diff --git a/lib/align.jar b/lib/align.jar
index b617a4c03e6f72ecf41cee79708d82e8667d6f0d..d64de955107d48f817e443ec91a0c063f7e7cc0b 100644
Binary files a/lib/align.jar and b/lib/align.jar differ
diff --git a/lib/alignsvc.jar b/lib/alignsvc.jar
index 79ee308336b33c1f79090e071bce3196e9b5d22b..02a704c0b030164bab51738c39eb99e8c2ca61eb 100644
Binary files a/lib/alignsvc.jar and b/lib/alignsvc.jar differ
diff --git a/lib/alignwn.jar b/lib/alignwn.jar
index 36c48297673541159fda01abb3ff46a46046c96a..e086c76dd2ba019029bbaffbe110a2508e2715ea 100644
Binary files a/lib/alignwn.jar and b/lib/alignwn.jar differ
diff --git a/lib/procalign.jar b/lib/procalign.jar
index 62aac3c435143583359ea73d4adb37380310aedb..5ac39934cef50cf9b253a24e7756baf4f7e94229 100644
Binary files a/lib/procalign.jar and b/lib/procalign.jar differ
diff --git a/rdf/srcalign.owl b/rdf/srcalign.owl
index 27d453ff6d521855356a2563b4e9b9254e20135a..5c4bbea031e76ced1c3586159d6bdf8954b47fc9 100644
--- a/rdf/srcalign.owl
+++ b/rdf/srcalign.owl
@@ -9,8 +9,8 @@
<type>11</type>
<uri1>http://www.example.org/ontology1</uri1>
<uri2>http://www.example.org/ontology2</uri2>
- <onto1>file://./rdf/onto1.owl</onto1>
- <onto2>file://./rdf/onto2.owl</onto2>
+ <onto1>file://localhost/Volumes/Phata/JAVA/alignapi/rdf/onto1.owl</onto1>
+ <onto2>file://localhost/Volumes/Phata/JAVA/alignapi/rdf/onto2.owl</onto2>
<map>
<Cell>
<entity1 rdf:resource='http://www.example.org/ontology1#journalarticle'/>
diff --git a/src/fr/inrialpes/exmo/align/util/GenPlot.java b/src/fr/inrialpes/exmo/align/util/GenPlot.java
index f7967e7f48b9bad5ea04bcc93db908031b2b07a7..f634ae8a1d9decd3280879c8e9b868f07497e267 100644
--- a/src/fr/inrialpes/exmo/align/util/GenPlot.java
+++ b/src/fr/inrialpes/exmo/align/util/GenPlot.java
@@ -300,24 +300,6 @@ public class GenPlot {
output.println("\\begin{document}");
output.println("\\date{today}");
output.println("");
- output.println("\\pgfuseplotmark{-}");
- output.println("\\pgfuseplotmark{|}");
- output.println("\\pgfuseplotmark{o}");
- output.println("\\pgfuseplotmark{asterisk}");
- output.println("\\pgfuseplotmark{star}");
- output.println("\\pgfuseplotmark{oplus}");
- output.println("\\pgfuseplotmark{oplus*}");
- output.println("\\pgfuseplotmark{otimes}");
- output.println("\\pgfuseplotmark{otimes*}");
- output.println("\\pgfuseplotmark{square}");
- output.println("\\pgfuseplotmark{square*}");
- output.println("\\pgfuseplotmark{triangle}");
- output.println("\\pgfuseplotmark{triangle*}");
- output.println("\\pgfuseplotmark{diamond}");
- output.println("\\pgfuseplotmark{diamond*}");
- output.println("\\pgfuseplotmark{pentagon}");
- output.println("\\pgfuseplotmark{pentagon*}");
- output.println("");
output.println("\n%% Plot generated by GenPlot of alignapi");
output.println("\\begin{tikzpicture}[cap=round]");
output.println("% Draw grid");
diff --git a/src/fr/inrialpes/exmo/align/util/GroupEval.java b/src/fr/inrialpes/exmo/align/util/GroupEval.java
index 7e2d8b75cb55a8f0751f62afb005a803428b105c..426c58b596dcb90049fe78ff0edb14c89241174a 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupEval.java
+++ b/src/fr/inrialpes/exmo/align/util/GroupEval.java
@@ -44,6 +44,7 @@ import java.io.FileOutputStream;
import java.net.URI;
import java.lang.Double;
import java.lang.Integer;
+import java.lang.Math;
import java.util.Hashtable;
import java.util.Vector;
import java.util.Enumeration;
@@ -282,6 +283,90 @@ public class GroupEval {
public static void print( Vector result ) {
if ( type.equals("html") ) printHTML( result );
else if ( type.equals("tex") ) printLATEX( result );
+ else if ( type.equals("triangle") ) printTRIANGLE( result );
+ }
+
+ public static void printTRIANGLE( Vector result ) {
+ // variables for computing iterative harmonic means
+ int expected = 0; // expected so far
+ int foundVect[]; // found so far
+ int correctVect[]; // correct so far
+ long timeVect[]; // time so far
+ double hMeansPrec[]; // Precision H-means so far
+ double hMeansRec[]; // Recall H-means so far
