@@ -108,6 +108,8 @@ public class MsfraggerGuiFrame extends javax.swing.JFrame {
108108 SimpleETable tableRawFiles ;
109109 SimpleUniqueTableModel <Path > tableModelRawFiles ;
110110 FileDrop tableRawFilesFileDrop ;
111+
112+ public static final SearchTypeProp DEFAULT_TYPE = SearchTypeProp .open ;
111113
112114 /**
113115 * Creates new form UmpireUnargetedDbSearchPanel
@@ -311,6 +313,8 @@ private void initComponents() {
311313 checkReportFilter = new javax .swing .JCheckBox ();
312314 textReportFilter = new javax .swing .JTextField ();
313315 checkCreateReport = new javax .swing .JCheckBox ();
316+ btnReportDefaultsClosed = new javax .swing .JButton ();
317+ btnReportDefaultsOpen = new javax .swing .JButton ();
314318 panelRun = new javax .swing .JPanel ();
315319 btnStop = new javax .swing .JButton ();
316320 btnClearConsole = new javax .swing .JButton ();
@@ -955,7 +959,6 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
955959 checkReportFilter .setSelected (true );
956960 checkReportFilter .setText ("Filter" );
957961
958- textReportFilter .setText (getDefaultTextReportFilter ());
959962 textReportFilter .setToolTipText ("<html>Additional flags for Philosopher<br/>\n --pepxml path-to-pepxml --protxml path-to-combined-protxml<br/>\n will be added automatically based on previous tabs." );
960963 textReportFilter .addFocusListener (new java .awt .event .FocusAdapter () {
961964 public void focusLost (java .awt .event .FocusEvent evt ) {
@@ -974,7 +977,7 @@ public void focusLost(java.awt.event.FocusEvent evt) {
974977 .addComponent (checkReportDbAnnotate , javax .swing .GroupLayout .DEFAULT_SIZE , javax .swing .GroupLayout .DEFAULT_SIZE , Short .MAX_VALUE ))
975978 .addPreferredGap (javax .swing .LayoutStyle .ComponentPlacement .UNRELATED )
976979 .addGroup (jPanel1Layout .createParallelGroup (javax .swing .GroupLayout .Alignment .LEADING )
977- .addComponent (textReportDbAnnotate )
980+ .addComponent (textReportDbAnnotate , javax . swing . GroupLayout . DEFAULT_SIZE , 461 , Short . MAX_VALUE )
978981 .addComponent (textReportFilter ))
979982 .addContainerGap ())
980983 );
@@ -992,10 +995,26 @@ public void focusLost(java.awt.event.FocusEvent evt) {
992995 .addContainerGap (javax .swing .GroupLayout .DEFAULT_SIZE , Short .MAX_VALUE ))
993996 );
994997
998+ loadLastReportFilter ();
999+
9951000 checkCreateReport .setSelected (true );
9961001 checkCreateReport .setText ("Create report" );
9971002 checkCreateReport .setToolTipText ("<html>Create tab separated report files with \n some statistics about search results." );
9981003
1004+ btnReportDefaultsClosed .setText ("Defaults Closed Search" );
1005+ btnReportDefaultsClosed .addActionListener (new java .awt .event .ActionListener () {
1006+ public void actionPerformed (java .awt .event .ActionEvent evt ) {
1007+ btnReportDefaultsClosedActionPerformed (evt );
1008+ }
1009+ });
1010+
1011+ btnReportDefaultsOpen .setText ("Defaults Open Search" );
1012+ btnReportDefaultsOpen .addActionListener (new java .awt .event .ActionListener () {
1013+ public void actionPerformed (java .awt .event .ActionEvent evt ) {
1014+ btnReportDefaultsOpenActionPerformed (evt );
1015+ }
1016+ });
1017+
9991018 javax .swing .GroupLayout panelReportLayout = new javax .swing .GroupLayout (panelReport );
10001019 panelReport .setLayout (panelReportLayout );
10011020 panelReportLayout .setHorizontalGroup (
@@ -1005,18 +1024,25 @@ public void focusLost(java.awt.event.FocusEvent evt) {
