diff --git a/html/relnotes.html b/html/relnotes.html
index c138c22c29ab32d65028d97873b32378ed12ece3..daf714c9b80f0cda51f919ea04657e2b1166a416 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -73,7 +73,8 @@ with a warning:
<li>Implemented <tt>extractss</tt> for ** alignments in <tt>DistanceAlignment</tt> (impl)</li>
<li>Changed default type of <tt>StringDistAlignment</tt> to "?*" for
preserving the previous behaviour (impl)</li>
-<li>Added level lines in the triangle display of <tt>GroupEval</tt> (util)</li>
+<li>Added level lines in the triangle display of <tt>GroupEval</tt> (cli)</li>
+<li>Implemented LaTeX output in <tt>GroupEval</tt> (cli)</li>
<li>Added <tt>BasicAlignment.deleteAllCells()</tt> (impl)</li>
<li>Added a guard in <tt>loadOntology</tt> for OWLAPI 3.0, in case the
ontology has no URI (ontowrap)</li>
diff --git a/src/fr/inrialpes/exmo/align/cli/GroupEval.java b/src/fr/inrialpes/exmo/align/cli/GroupEval.java
index fdc7b9a974d924ac923d7c3946323df40268edf8..458446d498116cd2da3ea2c33434e1382e4955a4 100644
--- a/src/fr/inrialpes/exmo/align/cli/GroupEval.java
+++ b/src/fr/inrialpes/exmo/align/cli/GroupEval.java
@@ -38,6 +38,7 @@ import fr.inrialpes.exmo.ontowrap.OntowrapException;
import java.io.File;
import java.io.PrintStream;
import java.io.FileOutputStream;
+import java.io.FileNotFoundException;
import java.lang.Integer;
import java.util.Hashtable;
import java.util.Vector;
@@ -280,9 +281,21 @@ public class GroupEval {
* This does not only print the results but compute the average as well
*/
public void print( Vector<Vector> result ) {
- if ( type.equals("html") ) printHTML( result );
- else if ( type.equals("tex") ) printLATEX( result );
- else if ( type.equals("triangle") ) printTRIANGLE( result );
+ PrintStream writer = null;
+ try {
+ if ( filename == null ) {
+ writer = System.out;
+ } else {
+ writer = new PrintStream(new FileOutputStream( filename ));
+ }
+ if ( type.equals("html") ) printHTML( result, writer );
+ else if ( type.equals("tex") ) printLATEX( result, writer );
+ else if ( type.equals("triangle") ) printTRIANGLE( result, writer );
+ } catch ( FileNotFoundException fnfex) {
+ fnfex.printStackTrace();
+ } finally {
+ writer.close();
+ }
}
/**
@@ -290,7 +303,7 @@ public class GroupEval {
* Added level lines provides by Christian Meilicke (U. Mannheim)
* See his program in comment below
*/
- public void printTRIANGLE( Vector<Vector> result ) {
+ public void printTRIANGLE( Vector<Vector> result, PrintStream writer ) {
// variables for computing iterative harmonic means
int expected = 0; // expected so far
int foundVect[]; // found so far
@@ -323,62 +336,62 @@ public class GroupEval {
}
}
}
- 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("%% Level lines for recall");
- System.out.println("\\draw[dashed] (10,0) arc (0:60:10cm) node[anchor=south east] {{\\tiny R=1.}};");
- System.out.println("\\draw[dotted,very thin] (9,0) arc (0:63:9cm) node[anchor=south east] {{\\tiny R=.9}};");
- System.out.println("\\draw[dotted,very thin] (8,0) arc (0:66:8cm) node[anchor=south east] {{\\tiny R=.8}};");
- System.out.println("\\draw[dotted,very thin] (7,0) arc (0:70:7cm) node[anchor=south east] {{\\tiny R=.7}};");
