X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=0957d28d1042e22f693c54055e504a0bf2f9800b;hb=aced09c4feeaf3406269442c14e54abeeb4cad81;hp=038477f169aaf831aa05dc39ac9558c431c6c484;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 038477f..0957d28 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -20,23 +20,58 @@ */ package jalview.gui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import javax.swing.*; - -import jalview.analysis.*; -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.schemes.*; +import jalview.analysis.AAFrequency; +import jalview.analysis.Conservation; +import jalview.commands.ChangeCaseCommand; +import jalview.commands.EditCommand; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.Annotation; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.FormatAdapter; +import jalview.io.SequenceAnnotationReport; +import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.NucleotideColourScheme; +import jalview.schemes.PIDColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; +import jalview.schemes.ResidueProperties; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.UserColourScheme; +import jalview.schemes.ZappoColourScheme; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; import jalview.util.UrlLink; +import java.awt.Color; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JColorChooser; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPopupMenu; +import javax.swing.JRadioButtonMenuItem; + /** * DOCUMENT ME! * @@ -74,6 +109,7 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); // protected JRadioButtonMenuItem covariationColour = new @@ -94,7 +130,9 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceSelDetails = new JMenuItem(); SequenceI sequence; + JMenuItem createGroupMenuItem = new JMenuItem(); + JMenuItem unGroupMenuItem = new JMenuItem(); JMenuItem outline = new JMenuItem(); @@ -126,11 +164,13 @@ public class PopupMenu extends JPopupMenu JMenu pdbMenu = new JMenu(); 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(); - + + // 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(); @@ -251,9 +291,12 @@ public class PopupMenu extends JPopupMenu { // TODO re JAL-860: optionally open dialog or provide a menu entry // allowing user to open just one structure per sequence - new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] - { pdb })[0], null, ap); - // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE); + // new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] + // { pdb })[0], null, ap); + new StructureViewer(ap.getStructureSelectionManager()) + .viewStructures(pdb, + ap.av.collateForPDB(new PDBEntry[] + { pdb })[0], null, ap); } }); @@ -288,25 +331,28 @@ public class PopupMenu extends JPopupMenu final String rnastruc = aa[i].getRNAStruc(); final String structureLine = aa[i].label; menuItem = new JMenuItem(); - menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine})); + menuItem.setText(MessageManager.formatMessage( + "label.2d_rna_structure_line", new String[] + { structureLine })); menuItem.addActionListener(new java.awt.event.ActionListener() - + { 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"); + // 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"); } }); viewStructureMenu.add(menuItem); @@ -326,13 +372,15 @@ public class PopupMenu extends JPopupMenu // TODO: make rnastrucF a bit more nice menuItem = new JMenuItem(); - menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()})); + menuItem.setText(MessageManager.formatMessage( + "label.2d_rna_sequence_name", new String[] + { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { // TODO: VARNA does'nt print gaps in the sequence - + new AppVarna(seq.getName() + " structure", seq, seq .getSequenceAsString(), rnastruc, seq.getName(), ap); @@ -345,7 +393,8 @@ public class PopupMenu extends JPopupMenu } - menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences")); + menuItem = new JMenuItem( + MessageManager.getString("action.hide_sequences")); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -358,7 +407,9 @@ public class PopupMenu extends JPopupMenu if (ap.av.getSelectionGroup() != null && ap.av.getSelectionGroup().getSize() > 1) { - menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()})); + menuItem = new JMenuItem(MessageManager.formatMessage( + "label.represent_group_with", new String[] + { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -376,7 +427,8 @@ public class PopupMenu extends JPopupMenu if (ap.av.adjustForHiddenSeqs(index) - ap.av.adjustForHiddenSeqs(index - 1) > 1) { - menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences")); + menuItem = new JMenuItem( + MessageManager.getString("action.reveal_sequences")); menuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -396,7 +448,8 @@ public class PopupMenu extends JPopupMenu if (ap.av.hasHiddenRows()) { { - menuItem = new JMenuItem(MessageManager.getString("action.reveal_all")); + menuItem = new JMenuItem( + MessageManager.getString("action.reveal_all")); menuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -415,12 +468,16 @@ public class PopupMenu extends JPopupMenu } SequenceGroup sg = ap.av.getSelectionGroup(); - boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false; + boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment() + .getGroups().contains(sg) : false; if (sg != null && sg.getSize() > 0) - { - groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()})); - groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group")); + { + groupName.setText(MessageManager.formatMessage("label.name_param", + new String[] + { sg.getName() })); + groupName.setText(MessageManager + .getString("label.edit_name_and_description_current_group")); if (sg.cs instanceof ZappoColourScheme) { @@ -470,8 +527,7 @@ public class PopupMenu extends JPopupMenu { purinePyrimidineColour.setSelected(true); } - - + /* * else if (sg.cs instanceof CovariationColourScheme) { * covariationColour.setSelected(true); } @@ -495,15 +551,15 @@ public class PopupMenu extends JPopupMenu buildGroupURLMenu(sg, groupLinks); } // Add a 'show all structures' for the current selection - Hashtable pdbe = new Hashtable(),reppdb=new Hashtable(); + Hashtable pdbe = new Hashtable(), reppdb = new Hashtable(); SequenceI sqass = null; for (SequenceI sq : ap.av.getSequenceSelection()) { Vector pes = (Vector) sq.getDatasetSequence() .getPDBId(); - if (pes != null) + if (pes != null && pes.size() > 0) { - reppdb.put(pes.get(0).getId(),pes.get(0)); + reppdb.put(pes.get(0).getId(), pes.get(0)); for (PDBEntry pe : pes) { pdbe.put(pe.getId(), pe); @@ -517,38 +573,50 @@ public class PopupMenu extends JPopupMenu if (pdbe.size() > 0) { final PDBEntry[] pe = pdbe.values().toArray( - new PDBEntry[pdbe.size()]),pr = reppdb.values().toArray( - new PDBEntry[reppdb.size()]); - final JMenuItem gpdbview,rpdbview; + 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)}))); + 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()}))); + 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.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 AppJmol(ap, pe, ap.av.collateForPDB(pe)); + new StructureViewer(ap.getStructureSelectionManager()) + .viewStructures(ap, pe, ap.av.collateForPDB(pe)); } }); - if (reppdb.size()>1 && 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")); + 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 AppJmol(ap, pr, ap.av.collateForPDB(pr)); + new StructureViewer(ap.getStructureSelectionManager()) + .viewStructures(ap, pr, ap.av.collateForPDB(pr)); } }); } @@ -565,7 +633,9 @@ public class PopupMenu extends JPopupMenu createGroupMenuItem.setVisible(true); unGroupMenuItem.setVisible(false); jMenu1.setText(MessageManager.getString("action.edit_new_group")); - } else { + } + else + { createGroupMenuItem.setVisible(false); unGroupMenuItem.setVisible(true); jMenu1.setText(MessageManager.getString("action.edit_group")); @@ -707,11 +777,18 @@ public class PopupMenu extends JPopupMenu // menu appears asap // sequence only URLs // ID/regex match URLs - groupLinksMenu = new JMenu(MessageManager.getString("action.group_link")); + groupLinksMenu = new JMenu( + MessageManager.getString("action.group_link")); JMenu[] linkMenus = new JMenu[] - { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")), - new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be - // created. + { null, new JMenu(MessageManager.getString("action.ids")), + new JMenu(MessageManager.getString("action.sequences")), + new JMenu(MessageManager.getString("action.ids_sequences")) }; // three + // types + // of url + // that + // might + // be + // created. SequenceI[] seqs = ap.av.getSelectionAsNewSequence(); String[][] idandseqs = GroupUrlLink.formStrings(seqs); Hashtable commonDbrefs = new Hashtable(); @@ -833,7 +910,8 @@ public class PopupMenu extends JPopupMenu } if (addMenu) { - groupLinksMenu = new JMenu(MessageManager.getString("action.group_link")); + groupLinksMenu = new JMenu( + MessageManager.getString("action.group_link")); for (int m = 0; m < linkMenus.length; m++) { if (linkMenus[m] != null @@ -859,7 +937,9 @@ public class PopupMenu extends JPopupMenu private void addshowLink(JMenu linkMenu, String label, final String url) { JMenuItem item = new JMenuItem(label); - item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url})); + item.setToolTipText(MessageManager.formatMessage( + "label.open_url_param", new String[] + { url })); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -894,7 +974,11 @@ public class PopupMenu extends JPopupMenu final GroupUrlLink urlgenerator, final Object[] urlstub) { JMenuItem item = new JMenuItem(label); - item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)})); + item.setToolTipText(MessageManager.formatMessage( + "label.open_url_seqs_param", + new Object[] + { urlgenerator.getUrl_prefix(), + urlgenerator.getNumberInvolved(urlstub) })); // TODO: put in info about what is being sent. item.addActionListener(new java.awt.event.ActionListener() { @@ -939,7 +1023,8 @@ public class PopupMenu extends JPopupMenu } }); sequenceMenu.setText(MessageManager.getString("label.sequence")); - sequenceName.setText(MessageManager.getString("label.edit_name_description")); + sequenceName.setText(MessageManager + .getString("label.edit_name_description")); sequenceName.