Changeset 3907

Timestamp:

Oct 21, 2010, 11:21:10 AM (13 years ago)

Author:

olle

Message:

Refs #700. New single-form version of routine for separating standard and advanced settings for X!Tandem searches:

1. Class/file gui/form/XTandemParameterSetForm.java in

client/servlet/ updated:

1. Public constructor XTandemParameterSetForm() update to place

fields and select boxes for standard settings in new field set,
that is open by default. These settings will no longer be added
to their original field sets, but will be kept in the original place
in the source code. Remaining advanced settings will be placed in
their original field sets, that are closed by default.

2. Class/file gui/form/XTandemParameterSetFormSimple.java in

client/servlet/ is removed, since it is no longer used.

3. English dictionary file locale/en/dictionary in client/servlet/

updated with new and changed entries for various string keys.

Location:

trunk/client/servlet/src

Files:

• locale/en/dictionary (modified) (1 diff)
• org/proteios/gui/form/XTandemParameterSetForm.java (modified) (16 diffs)
• org/proteios/gui/form/XTandemParameterSetFormSimple.java (deleted)

trunk/client/servlet/src/locale/en/dictionary

@@ -905 +905 @@
 XTandemOutputXslPath=XSL path
 XTandemParameterFile=X!Tandem Parameters File
-XTandemParameterSetListPath=X!Tandem - List path
-XTandemParameterSetOutput=X!Tandem - Output
-XTandemParameterSetProtein=X!Tandem - Protein
-XTandemParameterSetRefine=X!Tandem - Refine
-XTandemParameterSetResidue=X!Tandem - Residue
-XTandemParameterSetScoring=X!Tandem - Scoring
+XTandemParameterSetListPath=List path
+XTandemParameterSetOutput=Output
+XTandemParameterSetProtein=Protein
+XTandemParameterSetRefine=Refine
+XTandemParameterSetResidue=Residue
+XTandemParameterSetScoring=Scoring
 XTandemParameterSetsInDatabase=X!Tandem parameter sets in database
-XTandemParameterSetSpectrum=X!Tandem - Spectrum
+XTandemParameterSetSpectrum=Spectrum
+XTandemParameterSetStandardSettings=Standard Settings
 XTandemParameterSetStorage=X!Tandem parameter sets
 XTandemParameterSets=X!Tandem parameter sets