- System.out.println("\\draw[dotted,very thin] (6,0) arc (0:73:6cm) node[anchor=south east] {{\\tiny R=.6}};");
- System.out.println("\\draw[dotted,very thin] (5,0) arc (0:76:5cm) node[anchor=south east] {{\\tiny R=.5}};");
- System.out.println("\\draw[dotted,very thin] (4,0) arc (0:78:4cm) node[anchor=south east] {{\\tiny R=.4}};");
- System.out.println("\\draw[dotted,very thin] (3,0) arc (0:80:3cm) node[anchor=south east] {{\\tiny R=.3}};");
- System.out.println("\\draw[dotted,very thin] (2,0) arc (0:82:2cm) node[anchor=south east] {{\\tiny R=.2}};");
- System.out.println("\\draw[dotted,very thin] (1,0) arc (0:84:1cm) node[anchor=south east] {{\\tiny R=.1}};");
- System.out.println("%% Level lines for precision");
- System.out.println("\\draw[dashed] (0,0) arc (180:120:10cm) node[anchor=south west] {{\\tiny P=1.}};");
- System.out.println("\\draw[dotted,very thin] (1,0) arc (180:117:9cm) node[anchor=south west] {{\\tiny P=.9}};");
- System.out.println("\\draw[dotted,very thin] (2,0) arc (180:114:8cm) node[anchor=south west] {{\\tiny P=.8}};");
- System.out.println("\\draw[dotted,very thin] (3,0) arc (180:110:7cm) node[anchor=south west] {{\\tiny P=.7}};");
- System.out.println("\\draw[dotted,very thin] (4,0) arc (180:107:6cm) node[anchor=south west] {{\\tiny P=.6}};");
- System.out.println("\\draw[dotted,very thin] (5,0) arc (180:105:5cm) node[anchor=south west] {{\\tiny P=.5}};");
- System.out.println("\\draw[dotted,very thin] (6,0) arc (180:103:4cm) node[anchor=south west] {{\\tiny P=.4}};");
- System.out.println("\\draw[dotted,very thin] (7,0) arc (180:100:3cm) node[anchor=south west] {{\\tiny P=.3}};");
- System.out.println("\\draw[dotted,very thin] (8,0) arc (180:96:2cm) node[anchor=south west] {{\\tiny P=.2}};");
- System.out.println("\\draw[dotted,very thin] (9,0) arc (180:90:1cm) node[anchor=south west] {{\\tiny P=.1}};");
- System.out.println("%% Level lines for F-measure");
- System.out.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (0.56,3.29) (1.55,3.10) (2.46,2.68) (3.31,2.05) (4.12,1.19) (5.00,0.00) (6.42,1.79) (9.44,3.29)};");
- System.out.println("\\draw (0.56,3.29) node[anchor=south west] {\\tiny{F=0.5}};");
- System.out.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (0.92,4.19) (1.96,4.05) (2.95,3.78) (3.93,3.48) (5.00,3.32) (6.56,3.63) (9.08,4.19)};");
- System.out.println("\\draw (0.92,4.19) node[anchor=south west] {\\tiny{F=0.6}};");
- System.out.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (1.45,5.19) (2.59,5.11) (3.74,4.98) (5.00,4.90) (6.73,5.03) (8.55,5.19)};");
- System.out.println("\\draw (1.45,5.19) node[anchor=south west] {\\tiny{F=0.7}};");
- System.out.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (2.22,6.29) (3.54,6.27) (5.00,6.24) (6.91,6.28) (7.78,6.29)};");
- System.out.println("\\draw (2.22,6.29) node[anchor=south west] {\\tiny{F=0.8}};");
- System.out.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (3.35,7.47) (5.00,7.48) (6.65,7.47)};");
- System.out.println("\\draw (3.35,7.47) node[anchor=south west] {\\tiny{F=0.9}};");
-
- 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");
