X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=67bc00f3be024780d53242348bdb3036484d6a05;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=d87a62b755c99efddae11c9d9a8534f8f509c6cf;hpb=b65330720abd1329eac5fddbed9516b8302abe52;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index d87a62b..67bc00f 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,19 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * 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. - * + * * 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 . + * 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; /** @@ -85,8 +86,12 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceName = new JMenuItem(); - SequenceI sequence; + JMenuItem sequenceDetails = new JMenuItem(); + JMenuItem sequenceSelDetails = new JMenuItem(); + + SequenceI sequence; + JMenuItem createGroupMenuItem = new JMenuItem(); JMenuItem unGroupMenuItem = new JMenuItem(); JMenuItem outline = new JMenuItem(); @@ -162,8 +167,8 @@ public class PopupMenu extends JPopupMenu * @param links * @param groupLinks */ - public PopupMenu(final AlignmentPanel ap, final SequenceI seq, Vector links, - 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 @@ -236,8 +241,10 @@ 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); + // 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); } @@ -255,30 +262,31 @@ public class PopupMenu extends JPopupMenu } else { - if (ap.av.alignment.isNucleotide() == false) + if (ap.av.getAlignment().isNucleotide() == false) { - structureMenu.remove(viewStructureMenu); + structureMenu.remove(viewStructureMenu); } // structureMenu.remove(colStructureMenu); } - if (ap.av.alignment.isNucleotide() == true) + if (ap.av.getAlignment().isNucleotide() == true) { - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); for (int i = 0; i < aa.length; i++) { if (aa[i].getRNAStruc() != null) { final String rnastruc = aa[i].getRNAStruc(); - + final String structureLine = aa[i].label; menuItem = new JMenuItem(); - menuItem.setText("RNA structure - consensus"); + 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(seq.getSequenceAsString(), rnastruc, seq - .getName(), ap); + new AppVarna(structureLine, seq, seq.getSequenceAsString(), + rnastruc, seq.getName(), ap); } }); viewStructureMenu.add(menuItem); @@ -295,17 +303,18 @@ public class PopupMenu extends JPopupMenu if (seqAnno[i].getRNAStruc() != null) { final String rnastruc = seqAnno[i].getRNAStruc(); - - // TODO: make rnastrucF a bit more nice + + // TODO: make rnastrucF a bit more nice menuItem = new JMenuItem(); - menuItem.setText("RNA structure - "+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.getSequenceAsString(), rnastruc, seq - .getName(), ap); + new AppVarna(seq.getName() + " structure", seq, seq + .getSequenceAsString(), rnastruc, seq.getName(), + ap); } }); viewStructureMenu.add(menuItem); @@ -313,10 +322,9 @@ 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) @@ -329,7 +337,7 @@ 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) @@ -340,14 +348,14 @@ 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) @@ -364,9 +372,10 @@ public class PopupMenu extends JPopupMenu } } // for the case when no sequences are even visible - if (ap.av.hasHiddenRows) { + 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) @@ -385,11 +394,12 @@ 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."); + 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")); if (sg.cs instanceof ZappoColourScheme) { @@ -462,42 +472,63 @@ public class PopupMenu extends JPopupMenu buildGroupURLMenu(sg, groupLinks); } // Add a 'show all structures' for the current selection - Hashtable pdbe=new Hashtable(); - SequenceI sqass=null; - 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) + { + reppdb.put(pes.get(0).getId(),pes.get(0)); + for (PDBEntry pe : pes) { - pdbe.put(pe.getId(), pe); - if (sqass==null) + 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; - if (pdbe.size()==1) + 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("View structure for "+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() { - + @Override public void actionPerformed(ActionEvent e) { 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++) { @@ -542,7 +579,7 @@ public class PopupMenu extends JPopupMenu continue; } final String label = urlLink.getLabel(); - if (seq!=null && urlLink.isDynamic()) + if (seq != null && urlLink.isDynamic()) { // collect matching db-refs @@ -647,10 +684,10 @@ 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); @@ -773,7 +810,7 @@ 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 @@ -799,7 +836,7 @@ 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) @@ -834,16 +871,8 @@ 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) @@ -876,9 +905,9 @@ 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) @@ -886,8 +915,8 @@ 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) @@ -895,8 +924,25 @@ 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) @@ -904,8 +950,16 @@ 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) @@ -913,7 +967,7 @@ 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) @@ -921,8 +975,8 @@ 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() { @@ -931,7 +985,7 @@ public class PopupMenu extends JPopupMenu showBoxes_actionPerformed(); } }); - showText.setText("Text"); + showText.setText(MessageManager.getString("action.text")); showText.setState(true); showText.addActionListener(new ActionListener() { @@ -940,7 +994,7 @@ 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) @@ -948,7 +1002,7 @@ 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() { @@ -957,8 +1011,8 @@ 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) @@ -966,7 +1020,7 @@ 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) @@ -974,7 +1028,7 @@ 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) @@ -982,7 +1036,7 @@ 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) @@ -990,7 +1044,7 @@ 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) @@ -998,8 +1052,8 @@ 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) @@ -1007,7 +1061,7 @@ public class PopupMenu extends JPopupMenu pdbFromFile_actionPerformed(); } }); - enterPDB.setText("Enter PDB Id"); + enterPDB.setText(MessageManager.getString("label.enter_pdb_id")); enterPDB.