X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=6974d96780ca5238578a775b751c4812d665617a;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=4d23429720132ba91450e5555f3ee25598c96301;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 4d23429..6974d96 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * @@ -14,6 +14,7 @@ * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; @@ -24,7 +25,6 @@ import java.awt.event.*; import javax.swing.*; -import MCview.*; import jalview.analysis.*; import jalview.commands.*; import jalview.datamodel.*; @@ -32,6 +32,7 @@ import jalview.io.*; import jalview.schemes.*; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; +import jalview.util.MessageManager; import jalview.util.UrlLink; /** @@ -71,6 +72,7 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); // protected JRadioButtonMenuItem covariationColour = new // JRadioButtonMenuItem(); @@ -90,7 +92,7 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceSelDetails = new JMenuItem(); SequenceI sequence; - + JMenuItem createGroupMenuItem = new JMenuItem(); JMenuItem unGroupMenuItem = new JMenuItem(); JMenuItem outline = new JMenuItem(); @@ -122,7 +124,11 @@ 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(); + JMenuItem enterPDB = new JMenuItem(); JMenuItem discoverPDB = new JMenuItem(); @@ -193,6 +199,7 @@ public class PopupMenu extends JPopupMenu colours.add(PIDColour); colours.add(BLOSUM62Colour); colours.add(purinePyrimidineColour); + colours.add(RNAInteractionColour); // colours.add(covariationColour); for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) @@ -279,13 +286,25 @@ public class PopupMenu extends JPopupMenu final String rnastruc = aa[i].getRNAStruc(); final String structureLine = aa[i].label; menuItem = new JMenuItem(); - menuItem.setText("2D RNA " + 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) { - new AppVarna(structureLine, seq, seq.getSequenceAsString(), - rnastruc, seq.getName(), ap); + //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); @@ -305,12 +324,13 @@ public class PopupMenu extends JPopupMenu // TODO: make rnastrucF a bit more nice menuItem = new JMenuItem(); - menuItem.setText("2D RNA - " + 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); @@ -323,7 +343,7 @@ public class PopupMenu extends JPopupMenu } - menuItem = new JMenuItem("Hide Sequences"); + menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences")); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -336,7 +356,7 @@ public class PopupMenu extends JPopupMenu if (ap.av.getSelectionGroup() != null && ap.av.getSelectionGroup().getSize() > 1) { - menuItem = new JMenuItem("Represent Group with " + 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) @@ -354,7 +374,7 @@ public class PopupMenu extends JPopupMenu if (ap.av.adjustForHiddenSeqs(index) - ap.av.adjustForHiddenSeqs(index - 1) > 1) { - menuItem = new JMenuItem("Reveal Sequences"); + menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences")); menuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -374,7 +394,7 @@ public class PopupMenu extends JPopupMenu if (ap.av.hasHiddenRows()) { { - menuItem = new JMenuItem("Reveal All"); + menuItem = new JMenuItem(MessageManager.getString("action.reveal_all")); menuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -393,11 +413,12 @@ public class PopupMenu extends JPopupMenu } SequenceGroup sg = ap.av.getSelectionGroup(); + boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false; if (sg != null && sg.getSize() > 0) - { - groupName.setText("Name: " + sg.getName()); - groupName.setText("Edit name and description of 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) { @@ -447,6 +468,8 @@ public class PopupMenu extends JPopupMenu { purinePyrimidineColour.setSelected(true); } + + /* * else if (sg.cs instanceof CovariationColourScheme) { * covariationColour.setSelected(true); } @@ -470,7 +493,7 @@ public class PopupMenu extends JPopupMenu buildGroupURLMenu(sg, groupLinks); } // Add a 'show all structures' for the current selection - Hashtable pdbe = new Hashtable(); + Hashtable pdbe = new Hashtable(),reppdb=new Hashtable(); SequenceI sqass = null; for (SequenceI sq : ap.av.getSequenceSelection()) { @@ -478,6 +501,7 @@ public class PopupMenu extends JPopupMenu .getPDBId(); if (pes != null) { + reppdb.put(pes.get(0).getId(),pes.get(0)); for (PDBEntry pe : pes) { pdbe.put(pe.getId(), pe); @@ -491,19 +515,18 @@ public class PopupMenu extends JPopupMenu if (pdbe.size() > 0) { final PDBEntry[] pe = pdbe.values().toArray( - new PDBEntry[pdbe.size()]); - final JMenuItem gpdbview; + 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("View structure for " - + 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("View all " - + pdbe.size() + " structures.")); + structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()}))); } - gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment."); + gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment")); gpdbview.addActionListener(new ActionListener() { @@ -513,6 +536,20 @@ public class PopupMenu extends JPopupMenu new AppJmol(ap, pe, ap.av.collateForPDB(pe)); } }); + if (reppdb.size()>1 && reppdb.size() 0) { - JMenu linkMenu = new JMenu("Link"); + JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); Vector linkset = new Vector(); for (int i = 0; i < links.size(); i++) { @@ -662,10 +705,10 @@ public class PopupMenu extends JPopupMenu // menu appears asap // sequence only URLs // ID/regex match URLs - groupLinksMenu = new JMenu("Group Link"); + groupLinksMenu = new JMenu(MessageManager.getString("action.group_link")); JMenu[] linkMenus = new JMenu[] - { null, new JMenu("IDS"), new JMenu("Sequences"), - new JMenu("IDS and Sequences") }; // three types of url that might be + { 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); @@ -788,7 +831,7 @@ public class PopupMenu extends JPopupMenu } if (addMenu) { - groupLinksMenu = new JMenu("Group Links"); + groupLinksMenu = new JMenu(MessageManager.getString("action.group_link")); for (int m = 0; m < linkMenus.length; m++) { if (linkMenus[m] != null @@ -814,7 +857,7 @@ public class PopupMenu extends JPopupMenu private void addshowLink(JMenu linkMenu, String label, final String url) { JMenuItem item = new JMenuItem(label); - item.setToolTipText("open URL: " + url); + item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url})); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -849,16 +892,8 @@ public class PopupMenu extends JPopupMenu final GroupUrlLink urlgenerator, final Object[] urlstub) { JMenuItem item = new JMenuItem(label); - item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix() - + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO: - // put - // in - // info - // about - // what - // is - // being - // sent. + 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() { public void actionPerformed(ActionEvent e) @@ -891,9 +926,9 @@ public class PopupMenu extends JPopupMenu */ private void jbInit() throws Exception { - groupMenu.setText("Group"); - groupMenu.setText("Selection"); - groupName.setText("Name"); + groupMenu.setText(MessageManager.getString("label.group")); + groupMenu.setText(MessageManager.getString("label.selection")); + groupName.setText(MessageManager.getString("label.name")); groupName.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -901,8 +936,8 @@ public class PopupMenu extends JPopupMenu groupName_actionPerformed(); } }); - sequenceMenu.setText("Sequence"); - sequenceName.setText("Edit Name/Description"); + sequenceMenu.setText(MessageManager.getString("label.sequence")); + sequenceName.setText(MessageManager.getString("label.edit_name_description")); sequenceName.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -910,7 +945,7 @@ public class PopupMenu extends JPopupMenu sequenceName_actionPerformed(); } }); - sequenceDetails.setText("Sequence Details ..."); + sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "..."); sequenceDetails.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -918,7 +953,7 @@ public class PopupMenu extends JPopupMenu sequenceDetails_actionPerformed(); } }); - sequenceSelDetails.setText("Sequence Details ..."); + sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "..."); sequenceSelDetails .addActionListener(new java.awt.event.ActionListener() { @@ -928,7 +963,7 @@ public class PopupMenu extends JPopupMenu } }); PIDColour.setFocusPainted(false); - unGroupMenuItem.setText("Remove Group"); + unGroupMenuItem.setText(MessageManager.getString("action.remove_group")); unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -936,8 +971,16 @@ 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(); + } + }); - outline.setText("Border colour"); + outline.setText(MessageManager.getString("action.border_colour")); outline.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -945,7 +988,7 @@ public class PopupMenu extends JPopupMenu outline_actionPerformed(); } }); - nucleotideMenuItem.setText("Nucleotide"); + nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide")); nucleotideMenuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -953,8 +996,8 @@ public class PopupMenu extends JPopupMenu nucleotideMenuItem_actionPerformed(); } }); - colourMenu.setText("Group Colour"); - showBoxes.setText("Boxes"); + colourMenu.setText(MessageManager.getString("label.group_colour")); + showBoxes.setText(MessageManager.getString("action.boxes")); showBoxes.setState(true); showBoxes.addActionListener(new ActionListener() { @@ -963,7 +1006,7 @@ public class PopupMenu extends JPopupMenu showBoxes_actionPerformed(); } }); - showText.setText("Text"); + showText.setText(MessageManager.getString("action.text")); showText.setState(true); showText.addActionListener(new ActionListener() { @@ -972,7 +1015,7 @@ public class PopupMenu extends JPopupMenu showText_actionPerformed(); } }); - showColourText.setText("Colour Text"); + showColourText.setText(MessageManager.getString("label.colour_text")); showColourText.