+ writer.println("\\documentclass[11pt]{book}");
+ writer.println();
+ writer.println("\\usepackage{pgf}");
+ writer.println("\\usepackage{tikz}");
+ writer.println();
+ writer.println("\\begin{document}");
+ writer.println("\\date{today}");
+ writer.println("");
+ writer.println("\n%% Plot generated by GroupEval of alignapi");
+ writer.println("\\begin{tikzpicture}[cap=round]");
+ writer.println("% Draw grid");
+ //writer.println("\\draw[step=1cm,very thin,color=gray] (-0.2,-0.2) grid (10.0,9.0);");
+ writer.println("\\draw[|-|] (-0,0) -- (10,0);");
+ writer.println("%\\draw[dashed,very thin] (0,0) -- (5,8.66) -- (10,0);");
+ writer.println("\\draw[dashed,very thin] (10,0) arc (0:60:10cm);");
+ writer.println("\\draw[dashed,very thin] (0,0) arc (180:120:10cm);");
+
+ writer.println("%% Level lines for recall");
+ writer.println("\\draw[dashed] (10,0) arc (0:60:10cm) node[anchor=south east] {{\\tiny R=1.}};");
+ writer.println("\\draw[dotted,very thin] (9,0) arc (0:63:9cm) node[anchor=south east] {{\\tiny R=.9}};");
+ writer.println("\\draw[dotted,very thin] (8,0) arc (0:66:8cm) node[anchor=south east] {{\\tiny R=.8}};");
+ writer.println("\\draw[dotted,very thin] (7,0) arc (0:70:7cm) node[anchor=south east] {{\\tiny R=.7}};");
+ writer.println("\\draw[dotted,very thin] (6,0) arc (0:73:6cm) node[anchor=south east] {{\\tiny R=.6}};");
+ writer.println("\\draw[dotted,very thin] (5,0) arc (0:76:5cm) node[anchor=south east] {{\\tiny R=.5}};");
+ writer.println("\\draw[dotted,very thin] (4,0) arc (0:78:4cm) node[anchor=south east] {{\\tiny R=.4}};");
+ writer.println("\\draw[dotted,very thin] (3,0) arc (0:80:3cm) node[anchor=south east] {{\\tiny R=.3}};");
+ writer.println("\\draw[dotted,very thin] (2,0) arc (0:82:2cm) node[anchor=south east] {{\\tiny R=.2}};");
+ writer.println("\\draw[dotted,very thin] (1,0) arc (0:84:1cm) node[anchor=south east] {{\\tiny R=.1}};");
+ writer.println("%% Level lines for precision");
+ writer.println("\\draw[dashed] (0,0) arc (180:120:10cm) node[anchor=south west] {{\\tiny P=1.}};");
+ writer.println("\\draw[dotted,very thin] (1,0) arc (180:117:9cm) node[anchor=south west] {{\\tiny P=.9}};");
+ writer.println("\\draw[dotted,very thin] (2,0) arc (180:114:8cm) node[anchor=south west] {{\\tiny P=.8}};");
+ writer.println("\\draw[dotted,very thin] (3,0) arc (180:110:7cm) node[anchor=south west] {{\\tiny P=.7}};");
+ writer.println("\\draw[dotted,very thin] (4,0) arc (180:107:6cm) node[anchor=south west] {{\\tiny P=.6}};");
+ writer.println("\\draw[dotted,very thin] (5,0) arc (180:105:5cm) node[anchor=south west] {{\\tiny P=.5}};");
+ writer.println("\\draw[dotted,very thin] (6,0) arc (180:103:4cm) node[anchor=south west] {{\\tiny P=.4}};");
+ writer.println("\\draw[dotted,very thin] (7,0) arc (180:100:3cm) node[anchor=south west] {{\\tiny P=.3}};");
+ writer.println("\\draw[dotted,very thin] (8,0) arc (180:96:2cm) node[anchor=south west] {{\\tiny P=.2}};");
+ writer.println("\\draw[dotted,very thin] (9,0) arc (180:90:1cm) node[anchor=south west] {{\\tiny P=.1}};");
+ writer.println("%% Level lines for F-measure");
+ writer.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (0.56,3.29) (1.55,3.10) (2.46,2.68) (3.31,2.05) (4.12,1.19) (5.00,0.00) (6.42,1.79) (9.44,3.29)};");
