X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=25cad0ae528dc98385d038fdae2a247afd28f667;hb=3640aa8bd3308650c499f631fb2922cde429c43b;hp=82ce8359874e9964066a88f7d468c3544eaf4c2c;hpb=a0a45f042ee77368a0ff6c82caccb1b93d9e0f72;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 82ce835..25cad0a 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,19 +1,22 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, 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. * * 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; @@ -24,7 +27,6 @@ import java.awt.event.*; import javax.swing.*; -import MCview.*; import jalview.analysis.*; import jalview.commands.*; import jalview.datamodel.*; @@ -32,6 +34,7 @@ import jalview.io.*; import jalview.schemes.*; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; +import jalview.util.MessageManager; import jalview.util.UrlLink; /** @@ -69,10 +72,13 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); - + protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); - - //protected JRadioButtonMenuItem covariationColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); + + // protected JRadioButtonMenuItem covariationColour = new + // JRadioButtonMenuItem(); JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); @@ -84,7 +90,13 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceName = new JMenuItem(); - Sequence sequence; + JMenuItem sequenceDetails = new JMenuItem(); + + JMenuItem sequenceSelDetails = new JMenuItem(); + + SequenceI sequence; + + JMenuItem createGroupMenuItem = new JMenuItem(); JMenuItem unGroupMenuItem = new JMenuItem(); @@ -118,6 +130,12 @@ public class PopupMenu extends JPopupMenu JMenuItem pdbFromFile = new JMenuItem(); + // JBPNote: Commented these out - Should add these services via the web + // services menu system. + // JMenuItem ContraFold = new JMenuItem(); + + // JMenuItem RNAFold = new JMenuItem(); + JMenuItem enterPDB = new JMenuItem(); JMenuItem discoverPDB = new JMenuItem(); @@ -161,8 +179,8 @@ public class PopupMenu extends JPopupMenu * @param links * @param groupLinks */ - public PopupMenu(final AlignmentPanel ap, final Sequence seq, final Vector links, - final Vector groupLinks) + public PopupMenu(final AlignmentPanel ap, final SequenceI seq, + Vector links, Vector groupLinks) { // ///////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -188,7 +206,8 @@ public class PopupMenu extends JPopupMenu colours.add(PIDColour); colours.add(BLOSUM62Colour); colours.add(purinePyrimidineColour); - //colours.add(covariationColour); + colours.add(RNAInteractionColour); + // colours.add(covariationColour); for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) { @@ -214,11 +233,11 @@ public class PopupMenu extends JPopupMenu e.printStackTrace(); } + JMenuItem menuItem; if (seq != null) { sequenceMenu.setText(sequence.getName()); - JMenuItem menuItem; if (seq.getDatasetSequence().getPDBId() != null && seq.getDatasetSequence().getPDBId().size() > 0) { @@ -235,9 +254,14 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - // 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); + // 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 StructureViewer(ap.getStructureSelectionManager()) + .viewStructures(pdb, + ap.av.collateForPDB(new PDBEntry[] + { pdb })[0], null, ap); } }); @@ -253,42 +277,89 @@ public class PopupMenu extends JPopupMenu } } else - { - if(ap.av.alignment.isNucleotide()==false){ - structureMenu.remove(viewStructureMenu); - } + { + if (ap.av.getAlignment().isNucleotide() == false) + { + structureMenu.remove(viewStructureMenu); + } // structureMenu.remove(colStructureMenu); } - - if(ap.av.alignment.isNucleotide()==true){ - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); - String rnastruc=new String(); - for(int i=0; i 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) @@ -312,14 +385,15 @@ public class PopupMenu extends JPopupMenu sequenceMenu.add(menuItem); } - if (ap.av.hasHiddenRows) + if (ap.av.hasHiddenRows()) { - final int index = ap.av.alignment.findIndex(seq); + final int index = ap.av.getAlignment().findIndex(seq); 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) @@ -333,8 +407,14 @@ public class PopupMenu extends JPopupMenu }); add(menuItem); } - - menuItem = new JMenuItem("Reveal All"); + } + } + // for the case when no sequences are even visible + if (ap.av.hasHiddenRows()) + { + { + menuItem = new