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -980,7 +1023,7 @@ public class PopupMenu extends JPopupMenu showColourText_actionPerformed(); } }); - displayNonconserved.setText("Show Nonconserved"); + displayNonconserved.setText(MessageManager.getString("label.show_non_conversed")); displayNonconserved.setState(true); displayNonconserved.addActionListener(new ActionListener() { @@ -989,8 +1032,8 @@ public class PopupMenu extends JPopupMenu showNonconserved_actionPerformed(); } }); - editMenu.setText("Edit"); - cut.setText("Cut"); + editMenu.setText(MessageManager.getString("action.edit")); + cut.setText(MessageManager.getString("action.cut")); cut.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -998,7 +1041,7 @@ public class PopupMenu extends JPopupMenu cut_actionPerformed(); } }); - upperCase.setText("To Upper Case"); + upperCase.setText(MessageManager.getString("label.to_upper_case")); upperCase.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1006,7 +1049,7 @@ public class PopupMenu extends JPopupMenu changeCase(e); } }); - copy.setText("Copy"); + copy.setText(MessageManager.getString("action.copy")); copy.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1014,7 +1057,7 @@ public class PopupMenu extends JPopupMenu copy_actionPerformed(); } }); - lowerCase.setText("To Lower Case"); + lowerCase.setText(MessageManager.getString("label.to_lower_case")); lowerCase.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1022,7 +1065,7 @@ public class PopupMenu extends JPopupMenu changeCase(e); } }); - toggle.setText("Toggle Case"); + toggle.setText(MessageManager.getString("label.toggle_case")); toggle.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1030,8 +1073,8 @@ public class PopupMenu extends JPopupMenu changeCase(e); } }); - pdbMenu.setText("Associate Structure with Sequence"); - pdbFromFile.setText("From File"); + pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence")); + pdbFromFile.setText(MessageManager.getString("label.from_file")); pdbFromFile.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1039,7 +1082,33 @@ public class PopupMenu extends JPopupMenu pdbFromFile_actionPerformed(); } }); - enterPDB.setText("Enter PDB Id"); +// 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() { public void actionPerformed(ActionEvent e) @@ -1047,7 +1116,7 @@ public class PopupMenu extends JPopupMenu enterPDB_actionPerformed(); } }); - discoverPDB.setText("Discover PDB ids"); + discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids")); discoverPDB.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1055,8 +1124,8 @@ public class PopupMenu extends JPopupMenu discoverPDB_actionPerformed(); } }); - outputMenu.setText("Output to Textbox..."); - sequenceFeature.setText("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) @@ -1064,7 +1133,7 @@ public class PopupMenu extends JPopupMenu sequenceFeature_actionPerformed(); } }); - textColour.setText("Text Colour"); + textColour.setText(MessageManager.getString("label.text_colour")); textColour.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1072,11 +1141,11 @@ public class PopupMenu extends JPopupMenu textColour_actionPerformed(); } }); - jMenu1.setText("Group"); - structureMenu.setText("Structure"); - viewStructureMenu.setText("View Structure"); + jMenu1.setText(MessageManager.getString("label.group")); + structureMenu.setText(MessageManager.getString("label.structure")); + viewStructureMenu.setText(MessageManager.getString("label.view_structure")); // colStructureMenu.setText("Colour By Structure"); - editSequence.setText("Edit Sequence..."); + editSequence.setText(MessageManager.getString("label.edit_sequence") + "..."); editSequence.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) @@ -1098,6 +1167,8 @@ public class PopupMenu extends JPopupMenu groupMenu.add(editMenu); groupMenu.add(outputMenu); groupMenu.add(sequenceFeature); + groupMenu.add(createGroupMenuItem); + groupMenu.add(unGroupMenuItem); groupMenu.add(jMenu1); sequenceMenu.add(sequenceName); sequenceMenu.add(sequenceDetails); @@ -1114,9 +1185,10 @@ public class PopupMenu extends JPopupMenu colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideMenuItem); - if (ap.getAlignment().isNucleotide()) - { - 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); @@ -1151,10 +1223,12 @@ 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); pdbMenu.add(enterPDB); pdbMenu.add(discoverPDB); jMenu1.add(groupName); - jMenu1.add(unGroupMenuItem); jMenu1.add(colourMenu); jMenu1.add(showBoxes); jMenu1.add(showText); @@ -1164,7 +1238,7 @@ public class PopupMenu extends JPopupMenu structureMenu.add(pdbMenu); structureMenu.add(viewStructureMenu); // structureMenu.add(colStructureMenu); - noColourmenuItem.setText("None"); + noColourmenuItem.setText(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1173,7 +1247,7 @@ public class PopupMenu extends JPopupMenu } }); - clustalColour.setText("Clustalx colours"); + clustalColour.setText(MessageManager.getString("label.clustalx_colours")); clustalColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1181,7 +1255,7 @@ public class PopupMenu extends JPopupMenu clustalColour_actionPerformed(); } }); - zappoColour.setText("Zappo"); + zappoColour.setText(MessageManager.getString("label.zappo")); zappoColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1189,7 +1263,7 @@ public class PopupMenu extends JPopupMenu zappoColour_actionPerformed(); } }); - taylorColour.setText("Taylor"); + taylorColour.setText(MessageManager.getString("label.taylor")); taylorColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1197,7 +1271,7 @@ public class PopupMenu extends JPopupMenu taylorColour_actionPerformed(); } }); - hydrophobicityColour.setText("Hydrophobicity"); + hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity")); hydrophobicityColour .addActionListener(new java.awt.event.ActionListener() { @@ -1206,7 +1280,7 @@ public class PopupMenu extends JPopupMenu hydrophobicityColour_actionPerformed(); } }); - helixColour.setText("Helix propensity"); + helixColour.setText(MessageManager.getString("label.helix_propensity")); helixColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1214,7 +1288,7 @@ public class PopupMenu extends JPopupMenu helixColour_actionPerformed(); } }); - strandColour.setText("Strand propensity"); + strandColour.setText(MessageManager.getString("label.strand_propensity")); strandColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1222,7 +1296,7 @@ public class PopupMenu extends JPopupMenu strandColour_actionPerformed(); } }); - turnColour.setText("Turn propensity"); + turnColour.setText(MessageManager.getString("label.turn_propensity")); turnColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1230,7 +1304,7 @@ public class PopupMenu extends JPopupMenu turnColour_actionPerformed(); } }); - buriedColour.setText("Buried Index"); + buriedColour.setText(MessageManager.getString("label.buried_index")); buriedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1238,7 +1312,7 @@ public class PopupMenu extends JPopupMenu buriedColour_actionPerformed(); } }); - abovePIDColour.setText("Above % Identity"); + abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage")); abovePIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1246,7 +1320,7 @@ public class PopupMenu extends JPopupMenu abovePIDColour_actionPerformed(); } }); - userDefinedColour.setText("User Defined..."); + userDefinedColour.setText(MessageManager.getString("action.user_defined")); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1254,7 +1328,7 @@ public class PopupMenu extends JPopupMenu userDefinedColour_actionPerformed(e); } }); - PIDColour.setText("Percentage Identity"); + PIDColour.setText(MessageManager.getString("label.percentage_identity")); PIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1262,7 +1336,7 @@ public class PopupMenu extends JPopupMenu PIDColour_actionPerformed(); } }); - BLOSUM62Colour.setText("BLOSUM62"); + BLOSUM62Colour.setText(MessageManager.getString("label.blosum62")); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1270,7 +1344,7 @@ public class PopupMenu extends JPopupMenu BLOSUM62Colour_actionPerformed(); } }); - purinePyrimidineColour.setText("Purine/Pyrimidine"); + purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine")); purinePyrimidineColour .addActionListener(new java.awt.event.ActionListener() { @@ -1279,13 +1353,15 @@ public class PopupMenu extends JPopupMenu purinePyrimidineColour_actionPerformed(); } }); + + /* * covariationColour.addActionListener(new java.awt.event.ActionListener() { * public void actionPerformed(ActionEvent e) { * covariationColour_actionPerformed(); } }); */ - conservationMenuItem.setText("Conservation"); + conservationMenuItem.setText(MessageManager.getString("label.conservation")); conservationMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -1313,7 +1389,7 @@ public class PopupMenu extends JPopupMenu StringBuffer contents = new StringBuffer(); for (SequenceI seq : sequences) { - contents.append("

Annotation for " + seq.getDisplayId(true) + contents.append("

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