+ writer.println("\\draw (0.56,3.29) node[anchor=south west] {\\tiny{F=0.5}};");
+ writer.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (0.92,4.19) (1.96,4.05) (2.95,3.78) (3.93,3.48) (5.00,3.32) (6.56,3.63) (9.08,4.19)};");
+ writer.println("\\draw (0.92,4.19) node[anchor=south west] {\\tiny{F=0.6}};");
+ writer.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (1.45,5.19) (2.59,5.11) (3.74,4.98) (5.00,4.90) (6.73,5.03) (8.55,5.19)};");
+ writer.println("\\draw (1.45,5.19) node[anchor=south west] {\\tiny{F=0.7}};");
+ writer.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (2.22,6.29) (3.54,6.27) (5.00,6.24) (6.91,6.28) (7.78,6.29)};");
+ writer.println("\\draw (2.22,6.29) node[anchor=south west] {\\tiny{F=0.8}};");
+ writer.println("\\draw[very thin,densely dotted] plot[smooth] coordinates { (3.35,7.47) (5.00,7.48) (6.65,7.47)};");
+ writer.println("\\draw (3.35,7.47) node[anchor=south west] {\\tiny{F=0.9}};");
+
+ writer.println("\\draw (0,-0.3) node {$recall$};");
+ writer.println("\\draw (10,-0.3) node {$precision$};");
+ //writer.println("\\draw (0,-0.3) node {0.}; ");
+ //writer.println("\\draw (10,-0.3) node {1.}; ");
+ writer.println("% Plots");
int k = 0;
for ( String m: listAlgo ) {
double precision = (double)correctVect[k]/foundVect[k];
@@ -387,16 +400,321 @@ public class GroupEval {
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] {"+m+"};");
+ writer.println("\\draw plot[mark=+,] coordinates {("+a+","+b+")};");
+ writer.println("\\draw ("+(a+.01)+","+(b+.01)+") node[anchor=south west] {"+m+"};");
+ k++;
+ }
+ writer.println("\\end{tikzpicture}");
+ writer.println();
+ writer.println("\\end{document}");
+ }
+
+ public void printHTML( Vector<Vector> result, PrintStream writer ) {
+ // 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
+ Formatter formatter = new Formatter(writer);
+
+ fsize = format.length();
+ // JE: the h-means computation should be put out as well
+ // Print the header
+ if ( embedded != true ) writer.println("<html><head></head><body>");
+ writer.println("<table border='2' frame='sides' rules='groups'>");
+ writer.println("<colgroup align='center' />");
+ // for each algo <td spancol='2'>name</td>
+ for ( String m : listAlgo ) {
+ writer.println("<colgroup align='center' span='"+fsize+"' />");
+ }
+ // For each file do a
+ writer.println("<thead valign='top'><tr><th>algo</th>");
+ // for each algo <td spancol='2'>name</td>
+ for ( String m : listAlgo ) {
+ writer.println("<th colspan='"+fsize+"'>"+m+"</th>");
+ }
+ writer.println("</tr></thead><tbody><tr><td>test</td>");
+ // for each algo <td>Prec.</td><td>Rec.</td>
+ for ( String m : listAlgo ) {
+ for ( int i = 0; i < fsize; i++){
+ writer.print("<td>");
+ if ( format.charAt(i) == 'p' ) {
+ writer.print("Prec.");
+ } else if ( format.charAt(i) == 'f' ) {
+ writer.print("FMeas.");
+ } else if ( format.charAt(i) == 'o' ) {
+ writer.print("Over.");
+ } else if ( format.charAt(i) == 't' ) {
+ writer.print("Time");
+ } else if ( format.charAt(i) == 'r' ) {
+ writer.print("Rec.");
+ }
+ writer.println("</td>");
+ }
