From: j.procter@dundee.ac.uk Date: Thu, 3 Jul 2014 18:27:55 +0000 (-0700) Subject: Merge branch 'hotfix/JAL-1530' into develop X-Git-Tag: Jalview_2_9~180 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b72c67c9197942b0dabfc3980e0d1d5b41813091;hp=-c;p=jalview.git Merge branch 'hotfix/JAL-1530' into develop Conflicts: src/jalview/gui/PopupMenu.java --- b72c67c9197942b0dabfc3980e0d1d5b41813091 diff --combined src/jalview/gui/PopupMenu.java index 3cf4fe0,f5f92b9..ace4762 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@@ -1,21 -1,19 +1,21 @@@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * 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 . + * 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; @@@ -34,7 -32,7 +34,7 @@@ import jalview.io.* import jalview.schemes.*; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; -import jalview.util.MessageManager; +import jalview.util.MessageManager; import jalview.util.UrlLink; /** @@@ -75,8 -73,6 +75,8 @@@ public class PopupMenu extends JPopupMe protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); + // protected JRadioButtonMenuItem covariationColour = new // JRadioButtonMenuItem(); @@@ -95,9 -91,7 +95,9 @@@ JMenuItem sequenceSelDetails = new JMenuItem(); SequenceI sequence; + JMenuItem createGroupMenuItem = new JMenuItem(); + JMenuItem unGroupMenuItem = new JMenuItem(); JMenuItem outline = new JMenuItem(); @@@ -130,12 -124,6 +130,12 @@@ 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(); @@@ -206,7 -194,6 +206,7 @@@ 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++) @@@ -293,28 -280,13 +293,28 @@@ 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"); } }); viewStructureMenu.add(menuItem); @@@ -334,15 -306,12 +334,15 @@@ // 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); @@@ -355,8 -324,7 +355,8 @@@ } - 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) @@@ -369,9 -337,7 +369,9 @@@ 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) @@@ -389,8 -355,7 +389,8 @@@ 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) @@@ -410,8 -375,7 +410,8 @@@ 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) @@@ -430,16 -394,12 +430,16 @@@ } 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) { @@@ -489,7 -449,6 +489,7 @@@ { purinePyrimidineColour.setSelected(true); } + /* * else if (sg.cs instanceof CovariationColourScheme) { * covariationColour.setSelected(true); } @@@ -513,7 -472,7 +513,7 @@@ 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()) { @@@ -521,7 -480,7 +521,7 @@@ .getPDBId(); 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); @@@ -535,23 -494,18 +535,23 @@@ 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() { @@@ -561,15 -515,10 +561,15 @@@ new AppJmol(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() { @@@ -592,13 -541,11 +592,13 @@@ { createGroupMenuItem.setVisible(true); unGroupMenuItem.setVisible(false); - jMenu1.setText(MessageManager.getString("action.edit_new_group")); - } else { + jMenu1.setText(MessageManager.getString("action.edit_new_group")); + } + else + { createGroupMenuItem.setVisible(false); unGroupMenuItem.setVisible(true); - jMenu1.setText(MessageManager.getString("action.edit_group")); + jMenu1.setText(MessageManager.getString("action.edit_group")); } if (seq == null) @@@ -610,7 -557,7 +610,7 @@@ if (links != null && links.size() > 0) { - JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); + JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); Vector linkset = new Vector(); for (int i = 0; i < links.size(); i++) { @@@ -737,18 -684,11 +737,18 @@@ // 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(); @@@ -870,8 -810,7 +870,8 @@@ } 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 @@@ -897,9 -836,7 +897,9 @@@ 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) @@@ -934,12 -871,8 +934,12 @@@ 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)})); - // 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) @@@ -972,9 -905,9 +972,9 @@@ */ private void jbInit() throws Exception { - groupMenu.setText(MessageManager.getString("label.group")); - groupMenu.setText(MessageManager.getString("label.selection")); - groupName.setText(MessageManager.getString("label.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) @@@ -982,9 -915,8 +982,9 @@@ groupName_actionPerformed(); } }); - sequenceMenu.setText(MessageManager.getString("label.sequence")); - sequenceName.setText(MessageManager.getString("label.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) @@@ -992,8 -924,7 +992,8 @@@ 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) @@@ -1001,8 -932,7 +1001,8 @@@ sequenceDetails_actionPerformed(); } }); - sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "..."); + sequenceSelDetails.setText(MessageManager + .getString("label.sequence_details") + "..."); sequenceSelDetails .addActionListener(new java.awt.event.ActionListener() { @@@ -1012,8 -942,7 +1012,8 @@@ } }); 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) @@@ -1021,18 -950,16 +1021,18 @@@ 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.setText(MessageManager.getString("action.border_colour")); outline.