString(), inputName);
- //ImportExportUtils.addOntologiesToProject(inputName, importedUri);
- /*
- try {
- ImportExportControl ieControl = new ImportExportControl();
- URI uris[] = new URI[1];
- uris[0] = new File( owlPath).toURI();
- String[] importedModules = ieControl.importFileSystem(inputName, uris, null);
-
- //ieControl.addOntologies2Project(importedModules, inputName);
- } catch ( ControlException ex ) { }
- */
}
catch ( Exception ex ) { ex.printStackTrace();}
@@ -851,26 +784,13 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
}
if(!found) {
- //Properties proper = new Properties();
- //proper.put(IConfig.ONTOLOGY_LANGUAGE.toString(), IConfig.OntologyLanguage.OWL.toString());
new CreateProject( inputName, OWLManchesterProjectFactory.FACTORY_ID, new Properties()).run();
- //new CreateProject( inputName, DatamodelTypes.RAM, proper ).run();
-
}
- //ImportExportControl ieControl = new ImportExportControl();
- //ImportExportUtils ieControl = new ImportExportUtils();
-
URI uris[] = new URI[1];
uris[0] = new File(fn.getAbsolutePath()).toURI();
new OntologyFileSystemImport(inputName, new String[] {uris[0].toString()}).run();
-
- //String[] importedUri = new String[1];
- //importedUri[0] = ImportExportUtils.copyOntologyFileToProject(uris[0].toString(), inputName);
- //ImportExportUtils.addOntologiesToProject(inputName, importedUri);
- //ieControl.importFileSystem(inputName, uris, null);
-
}
}
catch ( Exception ex ) { ex.printStackTrace();};
@@ -994,50 +914,34 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
/**
* This function is taken from Alignment Server with processing Jar in Jar
+ * JE 2015: This is a lot of duplicated code and the code has aged!
*/
public static void implementations( Class<?> tosubclass, Set<String> list , String cp, boolean debug ){
Set<String> visited = new HashSet<String>();
- //String classPath = System.getProperty("java.class.path",".");
String classPath = cp;
int count=0;
- // Hack: this is not necessary
- //classPath = classPath.substring(0,classPath.lastIndexOf(File.pathSeparatorChar));
-
- //StringTokenizer tk = new StringTokenizer(classPath,File.pathSeparator);
StringTokenizer tk = new StringTokenizer(classPath, "," );
- //System.err.println("classPath for Impl.="+ classPath );
classPath = "";
while ( tk != null && tk.hasMoreTokens() ) {
StringTokenizer tk2 = tk;
tk = null;
- //System.err.println( "path" + tk2.toString());
// Iterate on Classpath
while ( tk2.hasMoreTokens() ) {
try {
URI nn = new URI( tk2.nextToken() );
- //System.err.println("token="+ nn);
File file = new File( nn );
if ( file.isDirectory() ) {
- //System.err.println("DIR "+file);
String subs[] = file.list();
for(int index = 0 ; index < subs.length ; index ++ ){
- //System.err.println("subs= "+subs[index]);
- // IF class
if ( subs[index].endsWith(".class") ) {
String classname = subs[index].substring(0,subs[index].length()-6);
- //System.err.println("classname= "+classname);
if (classname.startsWith(File.separator))
classname = classname.substring(1);
classname = classname.replace(File.separatorChar,'.');
try {
- // JE: Here there is a bug that is that it is not possible
- // to have ALL interfaces with this function!!!
- // This is really stupid but that's life
- // So it is compulsory that AlignmentProcess be declared
- // as implemented
- Class[] cls = Class.forName(classname).getInterfaces();
+ Class<?>[] cls = Class.forName(classname).getInterfaces();
for ( int i=0; i < cls.length ; i++ ){
if ( cls[i] == tosubclass ) {
if (debug ) System.err.println(" -j-> "+classname);
@@ -1072,15 +976,11 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
classname = classname.substring(0,len);
// Beware, in a Jarfile the separator is always "/"
// and it would not be dependent on the current system anyway.