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -947,7 +1032,8 @@ public class PopupMenu extends JPopupMenu sequenceName_actionPerformed(); } }); - sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "..."); + sequenceDetails.setText(MessageManager + .getString("label.sequence_details") + "..."); sequenceDetails.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -955,7 +1041,8 @@ public class PopupMenu extends JPopupMenu sequenceDetails_actionPerformed(); } }); - sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "..."); + sequenceSelDetails.setText(MessageManager + .getString("label.sequence_details") + "..."); sequenceSelDetails .addActionListener(new java.awt.event.ActionListener() { @@ -965,7 +1052,8 @@ public class PopupMenu extends JPopupMenu } }); PIDColour.setFocusPainted(false); - unGroupMenuItem.setText(MessageManager.getString("action.remove_group")); + unGroupMenuItem + .setText(MessageManager.getString("action.remove_group")); unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -973,14 +1061,16 @@ public class PopupMenu extends JPopupMenu unGroupMenuItem_actionPerformed(); } }); - createGroupMenuItem.setText(MessageManager.getString("action.create_group")); - createGroupMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - createGroupMenuItem_actionPerformed(); - } - }); + createGroupMenuItem.setText(MessageManager + .getString("action.create_group")); + createGroupMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + createGroupMenuItem_actionPerformed(); + } + }); outline.setText(MessageManager.getString("action.border_colour")); outline.addActionListener(new java.awt.event.ActionListener() @@ -990,7 +1080,8 @@ public class PopupMenu extends JPopupMenu outline_actionPerformed(); } }); - nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide")); + nucleotideMenuItem + .setText(MessageManager.getString("label.nucleotide")); nucleotideMenuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1025,7 +1116,8 @@ public class PopupMenu extends JPopupMenu showColourText_actionPerformed(); } }); - displayNonconserved.setText(MessageManager.getString("label.show_non_conversed")); + displayNonconserved.setText(MessageManager + .getString("label.show_non_conversed")); displayNonconserved.setState(true); displayNonconserved.addActionListener(new ActionListener() { @@ -1075,7 +1167,8 @@ public class PopupMenu extends JPopupMenu changeCase(e); } }); - pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence")); + pdbMenu.setText(MessageManager + .getString("label.associate_structure_with_sequence")); pdbFromFile.setText(MessageManager.getString("label.from_file")); pdbFromFile.addActionListener(new ActionListener() { @@ -1084,32 +1177,32 @@ 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(); -// } -// } -// }); + // 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() { @@ -1126,8 +1219,10 @@ public class PopupMenu extends JPopupMenu discoverPDB_actionPerformed(); } }); - outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "..."); - sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature")); + outputMenu.setText(MessageManager.getString("label.out_to_textbox") + + "..."); + sequenceFeature.setText(MessageManager + .getString("label.create_sequence_feature")); sequenceFeature.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1145,9 +1240,11 @@ public class PopupMenu extends JPopupMenu }); jMenu1.setText(MessageManager.getString("label.group")); structureMenu.setText(MessageManager.getString("label.structure")); - viewStructureMenu.setText(MessageManager.getString("label.view_structure")); + viewStructureMenu.setText(MessageManager + .getString("label.view_structure")); // colStructureMenu.setText("Colour By Structure"); - editSequence.setText(MessageManager.getString("label.edit_sequence") + "..."); + editSequence.setText(MessageManager.getString("label.edit_sequence") + + "..."); editSequence.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) @@ -1187,10 +1284,11 @@ public class PopupMenu extends JPopupMenu colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideMenuItem); - if (ap.getAlignment().isNucleotide()) { - // JBPNote - commented since the colourscheme isn't functional - // colourMenu.add(RNAInteractionColour); - colourMenu.add(purinePyrimidineColour); + if (ap.getAlignment().isNucleotide()) + { + // JBPNote - commented since the colourscheme isn't functional + // colourMenu.add(RNAInteractionColour); + colourMenu.add(purinePyrimidineColour); } // colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); @@ -1225,9 +1323,10 @@ public class PopupMenu extends JPopupMenu editMenu.add(lowerCase); editMenu.add(toggle); pdbMenu.add(pdbFromFile); - // JBPNote: These shouldn't be added here - should appear in a generic 'apply web service to this sequence