trunk/client/servlet/src/org/proteios/gui/form/XTandemParameterSetForm.java

@@ -201 +201 @@
   // Form field sets, fields, menus, and select boxes
   public Fieldset hiddenFieldContainerFS;
+  public Fieldset standardSettingsFS;
   //public Fieldset listPathFS;
   public Select<VString> listPathDefaultParametersSB;
@@ -315 +316 @@
     //List<String> selectedList = null;
     /*
-     * Spectrum field set is used for hidden fields from other field sets
-     */
-    spectrumFS = new Fieldset();
-    spectrumFS.setTitle("XTandemParameterSetSpectrum");
-    addFieldset(spectrumFS);
-    hiddenFieldContainerFS = spectrumFS;
+     * Standard settings field set
+     * 
+     * Standard settings field set is used for hidden fields from other field sets.
+     * Fields and select boxes in the standard settings field set
+     * are placed under the header of their original field set,
+     * in order to easier change what components are placed in
+     * the standard settings field set.
+     */
+    standardSettingsFS = new Fieldset();
+    standardSettingsFS.setTitle("XTandemParameterSetStandardSettings");
+    addFieldset(standardSettingsFS);
+    hiddenFieldContainerFS = standardSettingsFS;
     /*
      * List path field set
@@ -347 +354 @@
      * Spectrum field set
      */
-    // Spectrum field set already created
-    /*
     spectrumFS = new Fieldset();
     spectrumFS.setTitle("XTandemParameterSetSpectrum");
+    spectrumFS.setOpen(false);
     addFieldset(spectrumFS);
-    */
     // Spectrum, path
     spectrumPathF = new TextField<String>(VXTANDEM_SPECTRUM_PATH);
@@ -358 +363 @@
     // Spectrum, fragment monoisotopic mass error
     fragMiMassErrorF = new TextField<String>(VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR);
-    spectrumFS.add(fragMiMassErrorF);
+    //spectrumFS.add(fragMiMassErrorF);
+    standardSettingsFS.add(fragMiMassErrorF);
     // Spectrum, fragment monoisotopic mass error units
     validStringParam = VXTANDEM_SPECTRUM_FRAG_MI_MASS_ERROR_UNITS;
@@ -365 +371 @@
     stringList.add("ppm");
     fragMiMassErrorUnitsM = new Select<VString>(validStringParam, stringList, null);
-    spectrumFS.add(fragMiMassErrorUnitsM);
+    //spectrumFS.add(fragMiMassErrorUnitsM);
+    standardSettingsFS.add(fragMiMassErrorUnitsM);
     // Spectrum, parent monoisotopic mass error plus
     parentMiMassErrorPlusF = new TextField<String>(VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_PLUS);
-    spectrumFS.add(parentMiMassErrorPlusF);
+    //spectrumFS.add(parentMiMassErrorPlusF);
+    standardSettingsFS.add(parentMiMassErrorPlusF);
     // Spectrum, parent monoisotopic mass error minus
     parentMiMassErrorMinusF = new TextField<String>(VXTANDEM_SPECTRUM_PARENT_MI_MASS_ERROR_MINUS);
-    spectrumFS.add(parentMiMassErrorMinusF);
+    //spectrumFS.add(parentMiMassErrorMinusF);
+    standardSettingsFS.add(parentMiMassErrorMinusF);
     // Spectrum, parent monoisotopic mass isotope error
     validStringParam = VXTANDEM_SPECTRUM_PARENT_MI_MASS_ISOTOPE_ERROR;
@@ -385 +394 @@
     stringList.add("ppm");
     parentMiMassErrorUnitsM = new Select<VString>(validStringParam, stringList, null);
-    spectrumFS.add(parentMiMassErrorUnitsM);
+    //spectrumFS.add(parentMiMassErrorUnitsM);
+    standardSettingsFS.add(parentMiMassErrorUnitsM);
     // Spectrum, fragment mass type
     validStringParam = VXTANDEM_SPECTRUM_FRAG_MASS_TYPE;
@@ -432 +442 @@
     residueFS = new Fieldset();
     residueFS.setTitle("XTandemParameterSetResidue");
+    residueFS.setOpen(false);
     addFieldset(residueFS);
     // Residue, modification mass select
@@ -446 +457 @@
       .setLabel("XTandemResidueModificationMassSelect");
     residueModificationMassM.selectOption(null);
-    residueFS.add(residueModificationMassM);
+    //residueFS.add(residueModificationMassM);
+    standardSettingsFS.add(residueModificationMassM);
     // Residue, modification mass (own entered value)
     modificationMassF = new TextField<String>(VXTANDEM_RESIDUE_MODIFICATION_MASS);
     modificationMassF.setLabel("XTandemResidueModificationMassEnter");
-    residueFS.add(modificationMassF);
+    //residueFS.add(modificationMassF);
+    standardSettingsFS.add(modificationMassF);
     // Residue, potential modification mass select
     /*
@@ -466 +479 @@
       4,
       null);
-    residueFS.add(residuePotentialModificationMassSB);
+    //residueFS.add(residuePotentialModificationMassSB);
+    standardSettingsFS.add(residuePotentialModificationMassSB);
     // Residue, potential modification mass
     potentialModificationMassF = new TextField<String>(VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MASS);
     potentialModificationMassF
       .setLabel("XTandemResiduePotentialModificationMassEnter");
-    residueFS.add(potentialModificationMassF);
+    //residueFS.add(potentialModificationMassF);
+    standardSettingsFS.add(potentialModificationMassF);
     // Residue, potential modification motif
     potentialModificationMotifF = new TextField<String>(VXTANDEM_RESIDUE_POTENTIAL_MODIFICATION_MOTIF);
@@ -480 +495 @@
     proteinFS = new Fieldset();
     proteinFS.setTitle("XTandemParameterSetProtein");
+    proteinFS.setOpen(false);
     addFieldset(proteinFS);
     // Protein, taxon
@@ -495 +511 @@
       5,
       null);
-    proteinFS.add(taxonSB);
+    //proteinFS.add(taxonSB);
+    standardSettingsFS.add(taxonSB);
     // Taxon - Prokaryotes
     taxon1SB = createMultipleSelectBox(
@@ -503 +520 @@
       5,
       null);
-    proteinFS.add(taxon1SB);
+    //proteinFS.add(taxon1SB);
+    standardSettingsFS.add(taxon1SB);
     // Protein, cleavage site
     /*
@@ -549 +567 @@
     refineFS = new Fieldset();
     refineFS.setTitle("XTandemParameterSetRefine");
+    refineFS.setOpen(false);
     addFieldset(refineFS);
     // Refine
@@ -632 +651 @@
     scoringFS = new Fieldset();
     scoringFS.setTitle("XTandemParameterSetScoring");
+    scoringFS.setOpen(false);
     addFieldset(scoringFS);
     // Scoring, minimum ion count
@@ -702 +722 @@
     algorithmM = new Select<VString>(
       validStringParam, optionList);
-    scoringFS.add(algorithmM);
+    //scoringFS.add(algorithmM);
+    standardSettingsFS.add(algorithmM);
     /*
      * Output field set
@@ -708 +729 @@
     outputFS = new Fieldset();
     outputFS.setTitle("XTandemParameterSetOutput");
+    outputFS.setOpen(false);
     addFieldset(outputFS);
     // Output, path