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1040,8 -967,7 +1040,8 @@@ outline_actionPerformed(); } }); - nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide")); + nucleotideMenuItem + .setText(MessageManager.getString("label.nucleotide")); nucleotideMenuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1049,8 -975,8 +1049,8 @@@ nucleotideMenuItem_actionPerformed(); } }); - colourMenu.setText(MessageManager.getString("label.group_colour")); - showBoxes.setText(MessageManager.getString("action.boxes")); + colourMenu.setText(MessageManager.getString("label.group_colour")); + showBoxes.setText(MessageManager.getString("action.boxes")); showBoxes.setState(true); showBoxes.addActionListener(new ActionListener() { @@@ -1059,7 -985,7 +1059,7 @@@ showBoxes_actionPerformed(); } }); - showText.setText(MessageManager.getString("action.text")); + showText.setText(MessageManager.getString("action.text")); showText.setState(true); showText.addActionListener(new ActionListener() { @@@ -1068,7 -994,7 +1068,7 @@@ showText_actionPerformed(); } }); - showColourText.setText(MessageManager.getString("label.colour_text")); + showColourText.setText(MessageManager.getString("label.colour_text")); showColourText.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1076,8 -1002,7 +1076,8 @@@ 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() { @@@ -1086,8 -1011,8 +1086,8 @@@ showNonconserved_actionPerformed(); } }); - editMenu.setText(MessageManager.getString("action.edit")); - cut.setText(MessageManager.getString("action.cut")); + editMenu.setText(MessageManager.getString("action.edit")); + cut.setText(MessageManager.getString("action.cut")); cut.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1095,7 -1020,7 +1095,7 @@@ cut_actionPerformed(); } }); - upperCase.setText(MessageManager.getString("label.to_upper_case")); + upperCase.setText(MessageManager.getString("label.to_upper_case")); upperCase.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1103,7 -1028,7 +1103,7 @@@ changeCase(e); } }); - copy.setText(MessageManager.getString("action.copy")); + copy.setText(MessageManager.getString("action.copy")); copy.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1111,7 -1036,7 +1111,7 @@@ copy_actionPerformed(); } }); - lowerCase.setText(MessageManager.getString("label.to_lower_case")); + lowerCase.setText(MessageManager.getString("label.to_lower_case")); lowerCase.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1119,7 -1044,7 +1119,7 @@@ changeCase(e); } }); - toggle.setText(MessageManager.getString("label.toggle_case")); + toggle.setText(MessageManager.getString("label.toggle_case")); toggle.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1127,9 -1052,8 +1127,9 @@@ changeCase(e); } }); - pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence")); - pdbFromFile.setText(MessageManager.getString("label.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) @@@ -1137,33 -1061,7 +1137,33 @@@ pdbFromFile_actionPerformed(); } }); - enterPDB.setText(MessageManager.getString("label.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) @@@ -1171,7 -1069,7 +1171,7 @@@ enterPDB_actionPerformed(); } }); - discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids")); + discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids")); discoverPDB.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1179,10 -1077,8 +1179,10 @@@ 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) @@@ -1190,7 -1086,7 +1190,7 @@@ sequenceFeature_actionPerformed(); } }); - textColour.setText(MessageManager.getString("label.text_colour")); + textColour.setText(MessageManager.getString("label.text_colour")); textColour.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1198,13 -1094,11 +1198,13 @@@ textColour_actionPerformed(); } }); - jMenu1.setText(MessageManager.getString("label.group")); - structureMenu.setText(MessageManager.getString("label.structure")); - viewStructureMenu.setText(MessageManager.getString("label.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(MessageManager.getString("label.edit_sequence") + "..."); + editSequence.setText(MessageManager.getString("label.edit_sequence") + + "..."); editSequence.