JAL-1667 clean up commented codes in PopupMenu.java and StructureChooser.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 0a40af7..2244b03 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -125,9 +125,6 @@ public class PopupMenu extends JPopupMenu
 
   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 
-  // protected JRadioButtonMenuItem covariationColour = new
-  // JRadioButtonMenuItem();
-
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
 
   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
@@ -182,12 +179,6 @@ public class PopupMenu extends JPopupMenu
 
   JMenuItem pdbFromFile = new JMenuItem();
 
-  // JBPNote: Commented these out - Should add these services via the web
-  // services menu system.
-  // JMenuItem ContraFold = new JMenuItem();
-
-  // JMenuItem RNAFold = new JMenuItem();
-
   JMenuItem enterPDB = new JMenuItem();
 
   JMenuItem discoverPDB = new JMenuItem();
@@ -216,11 +207,8 @@ public class PopupMenu extends JPopupMenu
 
   JMenu viewStructureMenu = new JMenu();
 
-  // JMenu colStructureMenu = new JMenu();
   JMenuItem editSequence = new JMenuItem();
 
-  // JMenuItem annotationMenuItem = new JMenuItem();
-
   JMenu groupLinksMenu;
 
   JMenuItem hideInsertions = new JMenuItem();
@@ -273,7 +261,6 @@ public class PopupMenu extends JPopupMenu
     colours.add(BLOSUM62Colour);
     colours.add(purinePyrimidineColour);
     colours.add(RNAInteractionColour);
-    // colours.add(covariationColour);
 
     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
     {
@@ -378,7 +365,6 @@ public class PopupMenu extends JPopupMenu
         {
           structureMenu.remove(viewStructureMenu);
         }
-        // structureMenu.remove(colStructureMenu);
       }
       if (ap.av.getAlignment().isNucleotide() == true)
       {
@@ -399,19 +385,8 @@ public class PopupMenu extends JPopupMenu
               @Override
               public void actionPerformed(ActionEvent e)
               {
-                // // System.out.println("1:"+structureLine);
-                // System.out.println("1:sname" + seq.getName());
-                // System.out.println("2:seq" + seq);
-                //
-                // // System.out.println("3:"+seq.getSequenceAsString());
-                // System.out.println("3:strucseq" + rnastruc);
-                // // System.out.println("4:struc"+seq.getRNA());
-                // System.out.println("5:name" + seq.getName());
-                // System.out.println("6:ap" + ap);
                 new AppVarna(structureLine, seq, seq.getSequenceAsString(),
                         rnastruc, seq.getName(), ap);
-                // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
-                // seq.getName(), ap);
                 System.out.println("end");
               }
             });
@@ -419,7 +394,6 @@ public class PopupMenu extends JPopupMenu
           }
         }
 
-        // SequenceFeatures[] test = seq.getSequenceFeatures();
 