- //classname = classname.replaceAll(File.separator,".");
classname = classname.replaceAll("/",".");
-
- //System.err.println("classname in jar = "+classname);
-
try {
if ( classname.equals("org.apache.xalan.extensions.ExtensionHandlerGeneral") ) throw new ClassNotFoundException( "Stupid JAVA/Xalan bug");
Class<?> cl = Class.forName(classname);
- Class[] ints = cl.getInterfaces();
+ Class<?>[] ints = cl.getInterfaces();
for ( int i=0; i < ints.length ; i++ ){
if ( ints[i] == tosubclass ) {
if (debug ) System.err.println(" -j-> "+classname);
@@ -1096,11 +996,7 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
// This one has been added for OMWG, this is a bad error
}
} else if( classname.endsWith(".jar") ) {
- //If jarEntry is a jarfile
- //System.err.println( "jarEntry is a jarfile="+je.getName() );
InputStream jarSt = jar.getInputStream( (ZipEntry)je );
- // JE2010: START OF CRITICAL SECTION
- //File f = new File("tmpFileXXX"+ count++);
File f = File.createTempFile( "tmpFileXXX"+count++, "jar" );
try {
@@ -1129,18 +1025,13 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
classname2 = classname2.substring(0,len3);
// Beware, in a Jarfile the separator is always "/"
// and it would not be dependent on the current system anyway.
- //classname = classname.replaceAll(File.separator,".");
classname2 = classname2.replaceAll("/",".");
-
- //System.err.println("classname in jar in jar = "+classname2);
-
try {
if ( classname2.equals("org.apache.xalan.extensions.ExtensionHandlerGeneral") ) throw new ClassNotFoundException( "Stupid JAVA/Xalan bug");
Class<?> cl = Class.forName(classname2);
- Class[] ints = cl.getInterfaces();
+ Class<?>[] ints = cl.getInterfaces();
for ( int i=0; i < ints.length ; i++ ){
if ( ints[i] == tosubclass ) {
- //System.err.println(classname2 + " added");
list.add( classname2 );
}
}
@@ -1154,10 +1045,8 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
}
}//while
f.delete();
- // JE2010: END OF CRITICAL SECTION
} // else If endWith .jar
-
// Iterate on needed Jarfiles
// JE(caveat): this deals naively with Jar files,
// in particular it does not deal with section'ed MANISFESTs
@@ -1186,7 +1075,6 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
}
if ( !classPath.equals("") ) {
- //tk = new StringTokenizer(classPath,File.pathSeparator);
tk = new StringTokenizer(classPath,",");
classPath = "";
}
@@ -1204,8 +1092,6 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
implementations( toclass, list, cp, false );
} catch (ClassNotFoundException ex) {
System.err.println("Class "+interfaceName+" not found!");
- //System.err.flush();
- //System.err.close();
}
return list;
@@ -1216,17 +1102,12 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
// (with the same interface as for the Online version)
void offlineInit( boolean init ) {
online = false;
- //methods.removeAll();
serverAlignBox.removeAll();
- //localAlignBox.removeAll();
- //ontoBox1.removeAll();
- //ontoBox2.removeAll();
Bundle bundle = AlignmentPlugin.getDefault().getBundle();
Set<String> ms = new HashSet<String>();
String classpath = bundle.getHeaders().get("Bundle-ClassPath").toString();
- //System.out.println("classpath="+ classpath);
URL url = FileLocator.find( AlignmentPlugin.getDefault().getBundle(), new Path(""), null );
try {
@@ -1235,20 +1116,13 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
ioe.printStackTrace();
}
- //try {
- //System.setErr( new PrintStream( new File( alignFolder.getAbsolutePath() + File.separator + "debug.txt") ) );
- //System.err.println( "AlignmentPlugin bundle??? : "+AlignmentPlugin.getDefault().getBundle() );
- //System.err.println("url ="+ url.toString() );
-
if( ! url.toString().startsWith("jar") ) {
String[] files = classpath.split(",");
classpath = "";
for(int k=0; k < files.length; k++) {
- //System.err.println("files="+ files[k]);
classpath += url.toString()+files[k]+",";
}
