From fecc0f8bab5ea8327eb8602fce11a3177ecfd38e Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Wed, 25 Mar 2015 10:27:43 +0000 Subject: [PATCH] JAL-1667 clean up commented codes in PopupMenu.java and StructureChooser.java --- src/jalview/gui/PopupMenu.java | 119 +-------------------------------- src/jalview/gui/StructureChooser.java | 92 +------------------------ 2 files changed, 3 insertions(+), 208 deletions(-) diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 0a40af7..2244b03 100644 --- 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 --- 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 wantedFields = PDBDocFieldPreferences - // .getStructureSummaryFields(); - // Collection filteredResponse = new - // HashSet(); - // 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 reorderedStructuresSet = new - // LinkedHashSet(); - // 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); -- 1.7.10.2