         if (seq.getAnnotation() != null)
         {
@@ -639,50 +613,6 @@ public class PopupMenu extends JPopupMenu
                 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
                 new PDBEntry[reppdb.size()]);
         final JMenuItem gpdbview, rpdbview;
-        // if (pdbe.size() == 1)
-        // {
-        // structureMenu.add(gpdbview = new JMenuItem(MessageManager
-        // .formatMessage("label.view_structure_for", new String[]
-        // { sqass.getDisplayId(false) })));
-        // }
-        // else
-        // {
-        // structureMenu.add(gpdbview = new JMenuItem(MessageManager
-        // .formatMessage("label.view_all_structures", new String[]
-        // { new Integer(pdbe.size()).toString() })));
-        // }
-        // gpdbview.setToolTipText(MessageManager
-        // .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
-        // gpdbview.addActionListener(new ActionListener()
-        // {
-        //
-        // @Override
-        // public void actionPerformed(ActionEvent e)
-        // {
-        // new StructureViewer(ap.getStructureSelectionManager())
-        // .viewStructures(ap, pe, ap.av.collateForPDB(pe));
-        // }
-        // });
-        // if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
-        // {
-        // structureMenu.add(rpdbview = new JMenuItem(MessageManager
-        // .formatMessage(
-        // "label.view_all_representative_structures",
-        // new String[]
-        // { new Integer(reppdb.size()).toString() })));
-        // rpdbview.setToolTipText(MessageManager
-        // .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
-        // rpdbview.addActionListener(new ActionListener()
-        // {
-        //
-        // @Override
-        // public void actionPerformed(ActionEvent e)
-        // {
-        // new StructureViewer(ap.getStructureSelectionManager())
-        // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
-        // }
-        // });
-        // }
       }
     }
     else
@@ -1116,8 +1046,6 @@ public class PopupMenu extends JPopupMenu
       if (urlset != null)
       {
         int type = urlLink.getGroupURLType() & 3;
-        // System.out.println(urlLink.getGroupURLType()
-        // +" "+((String[])urlset[3])[0]);
         // first two bits ofurlLink type bitfield are sequenceids and sequences
         // TODO: FUTURE: ensure the groupURL menu structure can be generalised
         addshowLink(linkMenus[type], label
@@ -1428,32 +1356,7 @@ public class PopupMenu extends JPopupMenu
         pdbFromFile_actionPerformed();
       }
     });
-    // RNAFold.setText("From RNA Fold with predict2D");
-    // RNAFold.addActionListener(new ActionListener()
-    // {
-    // public void actionPerformed(ActionEvent e)
-    // {
-    // try {
-    // RNAFold_actionPerformed();
-    // } catch (Exception e1) {
-    // // TODO Auto-generated catch block
-    // e1.printStackTrace();
-    // }
-    // }
-    // });
-    // ContraFold.setText("From Contra Fold with predict2D");
-    // ContraFold.addActionListener(new ActionListener()
-    // {
-    // public void actionPerformed(ActionEvent e)
-    // {
-    // try {
-    // ContraFold_actionPerformed();
-    // } catch (Exception e1) {
-    // // TODO Auto-generated catch block
-    // e1.printStackTrace();
-    // }
-    // }
-    // });
+
     enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
     enterPDB.addActionListener(new ActionListener()
     {
@@ -1502,7 +1405,6 @@ public class PopupMenu extends JPopupMenu
       }
     });
     jMenu1.setText(MessageManager.getString("label.group"));
-    // structureMenu.setText(MessageManager.getString("label.structure"));
     structureMenu.setText(MessageManager.getString("label.view_structure"));
     structureMenu.addActionListener(new ActionListener()
     {
@@ -1606,10 +1508,8 @@ public class PopupMenu extends JPopupMenu
     if (ap.getAlignment().isNucleotide())
     {
       // JBPNote - commented since the colourscheme isn't functional
-      // colourMenu.add(RNAInteractionColour);
       colourMenu.add(purinePyrimidineColour);
     }
-    // colourMenu.add(covariationColour);
     colourMenu.add(userDefinedColour);
 
     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
@@ -1635,7 +1535,6 @@ public class PopupMenu extends JPopupMenu
     colourMenu.addSeparator();
     colourMenu.add(abovePIDColour);
     colourMenu.add(conservationMenuItem);
-    // colourMenu.add(annotationMenuItem);
     editMenu.add(copy);
     editMenu.add(cut);
     editMenu.add(editSequence);
@@ -1656,9 +1555,6 @@ public class PopupMenu extends JPopupMenu
     jMenu1.add(showColourText);
     jMenu1.add(outline);
     jMenu1.add(displayNonconserved);
-    // structureMenu.add(pdbMenu);
-    // structureMenu.add(viewStructureMenu);
-    // structureMenu.add(colStructureMenu);
     noColourmenuItem.setText(MessageManager.getString("label.none"));
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -2673,18 +2569,7 @@ public class PopupMenu extends JPopupMenu
 