- //System.err.println("classpath2="+ classpath);
ms = implementations( "org.semanticweb.owl.align.AlignmentProcess", classpath );
} else { // Plugin is a jarfile
String path = url.getFile();
@@ -1259,38 +1133,18 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
ms.remove("fr.inrialpes.exmo.align.impl.DistanceAlignment"); // this one is abstract
ms.remove("fr.inrialpes.exmo.align.ling.JWNLAlignment"); // requires WordNet
System.err.println("ms="+ms.size());
- //System.err.flush();
- //System.err.close();
methodList = new String[ms.size()];
int j=0;
for( String m : ms ) methodList[j++] = m;
- //methodList[0] = "fr.inrialpes.exmo.align.impl.method.NameEqAlignment";
- //methodList[1] = "fr.inrialpes.exmo.align.impl.method.StringDistAlignment";
- //methodList[2] = "fr.inrialpes.exmo.align.impl.method.SMOANameAlignment";
- //methodList[3] = "fr.inrialpes.exmo.align.impl.method.SubsDistNameAlignment";
- //methodList[4] = "fr.inrialpes.exmo.align.impl.method.StrucSubsDistAlignment";
- //methodList[5] = "fr.inrialpes.exmo.align.impl.method.NameAndPropertyAlignment";
- //methodList[6] = "fr.inrialpes.exmo.align.impl.method.ClassStructAlignment";
- //methodList[7] = "fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment";
-
if( methodList.length > 0 ) selectedMethod = methodList[0];
methods.removeAll();
methods.setItems( methodList );
methods.setEnabled(true);
methods.select(0);
methods.redraw();
- // }catch (IOException ioe){
- // ioe.printStackTrace();
- //System.err.flush();
- //System.err.close();
- // }
-
- //System.out.println( "alignFolder=" + alignFolder );
offlineAlign = new OfflineAlign( alignFolder, ontoFolder );
- //initButtons( false );
-
if ( init ) offlineAlign.getAllAlignFromFiles();
String[] list = offlineAlign.getAllAlign();
@@ -1299,7 +1153,6 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
if ( list.length > 0) {
forUniqueness = new String[list.length];
for(int i=0; i< list.length; i++){
- //System.out.println( "filename=" + list[i] );
File f = new File(list[i]);
forUniqueness[i] = f.getName();
}
@@ -1358,22 +1211,7 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
for ( int i=0; i < projects.length; i++ ) {
if ( projects[i]!=null ) {
IOntologyProject ontoProject = OntologyProjectManager.getDefault().getOntologyProject( projects[i] );
- // With the new version (2.3.0, 240+), it is not necessary to filter... but nothing gets local
- // This change has been made with Andreas Harth
- /*
- if( !online ) {
- Set<String> onto = ontoProject.getAvailableOntologyURIs();
- URI[] strSet = ontoProject.getOntologyFiles();
- //System.out.println("size of uris offline=" + strSet.length + "("+ projects[i] +")" );
- for(int k=0; k < strSet.length; k++) {
- String st = strSet[k].toString();
- if(st.startsWith("file:"))
- vec.put(st,projects[i]);
- }
- } else {
- */
Set<String> strSet = ontoProject.getAvailableOntologyURIs();
- //System.out.println("size of uris online=" + strSet.size() + "("+ projects[i] +")");
String[] uris = strSet.toArray( new String[0] );
for ( int k=0; k < uris.length; k++ ) {
vec.put( uris[k], projects[i] );
@@ -1384,7 +1222,6 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
}
}
} else {
- //System.out.printf("No Ontology Project !" );
return null;
}
} catch ( Exception ex ) { ex.printStackTrace();};
@@ -1395,13 +1232,10 @@ MessageDialog.openError(this.getSite().getShell(), "Error message",
String[] keys2 = vec.keySet().toArray(new String[0]);
if ( keys1.length > 0 ) {
- //ontoList = new String[ keys.length ];
- //ontoBox1.removeAll();
ontoBox1.setItems(keys1);
ontoBox1.select(0);
ontoBox1.redraw();
selectedOnto1 = keys1[0];
- //ontoBox2.removeAll();
ontoBox2.setItems(keys2);
ontoBox2.select(0);
ontoBox2.redraw();
diff --git a/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/OfflineAlign.java b/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/OfflineAlign.java