+ //writer.println("<td>Prec.</td><td>Rec.</td>");
+ }
+ writer.println("</tr></tbody><tbody>");
+ foundVect = new int[ listAlgo.size() ];
+ correctVect = new int[ listAlgo.size() ];
+ timeVect = new long[ listAlgo.size() ];
+ for( int k = listAlgo.size()-1; k >= 0; k-- ) {
+ foundVect[k] = 0;
+ correctVect[k] = 0;
+ timeVect[k] = 0;
+ }
+ // </tr>
+ // For each directory <tr>
+ boolean colored = false;
+ for ( Vector test : result ) {
+ int nexpected = -1;
+ if ( colored == true && color != null ){
+ colored = false;
+ writer.println("<tr bgcolor=\""+color+"\">");
+ } else {
+ colored = true;
+ writer.println("<tr>");
+ };
+ // Print the directory <td>bla</td>
+ writer.println("<td>"+(String)test.get(0)+"</td>");
+ // For each record print the values <td>bla</td>
+ 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 ){
+ expected += eval.getExpected();
+ nexpected = 0;
+ }
+ foundVect[k] += eval.getFound();
+ correctVect[k] += eval.getCorrect();
+ timeVect[k] += eval.getTime();
+
+ for ( int i = 0 ; i < fsize; i++){
+ writer.print("<td>");
+ if ( format.charAt(i) == 'p' ) {
+ formatter.format("%1.2f", eval.getPrecision());
+ } else if ( format.charAt(i) == 'f' ) {
+ formatter.format("%1.2f", eval.getFmeasure());
+ } else if ( format.charAt(i) == 'o' ) {
+ formatter.format("%1.2f", eval.getOverall());
+ } else if ( format.charAt(i) == 't' ) {
+ if ( eval.getTime() == 0 ){
+ writer.print("-");
+ } else {
+ formatter.format("%1.2f", eval.getTime());
+ }
+ } else if ( format.charAt(i) == 'r' ) {
+ formatter.format("%1.2f", eval.getRecall());
+ }
+ writer.println("</td>");
+ }
+ } else {
+ writer.println("<td>n/a</td><td>n/a</td>");
+ }
+ }
+ writer.println("</tr>");
+ }
+ writer.print("<tr bgcolor=\"yellow\"><td>H-mean</td>");
+ // Here we are computing a sheer average.
+ // While in the column results we print NaN when the returned
+ // alignment is empty,
+ // here we use the real values, i.e., add 0 to both correctVect and
+ // foundVect, so this is OK for computing the average.
+ int k = 0;
+ // ???
+ for ( String m : listAlgo ) {
+ double precision = (double)correctVect[k]/foundVect[k];
+ double recall = (double)correctVect[k]/expected;
+ for ( int i = 0 ; i < fsize; i++){
+ writer.print("<td>");
+ if ( format.charAt(i) == 'p' ) {
+ formatter.format("%1.2f", precision);
+ } else if ( format.charAt(i) == 'f' ) {
+ formatter.format("%1.2f", 2 * precision * recall / (precision + recall));
+ } else if ( format.charAt(i) == 'o' ) {
+ formatter.format("%1.2f", recall * (2 - (1 / precision)));
+ } else if ( format.charAt(i) == 't' ) {
+ if ( timeVect[k] == 0 ){
+ writer.print("-");
+ } else {
+ formatter.format("%1.2f", timeVect[k]);
+ }
+ } else if ( format.charAt(i) == 'r' ) {
+ formatter.format("%1.2f", recall);
+ }
+ writer.println("</td>");
+ };
+ k++;
+ }
+ writer.println("</tr>");
+ writer.println("</tbody></table>");
+ writer.println("<p><small>n/a: result alignment not provided or not readable<br />");
+ writer.println("NaN: division per zero, likely due to empty alignment.</small></p>");
+ if ( embedded != true ) writer.println("</body></html>");
+ }
+
+ public void printLATEX( Vector<Vector> result, PrintStream writer ) {