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -1015,7 +1069,7 @@ 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) @@ -1023,8 +1077,8 @@ 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) @@ -1032,7 +1086,7 @@ 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) @@ -1040,11 +1094,11 @@ 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) @@ -1052,22 +1106,25 @@ 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); @@ -1081,8 +1138,9 @@ 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()) + { + colourMenu.add(purinePyrimidineColour); } // colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); @@ -1120,7 +1178,6 @@ public class PopupMenu extends JPopupMenu pdbMenu.add(enterPDB); pdbMenu.add(discoverPDB); jMenu1.add(groupName); - jMenu1.add(unGroupMenuItem); jMenu1.add(colourMenu); jMenu1.add(showBoxes); jMenu1.add(showText); @@ -1130,7 +1187,7 @@ 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) @@ -1139,7 +1196,7 @@ 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) @@ -1147,7 +1204,7 @@ 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) @@ -1155,7 +1212,7 @@ 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) @@ -1163,7 +1220,7 @@ public class PopupMenu extends JPopupMenu taylorColour_actionPerformed(); } }); - hydrophobicityColour.setText("Hydrophobicity"); + hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity")); hydrophobicityColour .addActionListener(new java.awt.event.ActionListener() { @@ -1172,7 +1229,7 @@ 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) @@ -1180,7 +1237,7 @@ 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) @@ -1188,7 +1245,7 @@ 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) @@ -1196,7 +1253,7 @@ 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) @@ -1204,7 +1261,7 @@ 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) @@ -1212,7 +1269,7 @@ 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) @@ -1220,7 +1277,7 @@ 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) @@ -1228,7 +1285,7 @@ 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) @@ -1236,7 +1293,7 @@ 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() { @@ -1251,7 +1308,7 @@ public class PopupMenu extends JPopupMenu * covariationColour_actionPerformed(); } }); */ - conservationMenuItem.setText("Conservation"); + conservationMenuItem.setText(MessageManager.getString("label.conservation")); conservationMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -1262,6 +1319,43 @@ 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()); @@ -1288,9 +1382,7 @@ 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(); } @@ -1417,8 +1509,8 @@ 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()); @@ -1446,7 +1538,7 @@ public class PopupMenu extends JPopupMenu { SequenceGroup sg = getGroup(); - if (e.getActionCommand().equals("User Defined...")) + if (e.getSource().equals(userDefinedColour)) { new UserDefinedColours(ap, sg); } @@ -1471,8 +1563,8 @@ 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(); } @@ -1489,8 +1581,8 @@ 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(); } @@ -1523,9 +1615,10 @@ 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(); @@ -1557,7 +1650,7 @@ public class PopupMenu extends JPopupMenu sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD); - acg.predefinedColours = true; + acg.setPredefinedColours(true); sg.cs = acg; refresh(); @@ -1574,8 +1667,8 @@ 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) @@ -1599,7 +1692,7 @@ 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; @@ -1614,8 +1707,8 @@ 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) @@ -1628,8 +1721,8 @@ 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); } @@ -1653,10 +1746,15 @@ 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! @@ -1667,7 +1765,7 @@ 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) @@ -1724,9 +1822,8 @@ 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(); } @@ -1792,23 +1889,23 @@ 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); @@ -1823,7 +1920,7 @@ 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; @@ -1834,7 +1931,8 @@ public class PopupMenu extends JPopupMenu 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(); + AlignmentAnnotation[] nala = ap.av.getAlignment() + .getAlignmentAnnotation(); if (nala != null) { for (int i = 0; i < nala.length; i++) @@ -1853,8 +1951,8 @@ 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); @@ -1862,7 +1960,8 @@ 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); } } @@ -1870,7 +1969,7 @@ public class PopupMenu extends JPopupMenu 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) { @@ -1883,9 +1982,9 @@ public class PopupMenu extends JPopupMenu public void discoverPDB_actionPerformed() { - final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new SequenceI[] + 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() @@ -1948,16 +2047,16 @@ 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(); @@ -1976,16 +2075,16 @@ 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);