index c9f61478277f977efef13332da20b52299cbe36c..196fac8fe0083ee0961165721458c519b4eda6d1 100755
--- a/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/OfflineAlign.java
+++ b/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/OfflineAlign.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2007-2010, 2014
+ * Copyright (C) INRIA, 2007-2010, 2014-2015
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -82,7 +82,7 @@ public class OfflineAlign {
//uris.add( new URI(selectedNeOnOnto2 ) );
Object[] mparams = {};
Class<?> alignmentClass = Class.forName(method);
- Class[] cparams = {};
+ Class<?>[] cparams = {};
Constructor<?> alignmentConstructor = alignmentClass.getConstructor( cparams );
A1 = (AlignmentProcess)alignmentConstructor.newInstance(mparams);
OntologyFactory factory = null;
diff --git a/src/fr/inrialpes/exmo/align/cli/EvalAlign.java b/src/fr/inrialpes/exmo/align/cli/EvalAlign.java
index 4436aa5598c65f67ef2d22c9cbe3fd9bc4f10ef7..66a68ad6f90bee462f14c0bad8c16c850f118338 100644
--- a/src/fr/inrialpes/exmo/align/cli/EvalAlign.java
+++ b/src/fr/inrialpes/exmo/align/cli/EvalAlign.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2008, 2010-2014
+ * Copyright (C) INRIA, 2003-2008, 2010-2015
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -142,9 +142,9 @@ public class EvalAlign extends CommonCLI {
if ( evaluatorClass != null ) {
// Create evaluator object
try {
- Class[] cparams = { Alignment.class, Alignment.class };
+ Class<?>[] cparams = { Alignment.class, Alignment.class };
Constructor<?> evaluatorConstructor = evaluatorClass.getConstructor(cparams);
- Object [] mparams = { align1, align2};
+ Object[] mparams = { align1, align2};
eval = (Evaluator)evaluatorConstructor.newInstance(mparams);
} catch (InstantiationException ex) {
logger.debug( "IGNORED Exception", ex );
diff --git a/src/fr/inrialpes/exmo/align/cli/GenPlot.java b/src/fr/inrialpes/exmo/align/cli/GenPlot.java
index 91f967b94285b9b17f199d97fea6fcf0fc1acc18..d6eb3e8de592895e7161fad12589c2c640c7dd15 100644
--- a/src/fr/inrialpes/exmo/align/cli/GenPlot.java
+++ b/src/fr/inrialpes/exmo/align/cli/GenPlot.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2003-2014, INRIA
+ * Copyright (C) 2003-2015, INRIA
* Copyright (C) 2004, Universit� de Montr�al
*
* This program is free software; you can redistribute it and/or
@@ -150,12 +150,12 @@ public class GenPlot extends CommonCLI {
}
Class<?> graphClass = Class.forName( graphCN );
- Class[] cparams = {};
+ Class<?>[] cparams = {};
graphConstructor = graphClass.getConstructor( cparams );
// JE: This is not used
Class<?> evalClass = Class.forName( evalCN );
- Class[] caparams = { Alignment.class, Alignment.class };
+ Class<?>[] caparams = { Alignment.class, Alignment.class };
evalConstructor = evalClass.getConstructor( caparams );
// Collect correspondences from alignments in all directories
diff --git a/src/fr/inrialpes/exmo/align/cli/GroupAlign.java b/src/fr/inrialpes/exmo/align/cli/GroupAlign.java
index d13296fb3a2918522c0f2a3b7d6c697fc6d1ad97..ad6ae5debf5d1637cf551241f3d29b2da1570d21 100644
--- a/src/fr/inrialpes/exmo/align/cli/GroupAlign.java
+++ b/src/fr/inrialpes/exmo/align/cli/GroupAlign.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2003-2008, 2010-2014 INRIA
+ * Copyright (C) 2003-2008, 2010-2015 INRIA
* Copyright (C) 2004, Universit� de Montr�al
*
* This program is free software; you can redistribute it and/or
@@ -203,7 +203,7 @@ public class GroupAlign extends CommonCLI {
// Create alignment object
Object[] mparams = {};
- Class[] cparams = {};
+ Class<?>[] cparams = {};
Class<?> alignmentClass = Class.forName( alignmentClassName );
Constructor<?> alignmentConstructor = alignmentClass.getConstructor(cparams);
result = (AlignmentProcess)alignmentConstructor.newInstance( mparams );
@@ -231,7 +231,7 @@ public class GroupAlign extends CommonCLI {
AlignmentVisitor renderer = null;
try {
- Class[] cparams = { PrintWriter.class };