+ foundVect = new int[ listAlgo.size() ];
+ correctVect = new int[ listAlgo.size() ];
+ timeVect = new long[ listAlgo.size() ];
+ hMeansPrec = new double[ listAlgo.size() ];
+ hMeansRec = new double[ listAlgo.size() ];
+ for( int k = listAlgo.size()-1; k >= 0; k-- ) {
+ foundVect[k] = 0;
+ correctVect[k] = 0;
+ timeVect[k] = 0;
+ hMeansPrec[k] = 1.;
+ hMeansRec[k] = 1.;
+ }
+ for ( Enumeration e = result.elements() ; e.hasMoreElements() ;) {
+ int nexpected = -1;
+ int oexpected = 0;
+ Vector test = (Vector)e.nextElement();
+ Enumeration f = test.elements();
+ f.nextElement();
+ for( int k = 0 ; f.hasMoreElements() ; k++) {
+ PRecEvaluator eval = (PRecEvaluator)f.nextElement();
+ if ( eval != null ){
+ // iterative H-means computation
+ if ( nexpected == -1 ){
+ nexpected = eval.getExpected();
+ oexpected = expected;
+ expected = oexpected + nexpected;
+ }
+ int nfound = eval.getFound();
+ int ofound = foundVect[k];
+ foundVect[k] = ofound + nfound;
+ int ncorrect = eval.getCorrect();
+ int ocorrect = correctVect[k];
+ correctVect[k] = ocorrect + ncorrect;
+ timeVect[k] += eval.getTime();
+ }
+ }
+ }
+ System.out.println("\\documentclass[11pt]{book}");
+ System.out.println();
+ System.out.println("\\usepackage{pgf}");
+ System.out.println("\\usepackage{tikz}");
+ System.out.println();
+ System.out.println("\\begin{document}");
+ System.out.println("\\date{today}");
+ System.out.println("");
+ System.out.println("\n%% Plot generated by GenPlot of alignapi");
+ System.out.println("\\begin{tikzpicture}[cap=round]");
+ System.out.println("% Draw grid");
+ System.out.println("\\draw[step=1cm,very thin,color=gray] (-0.2,-0.2) grid (10.0,9.0);");
+ System.out.println("\\draw[|-|] (-0,0) -- (10,0);");
+ System.out.println("%\\draw[dashed,very thin] (0,0) -- (5,8.66) -- (10,0);");
+ System.out.println("\\draw[dashed,very thin] (10,0) arc (0:60:10cm);");
+ System.out.println("\\draw[dashed,very thin] (0,0) arc (180:120:10cm);");
+
+ System.out.println("\\draw (0,-0.3) node {$recall$}; ");
+ System.out.println("\\draw (10,-0.3) node {$precision$}; ");
+ //System.out.println("\\draw (0,-0.3) node {0.}; ");
+ //System.out.println("\\draw (10,-0.3) node {1.}; ");
+ System.out.println("% Plots");
+ int k = 0;
+ for ( Enumeration e = listAlgo.elements() ; e.hasMoreElements() ; k++) {
+ double precision = (double)correctVect[k]/foundVect[k];
+ double recall = (double)correctVect[k]/expected;
+ double prec2 = precision*precision;
+ double a = ((prec2-(recall*recall)+1)/2);
+ double b = java.lang.Math.sqrt( prec2 - (a*a) );
+ a = a*10; b = b*10; //for printing scale 10.
+ System.out.println("\\draw plot[mark=+,] coordinates {("+a+","+b+")};");
+ System.out.println("\\draw ("+(a+.01)+","+(b+.01)+") node[anchor=south west] {"+(String)e.nextElement()+"};");
+ }
+ System.out.println("\\end{tikzpicture}");
+ System.out.println();
+ System.out.println("\\end{document}");
}
public static void printLATEX( Vector result ) {
@@ -297,6 +382,8 @@ public class GroupEval {
double hMeansRec[]; // Recall H-means so far
PrintStream writer = null;
fsize = format.length();
+ // JE: the writer should be put out
+ // JE: the h-means computation should be put out as well
try {
// Print result
if ( filename == null ) {
@@ -480,7 +567,7 @@ public class GroupEval {
System.out.println("\t--output=filename -o filename\tSpecifies a file to which the output will go");
System.out.println("\t--reference=filename -r filename\tSpecifies the name of the reference alignment file (default: refalign.rdf)");
- System.out.println("\t--type=html|xml|tex|ascii -t html|xml|tex|ascii\tSpecifies the output format");
+ System.out.println("\t--type=html|xml|tex|ascii|triangle -t html|xml|tex|ascii\tSpecifies the output format");
System.out.println("\t--list=algo1,...,algon -l algo1,...,algon\tSequence of the filenames to consider");
System.out.println("\t--color=color -c color\tSpecifies if the output must color even lines of the output");
System.out.println("\t--debug[=n] -d [n]\t\tReport debug info at level n");