+ // 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
+ Formatter formatter = new Formatter(writer);
+
+ fsize = format.length();
+ // JE: the h-means computation should be put out as well
+ // Print the header
+ writer.println("\\documentclass[11pt]{book}");
+ writer.println();
+ writer.println("\\begin{document}");
+ writer.println("\\date{today}");
+ writer.println("");
+ writer.println("\n%% Plot generated by GroupEval of alignapi");
+ writer.println("\\setlength{\\tabcolsep}{3pt} % May be changed");
+ writer.println("\\begin{table}");
+ writer.print("\\begin{tabular}{|l||");
+ for ( int i = listAlgo.size(); i > 0; i-- ) {
+ for ( int j = fsize; j > 0; j-- ) writer.print("c");
+ writer.print("|");
+ }
+ writer.println("}");
+ writer.println("\\hline");
+ // For each file do a
+ writer.print("algo");
+ // for each algo <td spancol='2'>name</td>
+ for ( String m : listAlgo ) {
+ writer.print(" & \\multicolumn{"+fsize+"}{c|}{"+m+"}");
+ }
+ writer.println(" \\\\ \\hline");
+ writer.print("test");
+ // for each algo <td>Prec.</td><td>Rec.</td>
+ for ( String m : listAlgo ) {
+ for ( int i = 0; i < fsize; i++){
+ writer.print(" & ");
+ if ( format.charAt(i) == 'p' ) {
+ writer.print("Prec.");
+ } else if ( format.charAt(i) == 'f' ) {
+ writer.print("FMeas.");
+ } else if ( format.charAt(i) == 'o' ) {
+ writer.print("Over.");
+ } else if ( format.charAt(i) == 't' ) {
+ writer.print("Time");
+ } else if ( format.charAt(i) == 'r' ) {
+ writer.print("Rec.");
+ }
+ }
+ }
+ writer.println(" \\\\ \\hline");
+ foundVect = new int[ listAlgo.size() ];
+ correctVect = new int[ listAlgo.size() ];
+ timeVect = new long[ listAlgo.size() ];
+ for( int k = listAlgo.size()-1; k >= 0; k-- ) {
+ foundVect[k] = 0;
+ correctVect[k] = 0;
+ timeVect[k] = 0;
+ }
+ for ( Vector test : result ) {
+ int nexpected = -1;
+ // Print the directory
+ writer.print((String)test.get(0));
+ // For each record print the values
+ 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 ){
+ expected += eval.getExpected();
+ nexpected = 0;
+ }
+ foundVect[k] += eval.getFound();
+ correctVect[k] += eval.getCorrect();
+ timeVect[k] += eval.getTime();
+
+ for ( int i = 0 ; i < fsize; i++){
+ writer.print(" & ");
+ if ( format.charAt(i) == 'p' ) {
+ formatter.format("%1.2f", eval.getPrecision());
+ } else if ( format.charAt(i) == 'f' ) {
+ formatter.format("%1.2f", eval.getFmeasure());
+ } else if ( format.charAt(i) == 'o' ) {
+ formatter.format("%1.2f", eval.getOverall());
+ } else if ( format.charAt(i) == 't' ) {
+ if ( eval.getTime() == 0 ){
+ writer.print("-");
+ } else {
+ formatter.format("%1.2f", eval.getTime());
+ }
+ } else if ( format.charAt(i) == 'r' ) {
+ formatter.format("%1.2f", eval.getRecall());
+ }
+ }
+ } else {
+ writer.print(" & \\multicolumn{"+fsize+"}{c|}{n/a}");
+ }
+ }
+ writer.println(" \\\\");
+ }
+ writer.print("H-mean");
+ // Here we are computing a sheer average.
+ // While in the column results we print NaN when the returned
+ // alignment is empty,
+ // here we use the real values, i.e., add 0 to both correctVect and
+ // foundVect, so this is OK for computing the average.
+ int k = 0;
+ // ???