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) @@@ -1246,8 -1140,6 +1246,8 @@@ colourMenu.add(nucleotideMenuItem); if (ap.getAlignment().isNucleotide()) { + // JBPNote - commented since the colourscheme isn't functional + // colourMenu.add(RNAInteractionColour); colourMenu.add(purinePyrimidineColour); } // colourMenu.add(covariationColour); @@@ -1283,10 -1175,6 +1283,10 @@@ 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); @@@ -1299,7 -1187,7 +1299,7 @@@ structureMenu.add(pdbMenu); structureMenu.add(viewStructureMenu); // structureMenu.add(colStructureMenu); - noColourmenuItem.setText(MessageManager.getString("label.none")); + noColourmenuItem.setText(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1308,8 -1196,7 +1308,8 @@@ } }); - 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) @@@ -1317,7 -1204,7 +1317,7 @@@ clustalColour_actionPerformed(); } }); - zappoColour.setText(MessageManager.getString("label.zappo")); + zappoColour.setText(MessageManager.getString("label.zappo")); zappoColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1325,7 -1212,7 +1325,7 @@@ zappoColour_actionPerformed(); } }); - taylorColour.setText(MessageManager.getString("label.taylor")); + taylorColour.setText(MessageManager.getString("label.taylor")); taylorColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1333,8 -1220,7 +1333,8 @@@ taylorColour_actionPerformed(); } }); - hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity")); + hydrophobicityColour.setText(MessageManager + .getString("label.hydrophobicity")); hydrophobicityColour .addActionListener(new java.awt.event.ActionListener() { @@@ -1343,7 -1229,7 +1343,7 @@@ hydrophobicityColour_actionPerformed(); } }); - helixColour.setText(MessageManager.getString("label.helix_propensity")); + helixColour.setText(MessageManager.getString("label.helix_propensity")); helixColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1351,8 -1237,7 +1351,8 @@@ 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) @@@ -1360,7 -1245,7 +1360,7 @@@ strandColour_actionPerformed(); } }); - turnColour.setText(MessageManager.getString("label.turn_propensity")); + turnColour.setText(MessageManager.getString("label.turn_propensity")); turnColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1368,7 -1253,7 +1368,7 @@@ turnColour_actionPerformed(); } }); - buriedColour.setText(MessageManager.getString("label.buried_index")); + buriedColour.setText(MessageManager.getString("label.buried_index")); buriedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1376,8 -1261,7 +1376,8 @@@ 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) @@@ -1385,8 -1269,7 +1385,8 @@@ 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) @@@ -1394,8 -1277,7 +1394,8 @@@ 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) @@@ -1403,7 -1285,7 +1403,7 @@@ PIDColour_actionPerformed(); } }); - BLOSUM62Colour.setText(MessageManager.getString("label.blosum62")); + BLOSUM62Colour.setText(MessageManager.getString("label.blosum62")); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@@ -1411,8 -1293,7 +1411,8 @@@ BLOSUM62Colour_actionPerformed(); } }); - purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine")); + purinePyrimidineColour.setText(MessageManager + .getString("label.purine_pyrimidine")); purinePyrimidineColour .addActionListener(new java.awt.event.ActionListener() { @@@ -1421,15 -1302,13 +1421,15 @@@ 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() { @@@ -1457,12 -1336,8 +1457,12 @@@ 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, @@@ -1476,11 -1351,8 +1476,11 @@@ } 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); } @@@ -1666,7 -1538,7 +1666,7 @@@ { SequenceGroup sg = getGroup(); - if (e.getSource().equals(userDefinedColour)) + if (e.getSource().equals(userDefinedColour)) { new UserDefinedColours(ap, sg); } @@@ -1743,7 -1615,7 +1743,7 @@@ 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(), @@@ -1795,10 -1667,8 +1795,10 @@@ 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) @@@ -1837,12 -1707,8 +1837,12 @@@ 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) @@@ -1854,14 -1720,10 +1854,14 @@@ { 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(' ', '_')); @@@ -1888,11 -1750,9 +1888,11 @@@ 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(); } @@@ -1905,8 -1765,7 +1905,8 @@@ 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) @@@ -1960,10 -1819,11 +1960,10 @@@ 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(); } @@@ -2029,17 -1889,17 +2029,17 @@@ if (source == toggle) { - description = MessageManager.getString("label.toggle_case"); + description = MessageManager.getString("label.toggle_case"); caseChange = ChangeCaseCommand.TOGGLE_CASE; } else if (source == upperCase) { - description = MessageManager.getString("label.to_upper_case"); + description = MessageManager.getString("label.to_upper_case"); caseChange = ChangeCaseCommand.TO_UPPER; } else { - description = MessageManager.getString("label.to_lower_case"); + description = MessageManager.getString("label.to_lower_case"); caseChange = ChangeCaseCommand.TO_LOWER; } @@@ -2059,9 -1919,8 +2059,9 @@@ { 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; @@@ -2092,12 -1951,8 +2092,12 @@@ 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[]{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() })); ++ { sequence.getDisplayId(false) })); int value = chooser.showOpenDialog(null); @@@ -2111,24 -1966,10 +2111,24 @@@ } + // 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) { @@@ -2234,15 -2075,12 +2234,15 @@@ 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()),