   }
 
-  // JBNote: commented out - these won't be instantiated here...!
-  // public void RNAFold_actionPerformed() throws Exception
-  // {
-  // Predict2D P2D = new Predict2D();
-  // P2D.getStructure2DFromRNAFold("toto");
-  // }
-  //
-  // public void ContraFold_actionPerformed() throws Exception
-  // {
-  // Predict2D P2D = new Predict2D();
-  // P2D.getStructure2DFromContraFold("toto");
-  // }
+
   public void enterPDB_actionPerformed()
   {
     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 35c5791..3a54cc1 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -238,84 +238,6 @@ public class StructureChooser extends GStructureChooser
    */
   public void filterResultSet(final String fieldToFilterBy)
   {
-
-    // SwingWorker aWorker = new SwingWorker()
-    // {
-    // long startTime = System.currentTimeMillis();
-    //
-    // @Override
-    // protected Object doInBackground() throws Exception
-    // {
-    // lbl_loading.setVisible(true);
-    //
-    // Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
-    // .getStructureSummaryFields();
-    // Collection<PDBResponseSummary> filteredResponse = new
-    // HashSet<PDBResponseSummary>();
-    // for (SequenceI seq : selectedSequences)
-    // {
-    // PDBRestRequest pdbRequest = new PDBRestRequest();
-    // pdbRequest.setAllowEmptySeq(false);
-    // pdbRequest.setResponseSize(1);
-    // pdbRequest.setFieldToSearchBy("(text:");
-    // pdbRequest.setFieldToSortBy(fieldToFilterBy,
-    // !chk_invertFilter.isSelected());
-    // pdbRequest.setSearchTerm(buildQuery(seq) + ")");
-    // pdbRequest.setWantedFields(wantedFields);
-    // pdbRequest.setAssociatedSequence(seq.getName());
-    // pdbRestCleint = new PDBRestClient();
-    // PDBRestResponse resultList = pdbRestCleint
-    // .executeRequest(pdbRequest);
-    // lastPdbRequest = pdbRequest;
-    // if (resultList.getSearchSummary() != null
-    // && !resultList.getSearchSummary().isEmpty())
-    // {
-    // filteredResponse.addAll(resultList.getSearchSummary());
-    // }
-    // }
-    //
-    // if (!filteredResponse.isEmpty())
-    // {
-    // final int filterResponseCount = filteredResponse.size();
-    // Collection<PDBResponseSummary> reorderedStructuresSet = new
-    // LinkedHashSet<PDBResponseSummary>();
-    // reorderedStructuresSet.addAll(filteredResponse);
-    // reorderedStructuresSet.addAll(discoveredStructuresSet);
-    // tbl_summary.setModel(PDBRestResponse.getTableModel(
-    // lastPdbRequest, reorderedStructuresSet));
-    //
-    // // Update the model here
-    // // ListSelectionModel model = tbl_summary.getSelectionModel();
-    // // model.clearSelection();
-    // // model.addSelectionInterval(0, filterResponseCount - 1);
-    // // EventQueue.invokeLater(new Runnable()
-    // // {
-    // // public void run()
-    // // {
-    // // tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
-    //
-    // // }
-    // // });
-    // // Discard unwanted objects to make them eligible for garbage
-    // // collection
-    // reorderedStructuresSet = null;
-    // }
-    // return null;
-    // }
-    //
-    // public void done()
-    // {
-    // lbl_loading.setVisible(false);
-    // tbl_summary.addRowSelectionInterval(0, 2);
-    // String totalTime = (System.currentTimeMillis() - startTime)
-    // + " milli secs";
-    // mainFrame.setTitle("Structure Chooser - Filter time (" + totalTime
-    // + ")");
-    // validateSelections();
-    // }
-    // };
-    // aWorker.execute();
-
     Thread filterThread = new Thread(new Runnable()
     {
       @Override
@@ -360,21 +282,9 @@ public class StructureChooser extends GStructureChooser
             tbl_summary.setModel(PDBRestResponse.getTableModel(
                     lastPdbRequest, reorderedStructuresSet));
 
-            // Update the model here
-            // ListSelectionModel model = tbl_summary.getSelectionModel();
-            // model.clearSelection();
-            // model.addSelectionInterval(0, filterResponseCount - 1);
-            // EventQueue.invokeLater(new Runnable()
-            // {
-            // public void run()
-            // {
+            // Update table selection model here
             tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
 
-            // }
-            // });
-            // Discard unwanted objects to make them eligible for garbage
-            // collection
-            reorderedStructuresSet = null;
           }
 
           lbl_loading.setVisible(false);