10051024 .addGroup (panelReportLayout .createParallelGroup (javax .swing .GroupLayout .Alignment .LEADING )
10061025 .addGroup (panelReportLayout .createSequentialGroup ()
10071026 .addComponent (checkCreateReport )
1008- .addGap (0 , 531 , Short .MAX_VALUE ))
1027+ .addPreferredGap (javax .swing .LayoutStyle .ComponentPlacement .RELATED , javax .swing .GroupLayout .DEFAULT_SIZE , Short .MAX_VALUE )
1028+ .addComponent (btnReportDefaultsOpen )
1029+ .addPreferredGap (javax .swing .LayoutStyle .ComponentPlacement .RELATED )
1030+ .addComponent (btnReportDefaultsClosed ))
10091031 .addComponent (jPanel1 , javax .swing .GroupLayout .DEFAULT_SIZE , javax .swing .GroupLayout .DEFAULT_SIZE , Short .MAX_VALUE ))
10101032 .addContainerGap ())
10111033 );
10121034 panelReportLayout .setVerticalGroup (
10131035 panelReportLayout .createParallelGroup (javax .swing .GroupLayout .Alignment .LEADING )
10141036 .addGroup (panelReportLayout .createSequentialGroup ()
10151037 .addContainerGap ()
1016- .addComponent (checkCreateReport )
1017- .addPreferredGap (javax .swing .LayoutStyle .ComponentPlacement .UNRELATED )
1038+ .addGroup (panelReportLayout .createParallelGroup (javax .swing .GroupLayout .Alignment .LEADING )
1039+ .addComponent (checkCreateReport )
1040+ .addGroup (panelReportLayout .createParallelGroup (javax .swing .GroupLayout .Alignment .BASELINE )
1041+ .addComponent (btnReportDefaultsClosed )
1042+ .addComponent (btnReportDefaultsOpen )))
1043+ .addPreferredGap (javax .swing .LayoutStyle .ComponentPlacement .RELATED )
10181044 .addComponent (jPanel1 , javax .swing .GroupLayout .PREFERRED_SIZE , javax .swing .GroupLayout .DEFAULT_SIZE , javax .swing .GroupLayout .PREFERRED_SIZE )
1019- .addContainerGap (439 , Short .MAX_VALUE ))
1045+ .addContainerGap (436 , Short .MAX_VALUE ))
10201046 );
10211047
10221048 tabPane .addTab ("Report" , null , panelReport , "" );
@@ -1945,11 +1971,14 @@ private void btnLoadDefaultsOpenActionPerformed(java.awt.event.ActionEvent evt)
19451971 "Are you sure you want to load defaults for open search?\n "
19461972 + "It's a search with large precursor mass tolerance\n "
19471973 + "usually used to identify PTMs.\n "
1948- + "Will update parameters for MSFragger and both Prophets." , "Confirmation" , JOptionPane .OK_CANCEL_OPTION );
1974+ + "Will update parameters for MSFragger, both Prophets\n "
1975+ + "and Report Filter." , "Confirmation" , JOptionPane .OK_CANCEL_OPTION );
19491976 if (JOptionPane .OK_OPTION == confirmation ) {
19501977 fraggerPanel .loadDefaultsOpen ();
1951- loadDefaultsPeptideProphet (MsfraggerGuiFrame .SearchTypeProp .open );
1952- loadDefaultsProteinProphet (MsfraggerGuiFrame .SearchTypeProp .open );
1978+ MsfraggerGuiFrame .SearchTypeProp type = MsfraggerGuiFrame .SearchTypeProp .open ;
1979+ loadDefaultsPeptideProphet (type );
1980+ loadDefaultsProteinProphet (type );
1981+ loadDefaultsReportFilter (type );
19531982 }
19541983 }//GEN-LAST:event_btnLoadDefaultsOpenActionPerformed
19551984
@@ -1958,11 +1987,14 @@ private void btnLoadDefaultsClosedActionPerformed(java.awt.event.ActionEvent evt
19581987 "Are you sure you want to load defaults for open search?\n "
19591988 + "It's a search with large precursor mass tolerance\n "
19601989 + "usually used to identify PTMs.\n "
1961- + "Will update parameters for MSFragger and both Prophets." , "Confirmation" , JOptionPane .OK_CANCEL_OPTION );
1990+ + "Will update parameters for MSFragger, both Prophets\n "
1991+ + "and Report Filter." , "Confirmation" , JOptionPane .OK_CANCEL_OPTION );