+ Class<?>[] cparams = { PrintWriter.class };
Constructor<?> rendererConstructor =
Class.forName(rendererClass).getConstructor(cparams);
Object[] mparams = { (Object)writer };
diff --git a/src/fr/inrialpes/exmo/align/cli/GroupEval.java b/src/fr/inrialpes/exmo/align/cli/GroupEval.java
index 37a01e6fe6b6ff86773a3d0a1095319c8d8bbbf5..ff8a7679858e8d57e57a0e6497e96d3e6f10c3a0 100644
--- a/src/fr/inrialpes/exmo/align/cli/GroupEval.java
+++ b/src/fr/inrialpes/exmo/align/cli/GroupEval.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2003-2014, INRIA
+ * Copyright (C) 2003-2015, INRIA
* Copyright (C) 2004, Universit� de Montr�al
*
* This program is free software; you can redistribute it and/or
@@ -161,7 +161,7 @@ public class GroupEval extends CommonCLI {
}
Class<?> evalClass = Class.forName( classname );
- Class[] cparams = { Alignment.class, Alignment.class };
+ Class<?>[] cparams = { Alignment.class, Alignment.class };
evalConstructor = evalClass.getConstructor( cparams );
print( iterateDirectories() );
diff --git a/src/fr/inrialpes/exmo/align/cli/ParserPrinter.java b/src/fr/inrialpes/exmo/align/cli/ParserPrinter.java
index 73f32299ed0d99b93c563d07cfc4c3cb8d8937cc..1afcf2988b6bba7e5cc41de9e0795b6f92698644 100644
--- a/src/fr/inrialpes/exmo/align/cli/ParserPrinter.java
+++ b/src/fr/inrialpes/exmo/align/cli/ParserPrinter.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2004, 2007-2008, 2011-2014
+ * Copyright (C) INRIA, 2003-2004, 2007-2008, 2011-2015
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -142,7 +142,7 @@ public class ParserPrinter extends CommonCLI {
if ( parserClass == null ) aparser = new AlignmentParser();
else {
try {
- Class[] cparams = {};
+ Class<?>[] cparams = {};
Constructor<?> parserConstructor =
Class.forName(parserClass).getConstructor(cparams);
Object[] mparams = {};
@@ -189,7 +189,7 @@ public class ParserPrinter extends CommonCLI {
if ( rendererClass == null ) renderer = new RDFRendererVisitor( writer );
else {
try {
- Class[] cparams = { PrintWriter.class };
+ Class<?>[] cparams = { PrintWriter.class };
Constructor<?> rendererConstructor = Class.forName(rendererClass).getConstructor( cparams );
Object[] mparams = { (Object)writer };
renderer = (AlignmentVisitor) rendererConstructor.newInstance( mparams );
diff --git a/src/fr/inrialpes/exmo/align/cli/Procalign.java b/src/fr/inrialpes/exmo/align/cli/Procalign.java
index a4b6edd8c728d0d0af90a02e98ac718a8ca63590..170c902f3a1fc87e253ac76bd3007d930c355915 100644
--- a/src/fr/inrialpes/exmo/align/cli/Procalign.java
+++ b/src/fr/inrialpes/exmo/align/cli/Procalign.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2003-2008, 2010-2014 INRIA
+ * Copyright (C) 2003-2008, 2010-2015 INRIA
* Copyright (C) 2004, Universit� de Montr�al
*
* This program is free software; you can redistribute it and/or
@@ -164,7 +164,7 @@ public class Procalign extends CommonCLI {
// Create alignment object
Class<?> alignmentClass = Class.forName( alignmentClassName );
- Class[] cparams = {};
+ Class<?>[] cparams = {};
Constructor<?> alignmentConstructor = alignmentClass.getConstructor(cparams);
Object[] mparams = {};
result = (AlignmentProcess)alignmentConstructor.newInstance( mparams );
@@ -202,7 +202,7 @@ public class Procalign extends CommonCLI {
// Result printing (to be reimplemented with a default value)
try {
- Class[] cparams = { PrintWriter.class };
+ Class<?>[] cparams = { PrintWriter.class };
Constructor<?> rendererConstructor = Class.forName(rendererClass).getConstructor( cparams );
Object[] mparams = { (Object)writer };
renderer = (AlignmentVisitor) rendererConstructor.newInstance( mparams );
diff --git a/src/fr/inrialpes/exmo/align/cli/TestGen.java b/src/fr/inrialpes/exmo/align/cli/TestGen.java
index b7a192449f950890406e2dc1ec32a43af38db084..122e3256fe5f05afb30c379e083891097db3fd7d 100644
--- a/src/fr/inrialpes/exmo/align/cli/TestGen.java
