i- changed metadata for keyword expansion

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'/>

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");

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");