menu' - // pdbMenu.add(RNAFold); - // pdbMenu.add(ContraFold); + // JBPNote: These shouldn't be added here - should appear in a generic + // 'apply web service to this sequence menu' + // pdbMenu.add(RNAFold); + // pdbMenu.add(ContraFold); pdbMenu.add(enterPDB); pdbMenu.add(discoverPDB); jMenu1.add(groupName); @@ -1249,7 +1348,8 @@ public class PopupMenu extends JPopupMenu } }); - clustalColour.setText(MessageManager.getString("label.clustalx_colours")); + clustalColour.setText(MessageManager + .getString("label.clustalx_colours")); clustalColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1273,7 +1373,8 @@ public class PopupMenu extends JPopupMenu taylorColour_actionPerformed(); } }); - hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity")); + hydrophobicityColour.setText(MessageManager + .getString("label.hydrophobicity")); hydrophobicityColour .addActionListener(new java.awt.event.ActionListener() { @@ -1290,7 +1391,8 @@ public class PopupMenu extends JPopupMenu helixColour_actionPerformed(); } }); - strandColour.setText(MessageManager.getString("label.strand_propensity")); + strandColour.setText(MessageManager + .getString("label.strand_propensity")); strandColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1314,7 +1416,8 @@ public class PopupMenu extends JPopupMenu buriedColour_actionPerformed(); } }); - abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage")); + abovePIDColour.setText(MessageManager + .getString("label.above_identity_percentage")); abovePIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1322,7 +1425,8 @@ public class PopupMenu extends JPopupMenu abovePIDColour_actionPerformed(); } }); - userDefinedColour.setText(MessageManager.getString("action.user_defined")); + userDefinedColour.setText(MessageManager + .getString("action.user_defined")); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1330,7 +1434,8 @@ public class PopupMenu extends JPopupMenu userDefinedColour_actionPerformed(e); } }); - PIDColour.setText(MessageManager.getString("label.percentage_identity")); + PIDColour + .setText(MessageManager.getString("label.percentage_identity")); PIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1346,7 +1451,8 @@ public class PopupMenu extends JPopupMenu BLOSUM62Colour_actionPerformed(); } }); - purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine")); + purinePyrimidineColour.setText(MessageManager + .getString("label.purine_pyrimidine")); purinePyrimidineColour .addActionListener(new java.awt.event.ActionListener() { @@ -1355,15 +1461,15 @@ public class PopupMenu extends JPopupMenu purinePyrimidineColour_actionPerformed(); } }); - - + /* * covariationColour.addActionListener(new java.awt.event.ActionListener() { * public void actionPerformed(ActionEvent e) { * covariationColour_actionPerformed(); } }); */ - conservationMenuItem.setText(MessageManager.getString("label.conservation")); + conservationMenuItem.setText(MessageManager + .getString("label.conservation")); conservationMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -1391,8 +1497,12 @@ public class PopupMenu extends JPopupMenu StringBuffer contents = new StringBuffer(); for (SequenceI seq : sequences) { - contents.append("

" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)}) - + "

"); + contents.append("

" + + MessageManager + .formatMessage( + "label.create_sequence_details_report_annotation_for", + new String[] + { seq.getDisplayId(true) }) + "

"); new SequenceAnnotationReport(null) .createSequenceAnnotationReport( contents, @@ -1406,8 +1516,11 @@ public class PopupMenu extends JPopupMenu } cap.setText("" + contents.toString() + ""); - Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")})) - ,500, 400); + Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage( + "label.sequece_details_for", + (sequences.length == 1 ? new String[] + { sequences[0].getDisplayId(true) } : new String[] + { MessageManager.getString("label.selection") })), 500, 400); } @@ -1543,7 +1656,6 @@ public class PopupMenu extends JPopupMenu refresh(); } - /* * protected void covariationColour_actionPerformed() { getGroup().cs = new * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } @@ -1671,7 +1783,7 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { - // JBPNote: Conservation name shouldn't be i18n translated + // JBPNote: Conservation name shouldn't be i18n translated Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, sg.getSequences(ap.av .getHiddenRepSequences()), sg.getStartRes(), @@ -1723,8 +1835,10 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = getGroup(); EditNameDialog dialog = new EditNameDialog(sg.getName(), - sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ", - MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"), + sg.getDescription(), " " + + MessageManager.getString("label.group_name") + " ", + MessageManager.getString("label.group_description") + " ", + MessageManager.getString("label.edit_group_name_description"), ap.alignFrame); if (!dialog.accept) @@ -1763,8 +1877,12 @@ public