19621992 if (JOptionPane .OK_OPTION == confirmation ) {
19631993 fraggerPanel .loadDefaultsClosed ();
1964- loadDefaultsPeptideProphet (MsfraggerGuiFrame .SearchTypeProp .closed );
1965- loadDefaultsProteinProphet (MsfraggerGuiFrame .SearchTypeProp .closed );
1994+ MsfraggerGuiFrame .SearchTypeProp type = MsfraggerGuiFrame .SearchTypeProp .closed ;
1995+ loadDefaultsPeptideProphet (type );
1996+ loadDefaultsProteinProphet (type );
1997+ loadDefaultsReportFilter (type );
19661998 }
19671999 }//GEN-LAST:event_btnLoadDefaultsClosedActionPerformed
19682000
@@ -2000,6 +2032,14 @@ private void jButton1ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRS
20002032 btnAboutActionPerformed (null );
20012033 }//GEN-LAST:event_jButton1ActionPerformed
20022034
2035+ private void btnReportDefaultsClosedActionPerformed (java .awt .event .ActionEvent evt ) {//GEN-FIRST:event_btnReportDefaultsClosedActionPerformed
2036+ loadDefaultsReportFilter (SearchTypeProp .closed );
2037+ }//GEN-LAST:event_btnReportDefaultsClosedActionPerformed
2038+
2039+ private void btnReportDefaultsOpenActionPerformed (java .awt .event .ActionEvent evt ) {//GEN-FIRST:event_btnReportDefaultsOpenActionPerformed
2040+ loadDefaultsReportFilter (SearchTypeProp .open );
2041+ }//GEN-LAST:event_btnReportDefaultsOpenActionPerformed
2042+
20032043 public void loadLastPeptideProphet () {
20042044 String val = ThisAppProps .load (ThisAppProps .PROP_TEXT_CMD_PEPTIDE_PROPHET );
20052045 if (val != null ) {
@@ -2035,13 +2075,23 @@ public void loadDefaultsProteinProphet(SearchTypeProp type) {
20352075 txtProteinProphetCmdLineOpts .setText (val );
20362076 ThisAppProps .save (ThisAppProps .PROP_TEXT_CMD_PROTEIN_PROPHET , val );
20372077 }
2038-
2039- private String getDefaultTextReportFilter () {
2078+
2079+ private void loadLastReportFilter () {
20402080 String val = ThisAppProps .load (ThisAppProps .PROP_TEXTFIELD_REPORT_FILTER );
2041- if (StringUtils .isNullOrWhitespace (val )) {
2042- val = "" ;
2081+ if (val != null ) {
2082+ textReportFilter .setText (val );
2083+ } else {
2084+ loadDefaultsReportFilter (SearchTypeProp .open );
20432085 }
2044- return val ;
2086+ }
2087+
2088+ private void loadDefaultsReportFilter (SearchTypeProp type ) {
2089+ final String prop = ThisAppProps .PROP_TEXTFIELD_REPORT_FILTER + "." + type .name ();
2090+ java .util .ResourceBundle bundle = java .util .ResourceBundle .getBundle ("umich/msfragger/gui/Bundle" ); // NOI18N
2091+ String val = bundle .getString (prop );
2092+
2093+ textReportFilter .setText (val );
2094+ ThisAppProps .save (ThisAppProps .PROP_TEXTFIELD_REPORT_FILTER , val );
20452095 }
20462096
20472097 private String getFraggerLableJavaVer () {
@@ -2064,7 +2114,7 @@ private String getFraggerLableJavaVer() {
20642114
20652115 return sb .toString ();
20662116 }
2067-
2117+
20682118 public enum SearchTypeProp {open , closed }
20692119
20702120 private boolean validateAndSavePhilosopherPath (String path ) {
@@ -3395,6 +3445,8 @@ private String getDefaultBinPhilosopher() {
33953445 private javax .swing .JButton btnRawAddFolder ;
33963446 private javax .swing .JButton btnRawClear ;
33973447 private javax .swing .JButton btnRawRemove ;
3448+ private javax .swing .JButton btnReportDefaultsClosed ;
3449+ private javax .swing .JButton btnReportDefaultsOpen ;
33983450 private javax .swing .JButton btnRun ;
33993451 private javax .swing .JButton btnSelectPeptideProphetSeqDbPath ;
34003452 private javax .swing .JButton btnSelectWrkingDir ;
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