+++ b/src/fr/inrialpes/exmo/align/cli/TestGen.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) 2011-2014, INRIA
+ * Copyright (C) 2011-2015, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -121,7 +121,7 @@ public class TestGen extends CommonCLI {
TestSet tset = null;
try {
Class<?> testSetClass = Class.forName( methodName );
- Class[] cparams = {};
+ Class<?>[] cparams = {};
Constructor<?> testSetConstructor = testSetClass.getConstructor(cparams);
Object[] mparams = {};
tset = (TestSet)testSetConstructor.newInstance( mparams );
diff --git a/src/fr/inrialpes/exmo/align/gen/AlteratorFactory.java b/src/fr/inrialpes/exmo/align/gen/AlteratorFactory.java
index 708ba3a97d6b1f8a931d3ada95c444bdb3bad041..b10fb356fd6eccd608ee13142bad5d000553906d 100644
--- a/src/fr/inrialpes/exmo/align/gen/AlteratorFactory.java
+++ b/src/fr/inrialpes/exmo/align/gen/AlteratorFactory.java
@@ -1,7 +1,7 @@
/**
* $Id$
*
- * Copyright (C) INRIA, 2011, 2013-2014
+ * Copyright (C) INRIA, 2011, 2013-2015
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -47,7 +47,7 @@ public class AlteratorFactory {
try {
// This should also be a static getInstance!
Class<?> altClass = Class.forName(classname);
- Class[] cparams = {Class.forName("fr.inrialpes.exmo.align.gen.Alterator")};
+ Class<?>[] cparams = {Class.forName("fr.inrialpes.exmo.align.gen.Alterator")};
Constructor<?> altConstructor = altClass.getConstructor(cparams);
Object[] mparams = { om };
alt = (Alterator)altConstructor.newInstance(mparams);
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
index e881d376d5d47b5ad011e93657ef56dba99224e2..c6558a929c50af9a97647b0ccaabd1d8c93d3c49 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
@@ -260,7 +260,7 @@ public class BasicAlignment implements Alignment, Extensible {
}*/
};
- public Class getRelationType() {
+ public Class<? extends Relation> getRelationType() {
return relationType;
};
@@ -272,7 +272,7 @@ public class BasicAlignment implements Alignment, Extensible {
}
};
- public Class getConfidenceType() {
+ public Class<?> getConfidenceType() {
return confidenceType;
};
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java b/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java
index bcab44c475e1b8becd66e4d22e4f4b64acb6c6d1..a37d621c19136ccfd2dd98dd03775cf0c4df675c 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2009-2010, 2014
+ * Copyright (C) INRIA, 2009-2010, 2014-2015
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -340,7 +340,7 @@ public class BasicOntologyNetwork implements OntologyNetwork, Extensible {
try {
// Create alignment object
Class<?> alignmentClass = Class.forName( method );
- Class[] cparams = {};
+ Class<?>[] cparams = {};
Constructor<?> alignmentConstructor = alignmentClass.getConstructor(cparams);
Object[] mparams = {};
ap = (AlignmentProcess)alignmentConstructor.newInstance( mparams );
diff --git a/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java b/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java
index 03a6a48592fbafcdae3f777e94eb77f729ab067b..20bff41a7987ba18ce0226dfc6ca2452cfbb2005 100644
--- a/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/method/StringDistAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2011, 2013-2014
+ * Copyright (C) INRIA, 2003-2011, 2013-2015
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -104,7 +104,7 @@ public class StringDistAlignment extends DistanceAlignment implements AlignmentP
String f = params.getProperty("stringFunction");
try {
if ( f != null ) methodName = f.trim();
- Class[] mParams = { String.class, String.class };
+ Class<?>[] mParams = { String.class, String.class };
dissimilarity = StringDistances.class.getMethod( methodName, mParams );
} catch ( NoSuchMethodException e ) {
throw new AlignmentException( "Unknown method for StringDistAlignment : "+params.getProperty("stringFunction"), e );
