X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=aa1ab2177250cd3df74095613c6772ccdaf7fec2;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=453e6425ac2188cce04dc279054af29e445fe026;hpb=87ea83af3e209a8c3a4b19f9530a9c05b4541148;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 453e642..aa1ab21 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -1,35 +1,62 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * 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.appletgui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.analysis.*; -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.util.MessageManager; -import jalview.util.UrlLink; +import jalview.analysis.AAFrequency; +import jalview.analysis.Conservation; +import jalview.commands.ChangeCaseCommand; +import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; import jalview.io.AppletFormatAdapter; import jalview.io.SequenceAnnotationReport; +import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.NucleotideColourScheme; +import jalview.schemes.PIDColourScheme; +import jalview.schemes.ResidueProperties; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.ZappoColourScheme; +import jalview.util.MessageManager; +import jalview.util.UrlLink; + +import java.awt.CheckboxMenuItem; +import java.awt.Frame; +import java.awt.Menu; +import java.awt.MenuItem; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.util.Vector; public class APopupMenu extends java.awt.PopupMenu implements ActionListener, ItemListener @@ -70,6 +97,8 @@ public class APopupMenu extends java.awt.PopupMenu implements MenuItem unGroupMenuItem = new MenuItem(); + MenuItem createGroupMenuItem = new MenuItem(); + MenuItem nucleotideMenuItem = new MenuItem(); Menu colourMenu = new Menu(); @@ -82,17 +111,21 @@ public class APopupMenu extends java.awt.PopupMenu implements CheckboxMenuItem displayNonconserved = new CheckboxMenuItem(); - Menu editMenu = new Menu("Edit"); + Menu editMenu = new Menu(MessageManager.getString("action.edit")); - MenuItem copy = new MenuItem("Copy (Jalview Only)"); + MenuItem copy = new MenuItem( + MessageManager.getString("label.jalview_copy")); - MenuItem cut = new MenuItem("Cut (Jalview Only)"); + MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut")); - MenuItem toUpper = new MenuItem("To Upper Case"); + MenuItem toUpper = new MenuItem( + MessageManager.getString("label.to_upper_case")); - MenuItem toLower = new MenuItem("To Lower Case"); + MenuItem toLower = new MenuItem( + MessageManager.getString("label.to_lower_case")); - MenuItem toggleCase = new MenuItem("Toggle Case"); + MenuItem toggleCase = new MenuItem( + MessageManager.getString("label.toggle_case")); Menu outputmenu = new Menu(); @@ -104,15 +137,20 @@ public class APopupMenu extends java.awt.PopupMenu implements MenuItem repGroup = new MenuItem(); - MenuItem sequenceName = new MenuItem("Edit Name/Description"); + MenuItem sequenceName = new MenuItem( + MessageManager.getString("label.edit_name_description")); - MenuItem sequenceFeature = new MenuItem("Create Sequence Feature"); + MenuItem sequenceFeature = new MenuItem( + MessageManager.getString("label.create_sequence_feature")); - MenuItem editSequence = new MenuItem("Edit Sequence"); + MenuItem editSequence = new MenuItem( + MessageManager.getString("label.edit_sequence")); - MenuItem sequenceDetails = new MenuItem("Sequence Details ..."); + MenuItem sequenceDetails = new MenuItem( + MessageManager.getString("label.sequence_details") + "..."); - MenuItem selSeqDetails = new MenuItem("Sequence Details ..."); + MenuItem selSeqDetails = new MenuItem( + MessageManager.getString("label.sequence_details") + "..."); Sequence seq; @@ -160,15 +198,23 @@ public class APopupMenu extends java.awt.PopupMenu implements if (sg != null && sg.getSize() > 0) { - editGroupName.setLabel(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()})); + editGroupName.setLabel(MessageManager.formatMessage( + "label.name_param", new String[] + { sg.getName() })); showText.setState(sg.getDisplayText()); showColourText.setState(sg.getColourText()); showBoxes.setState(sg.getDisplayBoxes()); displayNonconserved.setState(sg.getShowNonconserved()); if (!ap.av.getAlignment().getGroups().contains(sg)) { + menu1.setLabel(MessageManager.getString("action.edit_new_group")); groupMenu.remove(unGroupMenuItem); } + else + { + menu1.setLabel(MessageManager.getString("action.edit_group")); + groupMenu.remove(createGroupMenuItem); + } } else @@ -179,7 +225,7 @@ public class APopupMenu extends java.awt.PopupMenu implements if (links != null && links.size() > 0) { - Menu linkMenu = new Menu("Link"); + Menu linkMenu = new Menu(MessageManager.getString("action.link")); String