@@ -309,6 +309,7 @@ private void initComponents() {
309309 ghostTextPepProph = new GhostText (textReportDbAnnotate , TEXT_SAME_SEQ_DB , defTextColor );
310310 checkReportFilter = new javax .swing .JCheckBox ();
311311 textReportFilter = new javax .swing .JTextField ();
312+ checkReportProteinLevelFdr = new javax .swing .JCheckBox ();
312313 checkCreateReport = new javax .swing .JCheckBox ();
313314 btnReportDefaultsClosed = new javax .swing .JButton ();
314315 btnReportDefaultsOpen = new javax .swing .JButton ();
@@ -963,19 +964,33 @@ public void focusLost(java.awt.event.FocusEvent evt) {
963964 }
964965 });
965966
967+ checkReportProteinLevelFdr .setSelected (true );
968+ checkReportProteinLevelFdr .setText ("Report Protein level FDR" );
969+ checkReportProteinLevelFdr .setToolTipText ("<html>Which FDR (False Discovery Rate) level to use:\n <ul>\n <li>Checked - Protein level FDR</li>\n <li>Unchecked - Peptide level FDR</li>\n </ul>" );
970+ checkReportProteinLevelFdr .addChangeListener (new javax .swing .event .ChangeListener () {
971+ public void stateChanged (javax .swing .event .ChangeEvent evt ) {
972+ checkReportProteinLevelFdrStateChanged (evt );
973+ }
974+ });
975+
966976 javax .swing .GroupLayout jPanel1Layout = new javax .swing .GroupLayout (jPanel1 );
967977 jPanel1 .setLayout (jPanel1Layout );
968978 jPanel1Layout .setHorizontalGroup (
969979 jPanel1Layout .createParallelGroup (javax .swing .GroupLayout .Alignment .LEADING )
970980 .addGroup (jPanel1Layout .createSequentialGroup ()
971981 .addContainerGap ()
972- .addGroup (jPanel1Layout .createParallelGroup (javax .swing .GroupLayout .Alignment .TRAILING , false )
973- .addComponent (checkReportFilter , javax .swing .GroupLayout .DEFAULT_SIZE , javax .swing .GroupLayout .DEFAULT_SIZE , Short .MAX_VALUE )
974- .addComponent (checkReportDbAnnotate , javax .swing .GroupLayout .DEFAULT_SIZE , javax .swing .GroupLayout .DEFAULT_SIZE , Short .MAX_VALUE ))
975- .addPreferredGap (javax .swing .LayoutStyle .ComponentPlacement .UNRELATED )
976982 .addGroup (jPanel1Layout .createParallelGroup (javax .swing .GroupLayout .Alignment .LEADING )
977- .addComponent (textReportDbAnnotate , javax .swing .GroupLayout .DEFAULT_SIZE , 461 , Short .MAX_VALUE )
978- .addComponent (textReportFilter ))
983+ .addGroup (jPanel1Layout .createSequentialGroup ()
984+ .addGroup (jPanel1Layout .createParallelGroup (javax .swing .GroupLayout .Alignment .TRAILING , false )
985+ .addComponent (checkReportFilter , javax .swing .GroupLayout .DEFAULT_SIZE , javax .swing .GroupLayout .DEFAULT_SIZE , Short .MAX_VALUE )
986+ .addComponent (checkReportDbAnnotate , javax .swing .GroupLayout .DEFAULT_SIZE , javax .swing .GroupLayout .DEFAULT_SIZE , Short .MAX_VALUE ))
987+ .addPreferredGap (javax .swing .LayoutStyle .ComponentPlacement .UNRELATED )
988+ .addGroup (jPanel1Layout .createParallelGroup (javax .swing .GroupLayout .Alignment .LEADING )
989+ .addComponent (textReportDbAnnotate , javax .swing .GroupLayout .DEFAULT_SIZE , 461 , Short .MAX_VALUE )
990+ .addComponent (textReportFilter )))
991+ .addGroup (jPanel1Layout .createSequentialGroup ()
992+ .addComponent (checkReportProteinLevelFdr )
993+ .addGap (0 , 0 , Short .MAX_VALUE )))
979994 .addContainerGap ())
980995 );
981996 jPanel1Layout .setVerticalGroup (
@@ -989,10 +1004,13 @@ public void focusLost(java.awt.event.FocusEvent evt) {
9891004 .addGroup (jPanel1Layout .createParallelGroup (javax .swing .GroupLayout .Alignment .BASELINE )
9901005 .addComponent (checkReportFilter )