+ for ( String m : listAlgo ) {
+ double precision = (double)correctVect[k]/foundVect[k];
+ double recall = (double)correctVect[k]/expected;
+ for ( int i = 0 ; i < fsize; i++){
+ writer.print(" & ");
+ if ( format.charAt(i) == 'p' ) {
+ formatter.format("%1.2f", precision);
+ } else if ( format.charAt(i) == 'f' ) {
+ formatter.format("%1.2f", 2 * precision * recall / (precision + recall));
+ } else if ( format.charAt(i) == 'o' ) {
+ formatter.format("%1.2f", recall * (2 - (1 / precision)));
+ } else if ( format.charAt(i) == 't' ) {
+ if ( timeVect[k] == 0 ){
+ writer.print("-");
+ } else {
+ formatter.format("%1.2f", timeVect[k]);
+ }
+ } else if ( format.charAt(i) == 'r' ) {
+ formatter.format("%1.2f", recall);
+ }
+ };
k++;
}
- System.out.println("\\end{tikzpicture}");
- System.out.println();
- System.out.println("\\end{document}");
+ writer.println(" \\\\ \\hline");
+ writer.println("\\end{tabular}");
+ writer.println("\\caption{Plot generated by GroupEval of alignapi \\protect\\footnote{n/a: result alignment not provided or not readable -- NaN: division per zero, likely due to empty alignment.}}");
+ writer.println("\\end{table}");
+ writer.println("\\end{document}");
}
- /*
+ public void usage() {
+ System.out.println("usage: GroupEval [options]");
+ System.out.println("options are:");
+ System.out.println("\t--format=prfot -r prfot\tSpecifies the output order (precision/recall/f-measure/overall/time)");
+ // Apparently not implemented
+ //System.out.println("\t--sup=algo -s algo\tSpecifies if dominant columns are algorithms or measure");
+ 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|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");
+ System.out.println("\t--help -h\t\t\tPrint this message");
+ System.err.print("\n"+GroupEval.class.getPackage().getImplementationTitle()+" "+GroupEval.class.getPackage().getImplementationVersion());
+ System.err.println(" ($Id$)\n");
+ }
+
+/*
// Here is the code provided by Christian Meilicke and modified by JE
// For computing the F-measure level line in the Triangle representation
// The class can be put in FMeasureLines.java and compiled.
@@ -493,13 +811,9 @@ public class FMeasureLines {
return new double[]{pp, pr};
}
}
- */
-
- public void printLATEX( Vector result ) {
- }
+*/
- /* A few comments on how and why computing "weighted harmonic means"
- (Jérôme Euzenat)
+/* A few comments on how and why computing "weighted harmonic means" (Jérôme Euzenat)
Let Ai be the found alignment for test i, let Ri be the reference alignment for test i.
Let |A| be the size of A, i.e., the number of correspondences.
@@ -543,182 +857,8 @@ and
correctVect[k] / expected
which the program does...
- */
- public void printHTML( Vector<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
- 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 ) {
- writer = System.out;
- } else {
- writer = new PrintStream(new FileOutputStream( filename ));
- }
- Formatter formatter = new Formatter(writer);
-
- // Print the header
- if ( embedded != true ) writer.println("<html><head></head><body>");
- writer.println("<table border='2' frame='sides' rules='groups'>");
- writer.println("<colgroup align='center' />");
- // for each algo <td spancol='2'>name</td>
- for ( String m : listAlgo ) {
- writer.println("<colgroup align='center' span='"+fsize+"' />");
- }
- // For each file do a
- writer.println("<thead valign='top'><tr><th>algo</th>");
- // for each algo <td spancol='2'>name</td>
- for ( String m : listAlgo ) {
- writer.println("<th colspan='"+fsize+"'>"+m+"</th>");
- }
- writer.println("</tr></thead><tbody><tr><td>test</td>");
- // for each algo <td>Prec.</td><td>Rec.</td>
- for ( String m : listAlgo ) {
- for ( int i = 0; i < fsize; i++){
- writer.print("<td>");
- if ( format.charAt(i) == 'p' ) {
- writer.print("Prec.");
- } else if ( format.charAt(i) == 'f' ) {
- writer.print("FMeas.");
- } else if ( format.charAt(i) == 'o' ) {
- writer.print("Over.");
- } else if ( format.charAt(i) == 't' ) {
- writer.print("Time");