class PopupMenu extends JPopupMenu void sequenceName_actionPerformed() { EditNameDialog dialog = new EditNameDialog(sequence.getName(), - sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ", - MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"), + sequence.getDescription(), + " " + MessageManager.getString("label.sequence_name") + + " ", + MessageManager.getString("label.sequence_description") + " ", + MessageManager + .getString("label.edit_sequence_name_description"), ap.alignFrame); if (!dialog.accept) @@ -1776,10 +1894,14 @@ public class PopupMenu extends JPopupMenu { if (dialog.getName().indexOf(" ") > -1) { - JOptionPane.showMessageDialog(ap, - MessageManager.getString("label.spaces_converted_to_backslashes"), - MessageManager.getString("label.no_spaces_allowed_sequence_name"), - JOptionPane.WARNING_MESSAGE); + JOptionPane + .showMessageDialog( + ap, + MessageManager + .getString("label.spaces_converted_to_backslashes"), + MessageManager + .getString("label.no_spaces_allowed_sequence_name"), + JOptionPane.WARNING_MESSAGE); } sequence.setName(dialog.getName().replace(' ', '_')); @@ -1806,9 +1928,11 @@ public class PopupMenu extends JPopupMenu ap.av.setSelectionGroup(null); refresh(); } + void createGroupMenuItem_actionPerformed() { - getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this + getGroup(); // implicitly creates group - note - should apply defaults / use + // standard alignment window logic for this refresh(); } @@ -1821,7 +1945,8 @@ public class PopupMenu extends JPopupMenu protected void outline_actionPerformed() { SequenceGroup sg = getGroup(); - Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"), + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_outline_colour"), Color.BLUE); if (col != null) @@ -1875,11 +2000,10 @@ public class PopupMenu extends JPopupMenu jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, - MessageManager.getString("label.web_browser_not_found_unix"), - MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE); + JOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString("label.web_browser_not_found_unix"), + MessageManager.getString("label.web_browser_not_found"), + JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } @@ -1975,31 +2099,17 @@ public class PopupMenu extends JPopupMenu { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, - MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500); + Desktop.addInternalFrame(cap, MessageManager.formatMessage( + "label.alignment_output_command", new String[] + { e.getActionCommand() }), 600, 500); String[] omitHidden = null; System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens // or we simply trust the user wants // wysiwig behaviour - SequenceGroup sg = ap.av.getSelectionGroup(); - ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection()); - omitHidden = ap.av.getViewAsString(true); - Alignment oal = new Alignment(ap.av.getSequenceSelection()); - AlignmentAnnotation[] nala = ap.av.getAlignment() - .getAlignmentAnnotation(); - if (nala != null) - { - for (int i = 0; i < nala.length; i++) - { - AlignmentAnnotation na = nala[i]; - oal.addAnnotation(na); - } - } - cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - oal, omitHidden, csel, sg)); - oal = null; + + cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), ap.av, true)); } public void pdbFromFile_actionPerformed() @@ -2007,8 +2117,12 @@ public class PopupMenu extends JPopupMenu jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)})); - chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()})); + chooser.setDialogTitle(MessageManager.formatMessage( + "label.select_pdb_file_for", new String[] + { sequence.getDisplayId(false) })); + chooser.setToolTipText(MessageManager.formatMessage( + "label.load_pdb_file_associate_with_sequence", new String[] + { sequence.getDisplayId(false) })); int value = chooser.showOpenDialog(null); @@ -2021,22 +2135,25 @@ 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"); -// } + + // 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, - MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE); + MessageManager.getString("label.enter_pdb_id"), + MessageManager.getString("label.enter_pdb_id"), + JOptionPane.QUESTION_MESSAGE); if (id != null && id.length() > 0) { @@ -2142,12 +2259,15 @@ public class PopupMenu extends JPopupMenu EditNameDialog dialog = new EditNameDialog( sequence.getSequenceAsString(sg.getStartRes(), - sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null, - MessageManager.getString("label.edit_sequence"), ap.alignFrame); + sg.getEndRes() + 1), null, + MessageManager.getString("label.edit_sequence"), null, + MessageManager.getString("label.edit_sequence"), + ap.alignFrame); if (dialog.accept) { - EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"), + EditCommand editCommand = new EditCommand( + MessageManager.getString("label.edit_sequences"), EditCommand.REPLACE, dialog.getName().replace(' ', ap.av.getGapCharacter()), sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),