JMenuItem( + MessageManager.getString("action.reveal_all")); menuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -353,11 +433,16 @@ public class PopupMenu extends JPopupMenu } SequenceGroup sg = ap.av.getSelectionGroup(); + boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment() + .getGroups().contains(sg) : false; - if (sg != null) + 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) { @@ -405,12 +490,13 @@ public class PopupMenu extends JPopupMenu } else if (sg.cs instanceof PurinePyrimidineColourScheme) { - purinePyrimidineColour.setSelected(true); + purinePyrimidineColour.setSelected(true); } - /* else if (sg.cs instanceof CovariationColourScheme) - { - covariationColour.setSelected(true); - }*/ + + /* + * else if (sg.cs instanceof CovariationColourScheme) { + * covariationColour.setSelected(true); } + */ else { noColourmenuItem.setSelected(true); @@ -430,32 +516,73 @@ public class PopupMenu extends JPopupMenu buildGroupURLMenu(sg, groupLinks); } // Add a 'show all structures' for the current selection - Hashtable pdbe=new Hashtable(); - for (SequenceI sq: ap.av.getSequenceSelection()) + 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) { - for (PDBEntry pe: pes) + Vector pes = (Vector) sq.getDatasetSequence() + .getPDBId(); + if (pes != null && pes.size()>0) + { + reppdb.put(pes.get(0).getId(), pes.get(0)); + for (PDBEntry pe : pes) { - pdbe.put(pe.getId(), pe); + pdbe.put(pe.getId(), pe); + if (sqass == null) + { + sqass = sq; + } } } } - if (pdbe.size()>0) + if (pdbe.size() > 0) { - final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]); - final JMenuItem gpdbview; - structureMenu.add(gpdbview=new JMenuItem("View "+pdbe.size()+" structures.")); - gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment."); + final PDBEntry[] pe = pdbe.values().toArray( + new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray( + new PDBEntry[reppdb.size()]); + final JMenuItem gpdbview, rpdbview; + if (pdbe.size() == 1) + { + structureMenu.add(gpdbview = new JMenuItem(MessageManager + .formatMessage("label.view_structure_for", new String[] + { sqass.getDisplayId(false) }))); + } + else + { + structureMenu.add(gpdbview = new JMenuItem(MessageManager + .formatMessage("label.view_all_structures", new String[] + { new Integer(pdbe.size()).toString() }))); + } + gpdbview.setToolTipText(MessageManager + .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment")); gpdbview.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { - new AppJmol(ap, pe, ap.av.collateForPDB(pe)); + new StructureViewer(ap.getStructureSelectionManager()).viewStructures(ap, pe, ap.av.collateForPDB(pe)); } }); + if (reppdb.size() > 1 && reppdb.size() < pdbe.size()) + { + structureMenu.add(rpdbview = new JMenuItem(MessageManager + .formatMessage( + "label.view_all_representative_structures", + new String[] + { new Integer(reppdb.size()).toString() }))); + rpdbview.setToolTipText(MessageManager + .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment")); + rpdbview.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + new StructureViewer(ap.getStructureSelectionManager()).viewStructures(ap, pr, ap.av.collateForPDB(pr)); + } + }); + } } } else @@ -464,9 +591,17 @@ public class PopupMenu extends JPopupMenu editMenu.setVisible(false); } - if (!ap.av.alignment.getGroups().contains(sg)) + if (!isDefinedGroup) { + createGroupMenuItem.setVisible(true); unGroupMenuItem.setVisible(false); + jMenu1.setText(MessageManager.getString("action.edit_new_group")); + } + else + { + createGroupMenuItem.setVisible(false); + unGroupMenuItem.setVisible(true); + jMenu1.setText(MessageManager.getString("action.edit_group")); } if (seq == null) @@ -478,7 +613,7 @@ public class PopupMenu extends JPopupMenu if (links != null && links.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++) { @@ -500,7 +635,7 @@ public class PopupMenu extends JPopupMenu continue; } final String label = urlLink.getLabel(); - if (urlLink.isDynamic()) + if (seq != null && urlLink.isDynamic()) { // collect matching db-refs @@ -605,11 +740,18 @@ 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 - // 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(); @@ -731,7 +873,8 @@ 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 @@ -757,7 +900,9 @@ 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) @@ -792,16 +937,12 @@ 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) @@ -834,9 +975,9 @@ 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) @@ -844,8 +985,9 @@ 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) @@ -853,8 +995,28 @@ public class PopupMenu extends JPopupMenu sequenceName_actionPerformed(); } }); + sequenceDetails.setText(MessageManager + .getString("label.sequence_details") + "..."); + sequenceDetails.