- } else if ( format.charAt(i) == 'r' ) {
- writer.print("Rec.");
- }
- writer.println("</td>");
- }
- //writer.println("<td>Prec.</td><td>Rec.</td>");
- }
- writer.println("</tr></tbody><tbody>");
- foundVect = new int[ listAlgo.size() ];
- correctVect = new int[ listAlgo.size() ];
- timeVect = new long[ listAlgo.size() ];
- for( int k = listAlgo.size()-1; k >= 0; k-- ) {
- foundVect[k] = 0;
- correctVect[k] = 0;
- timeVect[k] = 0;
- }
- // </tr>
- // For each directory <tr>
- boolean colored = false;
- for ( Vector test : result ) {
- int nexpected = -1;
- if ( colored == true && color != null ){
- colored = false;
- writer.println("<tr bgcolor=\""+color+"\">");
- } else {
- colored = true;
- writer.println("<tr>");
- };
- // Print the directory <td>bla</td>
- writer.println("<td>"+(String)test.get(0)+"</td>");
- // For each record print the values <td>bla</td>
- 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 ){
- expected += eval.getExpected();
- nexpected = 0;
- }
- foundVect[k] += eval.getFound();
- correctVect[k] += eval.getCorrect();
- timeVect[k] += eval.getTime();
-
- for ( int i = 0 ; i < fsize; i++){
- writer.print("<td>");
- if ( format.charAt(i) == 'p' ) {
- formatter.format("%1.2f", eval.getPrecision());
- } else if ( format.charAt(i) == 'f' ) {
- formatter.format("%1.2f", eval.getFmeasure());
- } else if ( format.charAt(i) == 'o' ) {
- formatter.format("%1.2f", eval.getOverall());
- } else if ( format.charAt(i) == 't' ) {
- if ( eval.getTime() == 0 ){
- writer.print("-");
- } else {
- formatter.format("%1.2f", eval.getTime());
- }
- } else if ( format.charAt(i) == 'r' ) {
- formatter.format("%1.2f", eval.getRecall());
- }
- writer.println("</td>");
- }
- } else {
- writer.println("<td>n/a</td><td>n/a</td>");
- }
- }
- writer.println("</tr>");
- }
- writer.print("<tr bgcolor=\"yellow\"><td>H-mean</td>");
- // Here we are computing a sheer average.
- // While in the column results we print NaN when the returned
- // alignment is empty,
- // here we use the real values, i.e., add 0 to both correctVect and
- // foundVect, so this is OK for computing the average.
- int k = 0;
- // ???
- for ( String m : listAlgo ) {
- double precision = (double)correctVect[k]/foundVect[k];
- double recall = (double)correctVect[k]/expected;
- for ( int i = 0 ; i < fsize; i++){
- writer.print("<td>");
- if ( format.charAt(i) == 'p' ) {
- formatter.format("%1.2f", precision);
- } else if ( format.charAt(i) == 'f' ) {
- formatter.format("%1.2f", 2 * precision * recall / (precision + recall));
- } else if ( format.charAt(i) == 'o' ) {
- formatter.format("%1.2f", recall * (2 - (1 / precision)));
- } else if ( format.charAt(i) == 't' ) {
- if ( timeVect[k] == 0 ){
- writer.print("-");
- } else {
- formatter.format("%1.2f", timeVect[k]);
- }
- } else if ( format.charAt(i) == 'r' ) {
- formatter.format("%1.2f", recall);
- }
- writer.println("</td>");
- };
- k++;
- }
- writer.println("</tr>");
- writer.println("</tbody></table>");
- writer.println("<p><small>n/a: result alignment not provided or not readable<br />");
- writer.println("NaN: division per zero, likely due to empty alignment.</small></p>");
- if ( embedded != true ) writer.println("</body></html>");
- writer.close();
- } catch (Exception ex) {
- ex.printStackTrace();
- }
- }
+*/
- public void usage() {
- System.out.println("usage: GroupEval [options]");
- System.out.println("options are:");
- System.out.println("\t--format=prfot -r prfot\tSpecifies the output order (precision/recall/f-measure/overall/time)");
- // Apparently not implemented
- //System.out.println("\t--sup=algo -s algo\tSpecifies if dominant columns are algorithms or measure");
- 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|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");
- System.out.println("\t--help -h\t\t\tPrint this message");
- System.err.print("\n"+GroupEval.class.getPackage().getImplementationTitle()+" "+GroupEval.class.getPackage().getImplementationVersion());
- System.err.println(" ($Id$)\n");
- }
}