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/GenericReflectiveVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/GenericReflectiveVisitor.java
index 00728c1d24a0d9f818d20106835ff54607983f07..1f8389197c6d09272a0e8113e8feae08b10ce77d 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/GenericReflectiveVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/GenericReflectiveVisitor.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2012-2014
+ * Copyright (C) INRIA, 2012-2015
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -59,7 +59,7 @@ public class GenericReflectiveVisitor {
}
if ( m == null ) {//newc == Object.class ) {
// logger.trace( "Searching for interfaces" );
- Class[] interfaces = c.getInterfaces();
+ Class<?>[] interfaces = c.getInterfaces();
for ( int i=0; i < interfaces.length; i++ ) {
if ( interfaces[i] != root ) {
String method = interfaces[i].getName();
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
index f7b2953d3676f77ca4208b30dbcad9901cd09fa8..23b2aeee97271632ba5f5bd70ad6f5ced7537d3f 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/RDFRendererVisitor.java
@@ -181,11 +181,11 @@ public class RDFRendererVisitor extends IndentedRendererVisitor implements Align
indentedOutputln("<" + SyntaxElement.LEVEL.print(DEF) + ">" + align.getLevel() + "</" + SyntaxElement.LEVEL.print(DEF) + ">");
indentedOutputln("<" + SyntaxElement.TYPE.print(DEF) + ">" + align.getType() + "</" + SyntaxElement.TYPE.print(DEF) + ">");
if ( align instanceof BasicAlignment ) {
- Class relationType = ((BasicAlignment)align).getRelationType();
+ Class<?> relationType = ((BasicAlignment)align).getRelationType();
if ( relationType != BasicRelation.class ) {
indentedOutputln("<" + SyntaxElement.RELATION_CLASS.print(DEF) + ">" + relationType.getName() + "</" + SyntaxElement.RELATION_CLASS.print(DEF) + ">");
}
- Class confidenceType = ((BasicAlignment)align).getConfidenceType();
+ Class<?> confidenceType = ((BasicAlignment)align).getConfidenceType();
if ( confidenceType != BasicConfidence.class ) {
indentedOutputln("<" + SyntaxElement.CONFIDENCE_CLASS.print(DEF) + ">" + confidenceType.getName() + "</" + SyntaxElement.CONFIDENCE_CLASS.print(DEF) + ">");
}
diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index 163d9fd67e02af183a9aa23a41318581ee06fed5..319cd3c122d7a814a8d652fdbd5b2acc27ee5def 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -522,7 +522,7 @@ public class AServProtocolManager implements Service {
new OutputStreamWriter( result, "UTF-8" )), true);
AlignmentVisitor renderer = null;
try {
- Class[] cparams = { PrintWriter.class };
+ Class<?>[] cparams = { PrintWriter.class };
Constructor<?> rendererConstructor = Class.forName( method ).getConstructor( cparams );
Object[] mparams = { (Object)writer };
renderer = (AlignmentVisitor) rendererConstructor.newInstance( mparams );
@@ -735,7 +735,7 @@ public class AServProtocolManager implements Service {
if ( classname == null ) classname = "fr.inrialpes.exmo.align.impl.eval.PRecEvaluator";
Evaluator eval = null;
try {
- Class[] cparams = { Alignment.class, Alignment.class };
+ Class<?>[] cparams = { Alignment.class, Alignment.class };
Class<?> evaluatorClass = Class.forName( classname );
Constructor<?> evaluatorConstructor = evaluatorClass.getConstructor( cparams );
Object [] mparams = { (Object)ref, (Object)al };
@@ -1542,7 +1542,7 @@ public class AServProtocolManager implements Service {
if ( method == null )
method = "fr.inrialpes.exmo.align.impl.method.StringDistAlignment";
Class<?> alignmentClass = Class.forName(method);
- Class[] cparams = {};
+ Class<?>[] cparams = {};
Constructor<?> alignmentConstructor = alignmentClass.getConstructor( cparams );
Object[] mparams = {};
AlignmentProcess aresult = (AlignmentProcess)alignmentConstructor.newInstance( mparams );
diff --git a/src/fr/inrialpes/exmo/align/service/EDOALSQLCache.java b/src/fr/inrialpes/exmo/align/service/EDOALSQLCache.java