9911006 .addComponent (textReportFilter , javax .swing .GroupLayout .PREFERRED_SIZE , javax .swing .GroupLayout .DEFAULT_SIZE , javax .swing .GroupLayout .PREFERRED_SIZE ))
1007+ .addPreferredGap (javax .swing .LayoutStyle .ComponentPlacement .RELATED )
1008+ .addComponent (checkReportProteinLevelFdr )
9921009 .addContainerGap (javax .swing .GroupLayout .DEFAULT_SIZE , Short .MAX_VALUE ))
9931010 );
9941011
9951012 loadLastReportFilter ();
1013+ loadLastReportProteinLevelFdr ();
9961014
9971015 checkCreateReport .setSelected (true );
9981016 checkCreateReport .setText ("Create report" );
@@ -1039,7 +1057,7 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
10391057 .addComponent (btnReportDefaultsOpen )))
10401058 .addPreferredGap (javax .swing .LayoutStyle .ComponentPlacement .RELATED )
10411059 .addComponent (jPanel1 , javax .swing .GroupLayout .PREFERRED_SIZE , javax .swing .GroupLayout .DEFAULT_SIZE , javax .swing .GroupLayout .PREFERRED_SIZE )
1042- .addContainerGap (436 , Short .MAX_VALUE ))
1060+ .addContainerGap (415 , Short .MAX_VALUE ))
10431061 );
10441062
10451063 tabPane .addTab ("Report" , null , panelReport , "" );
@@ -2037,6 +2055,11 @@ private void btnReportDefaultsOpenActionPerformed(java.awt.event.ActionEvent evt
20372055 loadDefaultsReportFilter (SearchTypeProp .open );
20382056 }//GEN-LAST:event_btnReportDefaultsOpenActionPerformed
20392057
2058+ private void checkReportProteinLevelFdrStateChanged (javax .swing .event .ChangeEvent evt ) {//GEN-FIRST:event_checkReportProteinLevelFdrStateChanged
2059+ boolean selected = checkReportProteinLevelFdr .isSelected ();
2060+ ThisAppProps .save (ThisAppProps .PROP_CHECKBOX_REPORT_PROTEIN_LEVEL_FDR , Boolean .toString (selected ));
2061+ }//GEN-LAST:event_checkReportProteinLevelFdrStateChanged
2062+
20402063 public void loadLastPeptideProphet () {
20412064 String val = ThisAppProps .load (ThisAppProps .PROP_TEXT_CMD_PEPTIDE_PROPHET );
20422065 if (val != null ) {
@@ -2112,6 +2135,16 @@ private String getFraggerLableJavaVer() {
21122135 return sb .toString ();
21132136 }
21142137
2138+ private void loadLastReportProteinLevelFdr () {
2139+ String v = ThisAppProps .load (ThisAppProps .PROP_CHECKBOX_REPORT_PROTEIN_LEVEL_FDR );
2140+ if (v == null ) {
2141+ checkReportProteinLevelFdr .setSelected (true );
2142+ } else {
2143+ Boolean wasSelected = Boolean .valueOf (v );
2144+ checkReportProteinLevelFdr .setSelected (wasSelected );
2145+ }
2146+ }
2147+
21152148 public enum SearchTypeProp {open , closed }
21162149
21172150 private boolean validateAndSavePhilosopherPath (String path ) {
@@ -3155,8 +3188,10 @@ private List<ProcessBuilder> processBuildersReport(String programsDir, String wo
31553188 }
31563189 cmd .add ("--pepxml" );
31573190 cmd .add (workingDir );
3158- cmd .add ("--protxml" );
3159- cmd .add (combinedProtFilePath .toString ());
3191+ if (checkReportProteinLevelFdr .isSelected ()) {
3192+ cmd .add ("--protxml" );
3193+ cmd .add (combinedProtFilePath .toString ());
3194+ }
31603195 builders .add (new ProcessBuilder (cmd ));
31613196 }
31623197
@@ -3437,6 +3472,7 @@ private String getDefaultBinPhilosopher() {
34373472 private javax .swing .JCheckBox checkDryRun ;
34383473 private javax .swing .JCheckBox checkReportDbAnnotate ;
34393474 private javax .swing .JCheckBox checkReportFilter ;
3475+ private javax .swing .JCheckBox checkReportProteinLevelFdr ;
34403476 private javax .swing .JCheckBox chkProteinProphetInteractStar ;
34413477 private javax .swing .JCheckBox chkRunPeptideProphet ;
34423478 private javax .swing .JCheckBox chkRunProteinProphet ;
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