"); new SequenceAnnotationReport(null) .createSequenceAnnotationReport( @@ -1328,9 +1404,8 @@ public class PopupMenu extends JPopupMenu } cap.setText("" + contents.toString() + ""); - Desktop.instance.addInternalFrame(cap, "Sequence Details for " - + (sequences.length == 1 ? sequences[0].getDisplayId(true) - : "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); } @@ -1466,6 +1541,7 @@ public class PopupMenu extends JPopupMenu refresh(); } + /* * protected void covariationColour_actionPerformed() { getGroup().cs = new * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } @@ -1516,7 +1592,7 @@ public class PopupMenu extends JPopupMenu { SequenceGroup sg = getGroup(); - if (e.getActionCommand().equals("User Defined...")) + if (e.getSource().equals(userDefinedColour)) { new UserDefinedColours(ap, sg); } @@ -1593,6 +1669,7 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { + // JBPNote: Conservation name shouldn't be i18n translated Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, sg.getSequences(ap.av .getHiddenRepSequences()), sg.getStartRes(), @@ -1627,7 +1704,7 @@ public class PopupMenu extends JPopupMenu sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD); - acg.predefinedColours = true; + acg.setPredefinedColours(true); sg.cs = acg; refresh(); @@ -1644,8 +1721,8 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = getGroup(); EditNameDialog dialog = new EditNameDialog(sg.getName(), - sg.getDescription(), " Group Name ", - "Group Description ", "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) @@ -1684,8 +1761,8 @@ public class PopupMenu extends JPopupMenu void sequenceName_actionPerformed() { EditNameDialog dialog = new EditNameDialog(sequence.getName(), - sequence.getDescription(), " Sequence Name ", - "Sequence Description ", "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) @@ -1698,8 +1775,8 @@ public class PopupMenu extends JPopupMenu if (dialog.getName().indexOf(" ") > -1) { JOptionPane.showMessageDialog(ap, - "Spaces have been converted to \"_\"", - "No spaces allowed in Sequence Name", + MessageManager.getString("label.spaces_converted_to_backslashes"), + MessageManager.getString("label.no_spaces_allowed_sequence_name"), JOptionPane.WARNING_MESSAGE); } @@ -1727,6 +1804,11 @@ 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 + refresh(); + } /** * DOCUMENT ME! @@ -1737,7 +1819,7 @@ public class PopupMenu extends JPopupMenu protected void outline_actionPerformed() { SequenceGroup sg = getGroup(); - Color col = JColorChooser.showDialog(this, "Select Outline Colour", + Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"), Color.BLUE); if (col != null) @@ -1794,9 +1876,8 @@ public class PopupMenu extends JPopupMenu JOptionPane .showInternalMessageDialog( Desktop.desktop, - "Unixers: Couldn't find default web browser." - + "\nAdd the full path to your browser in Preferences.", - "Web browser not found", JOptionPane.WARNING_MESSAGE); + MessageManager.getString("label.web_browser_not_found_unix"), + MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } @@ -1862,17 +1943,17 @@ public class PopupMenu extends JPopupMenu if (source == toggle) { - description = "Toggle Case"; + description = MessageManager.getString("label.toggle_case"); caseChange = ChangeCaseCommand.TOGGLE_CASE; } else if (source == upperCase) { - description = "To Upper Case"; + description = MessageManager.getString("label.to_upper_case"); caseChange = ChangeCaseCommand.TO_UPPER; } else { - description = "To Lower Case"; + description = MessageManager.getString("label.to_lower_case"); caseChange = ChangeCaseCommand.TO_LOWER; } @@ -1893,7 +1974,7 @@ public class PopupMenu extends JPopupMenu CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); Desktop.addInternalFrame(cap, - "Alignment output - " + e.getActionCommand(), 600, 500); + MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500); String[] omitHidden = null; @@ -1924,10 +2005,8 @@ 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("Select a PDB file for " - + sequence.getDisplayId(false)); - chooser.setToolTipText("Load a PDB file and associate it with sequence '" - + sequence.getDisplayId(false) + "'"); + 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()})); int value = chooser.showOpenDialog(null); @@ -1940,11 +2019,22 @@ 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, - "Enter PDB Id", "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) { @@ -2050,12 +2140,12 @@ public class PopupMenu extends JPopupMenu EditNameDialog dialog = new EditNameDialog( sequence.getSequenceAsString(sg.getStartRes(), - sg.getEndRes() + 1), null, "Edit Sequence ", null, - "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("Edit Sequences", + EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"), EditCommand.REPLACE, dialog.getName().replace(' ', ap.av.getGapCharacter()), sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),