index b152b3b9053e23ae29719fab469a2204a19431f0..fe0bf95e0b117a0fca6c12763cd2d4ede8e29520 100644
--- a/src/fr/inrialpes/exmo/align/service/EDOALSQLCache.java
+++ b/src/fr/inrialpes/exmo/align/service/EDOALSQLCache.java
@@ -889,7 +889,7 @@ public class EDOALSQLCache {
// (play with NULL)
public Apply extractApply( long intid ) throws SQLException, AlignmentException {
try ( Statement st = service.getConnection().createStatement() ) {
- ResultSet rs = createStatement().executeQuery( "SELECT operation FROM apply WHERE intid='"+intid+"'" );
+ ResultSet rs = st.executeQuery( "SELECT operation FROM apply WHERE intid='"+intid+"'" );
if ( rs.next() ) {
try {
URI opuri = new URI( rs.getString( "operation" ) );
diff --git a/src/fr/inrialpes/exmo/align/service/HTTPTransport.java b/src/fr/inrialpes/exmo/align/service/HTTPTransport.java
index e37b53aa3add2b29e187ab325320e7fb8df9187a..01702616b4b8374efd4c73b6c4190207523adf03 100644
--- a/src/fr/inrialpes/exmo/align/service/HTTPTransport.java
+++ b/src/fr/inrialpes/exmo/align/service/HTTPTransport.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2006-2014
+ * Copyright (C) INRIA, 2006-2015
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -110,9 +110,9 @@ public class HTTPTransport {
// I do not decode them here because it is useless
// See below how it is done.
Properties header = new Properties();
- Enumeration headerNames = request.getHeaderNames();
+ Enumeration<String> headerNames = request.getHeaderNames();
while( headerNames.hasMoreElements() ) {
- String headerName = (String)headerNames.nextElement();
+ String headerName = headerNames.nextElement();
header.setProperty( headerName, request.getHeader(headerName) );
}
diff --git a/src/fr/inrialpes/exmo/align/service/SQLCache.java b/src/fr/inrialpes/exmo/align/service/SQLCache.java
index d95428e4c3f383bc9cd5833e5ac6f4413f469569..627c7c79193ab6c7afd2b8e2ca7a9d5dd7869153 100644
--- a/src/fr/inrialpes/exmo/align/service/SQLCache.java
+++ b/src/fr/inrialpes/exmo/align/service/SQLCache.java
@@ -311,7 +311,7 @@ public class SQLCache extends VolatilCache implements Cache {
}
}
- public void retrieveOntology( String uri, Ontology ob ) throws SQLException, AlignmentException, URISyntaxException {
+ public void retrieveOntology( String uri, Ontology<?> ob ) throws SQLException, AlignmentException, URISyntaxException {
Statement st = createStatement();
ResultSet rs = st.executeQuery( "SELECT * FROM ontology WHERE uri = '" + uri +"'" );
if ( rs.next() ) {
@@ -571,12 +571,12 @@ public class SQLCache extends VolatilCache implements Cache {
alignment.getOntology2URI(),
alignment.getFile2(),
alignment.getOntologyObject2() );
- Class relClass = alignment.getRelationType();
+ Class<?> relClass = alignment.getRelationType();
String relClassName = null;
if ( relClass != BasicRelation.class ) {
relClassName = relClass.getName();
}
- Class confClass = alignment.getConfidenceType();
+ Class<?> confClass = alignment.getConfidenceType();
String confClassName = null;
if ( confClass != BasicConfidence.class ) {
confClassName = confClass.getName();
diff --git a/src/fr/inrialpes/exmo/ontowrap/OntologyFactory.java b/src/fr/inrialpes/exmo/ontowrap/OntologyFactory.java
index 344b6f194867272f50ccbf8184a1306df35eed3d..84077c067aab75ed64ef50bfba6d0bacefe17f95 100644
--- a/src/fr/inrialpes/exmo/ontowrap/OntologyFactory.java
+++ b/src/fr/inrialpes/exmo/ontowrap/OntologyFactory.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2008, 2010-2014
+ * Copyright (C) INRIA, 2008, 2010-2015
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -111,7 +111,7 @@ public abstract class OntologyFactory {
try {
// This should also be a static getInstance!
Class<?> ofClass = Class.forName( apiName );
- Class[] cparams = {};
+ Class<?>[] cparams = {};
java.lang.reflect.Constructor<?> ofConstructor = ofClass.getConstructor( cparams );
Object[] mparams = {};
of = (OntologyFactory)ofConstructor.newInstance(mparams);