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceDetails_actionPerformed(); + } + }); + sequenceSelDetails.setText(MessageManager + .getString("label.sequence_details") + "..."); + sequenceSelDetails + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceSelectionDetails_actionPerformed(); + } + }); 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) @@ -862,8 +1024,18 @@ 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) @@ -871,7 +1043,8 @@ 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) @@ -879,8 +1052,8 @@ 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() { @@ -889,7 +1062,7 @@ public class PopupMenu extends JPopupMenu showBoxes_actionPerformed(); } }); - showText.setText("Text"); + showText.setText(MessageManager.getString("action.text")); showText.setState(true); showText.addActionListener(new ActionListener() { @@ -898,7 +1071,7 @@ 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) @@ -906,7 +1079,8 @@ 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() { @@ -915,8 +1089,8 @@ 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) @@ -924,7 +1098,7 @@ 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) @@ -932,7 +1106,7 @@ 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) @@ -940,7 +1114,7 @@ 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) @@ -948,7 +1122,7 @@ 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) @@ -956,8 +1130,9 @@ 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) @@ -965,7 +1140,33 @@ 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) @@ -973,7 +1174,7 @@ 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) @@ -981,8 +1182,10 @@ 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) @@ -990,7 +1193,7 @@ 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) @@ -998,11 +1201,13 @@ 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) @@ -1010,22 +1215,25 @@ public class PopupMenu extends JPopupMenu editSequence_actionPerformed(actionEvent); } }); + /* * annotationMenuItem.setText("By Annotation"); * annotationMenuItem.addActionListener(new ActionListener() { public void * actionPerformed(ActionEvent actionEvent) { * annotationMenuItem_actionPerformed(actionEvent); } }); */ - + groupMenu.add(sequenceSelDetails); add(groupMenu); - add(sequenceMenu); this.add(structureMenu); groupMenu.add(editMenu); groupMenu.add(outputMenu); groupMenu.add(sequenceFeature); + groupMenu.add(createGroupMenuItem); + groupMenu.add(unGroupMenuItem); groupMenu.add(jMenu1); sequenceMenu.add(sequenceName); + sequenceMenu.add(sequenceDetails); colourMenu.add(textColour); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); @@ -1039,8 +1247,13 @@ public class PopupMenu extends JPopupMenu colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideMenuItem); - colourMenu.add(purinePyrimidineColour); - //colourMenu.add(covariationColour); + if (ap.getAlignment().isNucleotide()) + { + // JBPNote - commented since the colourscheme isn't functional + // colourMenu.add(RNAInteractionColour); + colourMenu.add(purinePyrimidineColour); + } + // colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) @@ -1073,10 +1286,13 @@ 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); @@ -1086,7 +1302,7 @@ 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) @@ -1095,7 +1311,8 @@ 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) @@ -1103,7 +1320,7 @@ 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) @@ -1111,7 +1328,7 @@ 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) @@ -1119,7 +1336,8 @@ public class PopupMenu extends JPopupMenu taylorColour_actionPerformed(); } }); - hydrophobicityColour.setText("Hydrophobicity"); + hydrophobicityColour.setText(MessageManager + .getString("label.hydrophobicity")); hydrophobicityColour .addActionListener(new java.awt.event.ActionListener() { @@ -1128,7 +1346,7 @@ 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) @@ -1136,7 +1354,8 @@ 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) @@ -1144,7 +1363,7 @@ 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) @@ -1152,7 +1371,7 @@ 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) @@ -1160,7 +1379,8 @@ 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) @@ -1168,7 +1388,8 @@ 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) @@ -1176,7 +1397,8 @@ 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) @@ -1184,7 +1406,7 @@ 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) @@ -1192,24 +1414,25 @@ public class PopupMenu extends JPopupMenu BLOSUM62Colour_actionPerformed(); } }); - purinePyrimidineColour.setText("Purine/Pyrimidine"); - purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - purinePyrimidineColour_actionPerformed(); - } - }); - /* - covariationColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - covariationColour_actionPerformed(); - } - });*/ - - conservationMenuItem.setText("Conservation"); + purinePyrimidineColour.setText(MessageManager + .getString("label.purine_pyrimidine")); + purinePyrimidineColour + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + purinePyrimidineColour_actionPerformed(); + } + }); + + /* + * covariationColour.addActionListener(new java.awt.event.ActionListener() { + * public void actionPerformed(ActionEvent e) { + * covariationColour_actionPerformed(); } }); + */ + + conservationMenuItem.setText(MessageManager + .getString("label.conservation")); conservationMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -1220,6 +1443,50 @@ public class PopupMenu extends JPopupMenu }); } + protected void sequenceSelectionDetails_actionPerformed() + { + createSequenceDetailsReport(ap.av.getSequenceSelection()); + } + + protected void sequenceDetails_actionPerformed() + { + createSequenceDetailsReport(new SequenceI[] + { sequence }); + } + + public void createSequenceDetailsReport(SequenceI[] sequences) + { + CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); + StringBuffer contents = new StringBuffer(); + for (SequenceI seq : sequences) + { + contents.append("

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

"); + new SequenceAnnotationReport(null) + .createSequenceAnnotationReport( + contents, + seq, + true, + true, + false, + (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax + : null); + contents.append("

"); + } + 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); + + } + protected void showNonconserved_actionPerformed() { getGroup().setShowNonconserved(displayNonconserved.isSelected()); @@ -1246,9 +1513,7 @@ public class PopupMenu extends JPopupMenu protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme( - sg.getSequences(ap.av.hiddenRepSequences), - ap.av.alignment.getWidth()); + sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); refresh(); } @@ -1347,19 +1612,17 @@ public class PopupMenu extends JPopupMenu getGroup().cs = new NucleotideColourScheme(); refresh(); } - + protected void purinePyrimidineColour_actionPerformed() { getGroup().cs = new PurinePyrimidineColourScheme(); refresh(); } + /* - protected void covariationColour_actionPerformed() - { - getGroup().cs = new CovariationColourScheme(sequence.getAnnotation()[0]); - refresh(); - } -*/ + * protected void covariationColour_actionPerformed() { getGroup().cs = new + * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } + */ /** * DOCUMENT ME! * @@ -1377,8 +1640,8 @@ public class PopupMenu extends JPopupMenu if (abovePIDColour.isSelected()) { sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), - sg.getEndRes() + 1)); + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); @@ -1406,7 +1669,7 @@ public class PopupMenu extends JPopupMenu { SequenceGroup sg = getGroup(); - if (e.getActionCommand().equals("User Defined...")) + if (e.getSource().equals(userDefinedColour)) { new UserDefinedColours(ap, sg); } @@ -1431,8 +1694,8 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), - sg.getEndRes() + 1)); + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1449,8 +1712,8 @@ public class PopupMenu extends JPopupMenu sg.cs = new Blosum62ColourScheme(); sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), - sg.getEndRes() + 1)); + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1483,13 +1746,14 @@ 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.hiddenRepSequences), sg.getStartRes(), + ResidueProperties.propHash, 3, sg.getSequences(ap.av + .getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); - c.verdict(false, ap.av.ConsPercGaps); + c.verdict(false, ap.av.getConsPercGaps()); sg.cs.setConservation(c); @@ -1517,7 +1781,7 @@ public class PopupMenu extends JPopupMenu sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD); - acg.predefinedColours = true; + acg.setPredefinedColours(true); sg.cs = acg; refresh(); @@ -1534,8 +1798,10 @@ 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) @@ -1559,7 +1825,7 @@ public class PopupMenu extends JPopupMenu // this method won't add a new group if it already exists if (sg != null) { - ap.av.alignment.addGroup(sg); + ap.av.getAlignment().addGroup(sg); } return sg; @@ -1574,8 +1840,12 @@ 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) @@ -1587,10 +1857,14 @@ public class PopupMenu extends JPopupMenu { if (dialog.getName().indexOf(" ") > -1) { - JOptionPane.showMessageDialog(ap, - "Spaces have been converted to \"_\"", - "No spaces allowed in 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(' ', '_')); @@ -1613,11 +1887,18 @@ public class PopupMenu extends JPopupMenu void unGroupMenuItem_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); - ap.av.alignment.deleteGroup(sg); + ap.av.getAlignment().deleteGroup(sg); 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! * @@ -1627,7 +1908,8 @@ 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) @@ -1681,12 +1963,10 @@ public class PopupMenu extends JPopupMenu jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - 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); + JOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString("label.web_browser_not_found_unix"), + MessageManager.getString("label.web_browser_not_found"), + JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } @@ -1752,23 +2032,23 @@ 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; } ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, - sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, - caseChange); + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); @@ -1782,30 +2062,30 @@ public class PopupMenu extends JPopupMenu { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, - "Alignment output - " + 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.alignment.getAlignmentAnnotation(); - if (nala != null) + + AlignmentView selvew = ap.av.getAlignmentView(true, false); + AlignmentI aselview = selvew.getVisibleAlignment(ap.av + .getGapCharacter()); + List ala = (ap.av + .getVisibleAlignmentAnnotation(true)); + if (ala != null) { - for (int i = 0; i < nala.length; i++) + for (AlignmentAnnotation aa : ala) { - AlignmentAnnotation na = nala[i]; - oal.addAnnotation(na); + aselview.addAnnotation(aa); } } cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - oal, omitHidden, csel, sg)); - oal = null; + aselview, null, null, null)); } public void pdbFromFile_actionPerformed() @@ -1813,8 +2093,12 @@ 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("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[] + { sequence.getDisplayId(false) })); int value = chooser.showOpenDialog(null); @@ -1822,15 +2106,30 @@ public class PopupMenu extends JPopupMenu { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true); + new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, + jalview.io.AppletFormatAdapter.FILE, sequence, true); } } + // 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) { @@ -1843,9 +2142,9 @@ public class PopupMenu extends JPopupMenu public void discoverPDB_actionPerformed() { - final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[] + final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[] { sequence } - : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment)); + : ap.av.getSequenceSelection()); Thread discpdb = new Thread(new Runnable() { public void run() @@ -1908,16 +2207,16 @@ public class PopupMenu extends JPopupMenu public void colourByStructure(String pdbid) { - Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure( - sequence, pdbid); + Annotation[] anots = ap.av.getStructureSelectionManager() + .colourSequenceFromStructure(sequence, pdbid); AlignmentAnnotation an = new AlignmentAnnotation("Structure", "Coloured by " + pdbid, anots); - ap.av.alignment.addAnnotation(an); + ap.av.getAlignment().addAnnotation(an); an.createSequenceMapping(sequence, 0, true); // an.adjustForAlignment(); - ap.av.alignment.setAnnotationIndex(an, 0); + ap.av.getAlignment().setAnnotationIndex(an, 0); ap.adjustAnnotationHeight(); @@ -1936,16 +2235,19 @@ 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.hiddenRepSequences), - sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment); + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); ap.alignFrame.addHistoryItem(editCommand);