link; for (int i = 0; i < links.size(); i++) { @@ -301,7 +347,9 @@ public class APopupMenu extends java.awt.PopupMenu implements if (seq != null) { seqMenu.setLabel(seq.getName()); - repGroup.setLabel(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()})); + repGroup.setLabel(MessageManager.formatMessage( + "label.represent_group_with", new String[] + { seq.getName() })); } else { @@ -458,6 +506,11 @@ public class APopupMenu extends java.awt.PopupMenu implements unGroupMenuItem_actionPerformed(); } + else if (source == createGroupMenuItem) + { + createGroupMenuItem_actionPerformed(); + } + else if (source == sequenceName) { editName(); @@ -520,7 +573,9 @@ public class APopupMenu extends java.awt.PopupMenu implements if (sg != null) { if (seq == null) + { seq = (Sequence) sg.getSequenceAt(0); + } EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString( sg.getStartRes(), sg.getEndRes() + 1), null, @@ -530,8 +585,8 @@ public class APopupMenu extends java.awt.PopupMenu implements if (dialog.accept) { - EditCommand editCommand = new EditCommand("Edit Sequences", - EditCommand.REPLACE, dialog.getName().replace(' ', + EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"), + Action.REPLACE, dialog.getName().replace(' ', ap.av.getGapCharacter()), sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1, @@ -618,7 +673,7 @@ public class APopupMenu extends java.awt.PopupMenu implements features, true, ap)) { ap.alignFrame.sequenceFeatures.setState(true); - ap.av.showSequenceFeatures(true); + ap.av.setShowSequenceFeatures(true);; ap.highlightSearchResults(null); } } @@ -635,16 +690,16 @@ public class APopupMenu extends java.awt.PopupMenu implements Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, - "Selection output - " + e.getActionCommand(), 600, 500); + jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + "label.selection_output_command", new String[] + { e.getActionCommand() }), 600, 500); // JBPNote: getSelectionAsNewSequence behaviour has changed - this method // now returns a full copy of sequence data // TODO consider using getSequenceSelection instead here cap.setText(new jalview.io.AppletFormatAdapter().formatSequences( - e.getActionCommand(), - new Alignment(ap.av.getSelectionAsNewSequence()), - ap.av.showJVSuffix)); + e.getActionCommand(), + ap.av.showJVSuffix, ap.av, true)); } @@ -667,8 +722,9 @@ public class APopupMenu extends java.awt.PopupMenu implements StringBuffer contents = new StringBuffer(); for (SequenceI seq : sequences) { - contents.append("

Annotation for " + seq.getDisplayId(true) - + "

"); + contents.append(MessageManager.formatMessage( + "label.annotation_for_displayid", new String[] + { seq.getDisplayId(true) })); new SequenceAnnotationReport(null) .createSequenceAnnotationReport( contents, @@ -676,7 +732,7 @@ public class APopupMenu extends java.awt.PopupMenu implements true, true, false, - (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax + (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax() : null); contents.append("

"); } @@ -685,7 +741,9 @@ public class APopupMenu extends java.awt.PopupMenu implements jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for " + (sequences.length == 1 ? sequences[0].getDisplayId(true) : "Selection"), 600, 500); - cap.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()})); + cap.setText(MessageManager.formatMessage("label.html_content", + new String[] + { contents.toString() })); } void editName() @@ -710,11 +768,15 @@ public class APopupMenu extends java.awt.PopupMenu implements PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement(); if (ap.av.applet.jmolAvailable) + { new jalview.appletgui.AppletJmol(entry, new Sequence[] { seq }, null, ap, AppletFormatAdapter.URL); + } else + { new MCview.AppletPDBViewer(entry, new Sequence[] { seq }, null, ap, AppletFormatAdapter.URL); + } } else @@ -724,36 +786,43 @@ public class APopupMenu extends java.awt.PopupMenu implements cap.setPDBImport(seq); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, - MessageManager.formatMessage("label.paste_pdb_file_for_sequence", new String[]{seq.getName()}), 400, 300); + jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + "label.paste_pdb_file_for_sequence", new String[] + { seq.getName() }), 400, 300); } } private void jbInit() throws Exception { - groupMenu.setLabel(MessageManager.getString("label.group")); groupMenu.setLabel(MessageManager.getString("label.selection")); sequenceFeature.addActionListener(this); editGroupName.addActionListener(this); - unGroupMenuItem.setLabel(MessageManager.getString("action.remove_group")); + unGroupMenuItem.setLabel(MessageManager + .getString("action.remove_group")); unGroupMenuItem.addActionListener(this); - nucleotideMenuItem.setLabel(MessageManager.getString("label.nucleotide")); + createGroupMenuItem.setLabel(MessageManager + .getString("action.create_group")); + createGroupMenuItem.addActionListener(this); + + nucleotideMenuItem.setLabel(MessageManager + .getString("label.nucleotide")); nucleotideMenuItem.addActionListener(this); conservationMenuItem.addItemListener(this); abovePIDColour.addItemListener(this); colourMenu.setLabel(MessageManager.getString("label.group_colour")); - showBoxes.setLabel(MessageManager.getString("label.boxes")); + showBoxes.setLabel(MessageManager.getString("action.boxes")); showBoxes.setState(true); showBoxes.addItemListener(this); sequenceName.addActionListener(this); sequenceDetails.addActionListener(this); selSeqDetails.addActionListener(this); - displayNonconserved.setLabel(MessageManager.getString("label.show_non_conversed")); + displayNonconserved.setLabel(MessageManager + .getString("label.show_non_conversed")); displayNonconserved.setState(false); displayNonconserved.addItemListener(this); - showText.setLabel(MessageManager.getString("label.text")); + showText.setLabel(MessageManager.getString("action.text")); showText.addItemListener(this); showColourText.setLabel(MessageManager.getString("label.colour_text")); showColourText.addItemListener(this); @@ -761,20 +830,23 @@ public class APopupMenu extends java.awt.PopupMenu implements seqMenu.setLabel(MessageManager.getString("label.sequence")); pdb.setLabel(MessageManager.getString("label.view_pdb_structure")); hideSeqs.setLabel(MessageManager.getString("action.hide_sequences")); - repGroup.setLabel(MessageManager.getString("label.represent_group_with")); + repGroup.setLabel(MessageManager.formatMessage( + "label.represent_group_with", new String[] + { "" })); revealAll.setLabel(MessageManager.getString("action.reveal_all")); revealSeq.setLabel(MessageManager.getString("action.reveal_sequences")); - menu1.setLabel(MessageManager.getString("label.group")); + menu1.setLabel(MessageManager.getString("label.group") + ":"); add(groupMenu); this.add(seqMenu); this.add(hideSeqs); this.add(revealSeq); this.add(revealAll); // groupMenu.add(selSeqDetails); - groupMenu.add(editGroupName); groupMenu.add(editMenu); groupMenu.add(outputmenu); groupMenu.add(sequenceFeature); + groupMenu.add(createGroupMenuItem); + groupMenu.add(unGroupMenuItem); groupMenu.add(menu1); colourMenu.add(noColourmenuItem); @@ -794,34 +866,34 @@ public class APopupMenu extends java.awt.PopupMenu implements colourMenu.add(abovePIDColour); colourMenu.add(conservationMenuItem); - noColourmenuItem.setLabel("None"); + noColourmenuItem.setLabel(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(this); - clustalColour.setLabel("Clustalx colours"); + clustalColour.setLabel(MessageManager.getString("label.clustalx_colours")); clustalColour.addActionListener(this); - zappoColour.setLabel("Zappo"); + zappoColour.setLabel(MessageManager.getString("label.zappo")); zappoColour.addActionListener(this); - taylorColour.setLabel("Taylor"); + taylorColour.setLabel(MessageManager.getString("label.taylor")); taylorColour.addActionListener(this); - hydrophobicityColour.setLabel("Hydrophobicity"); + hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity")); hydrophobicityColour.addActionListener(this); - helixColour.setLabel("Helix propensity"); + helixColour.setLabel(MessageManager.getString("label.helix_propensity")); helixColour.addActionListener(this); - strandColour.setLabel("Strand propensity"); + strandColour.setLabel(MessageManager.getString("label.strand_propensity")); strandColour.addActionListener(this); - turnColour.setLabel("Turn propensity"); + turnColour.setLabel(MessageManager.getString("label.turn_propensity")); turnColour.addActionListener(this); - buriedColour.setLabel("Buried Index"); + buriedColour.setLabel(MessageManager.getString("label.buried_index")); buriedColour.addActionListener(this); - abovePIDColour.setLabel("Above % Identity"); + abovePIDColour.setLabel(MessageManager.getString("label.above_identity_percentage")); - userDefinedColour.setLabel("User Defined"); + userDefinedColour.setLabel(MessageManager.getString("action.user_defined")); userDefinedColour.addActionListener(this); - PIDColour.setLabel("Percentage Identity"); + PIDColour.setLabel(MessageManager.getString("action.percentage_identity")); PIDColour.addActionListener(this); BLOSUM62Colour.setLabel("BLOSUM62"); BLOSUM62Colour.addActionListener(this); - conservationMenuItem.setLabel("Conservation"); + conservationMenuItem.setLabel(MessageManager.getString("label.conservation")); editMenu.add(copy); copy.addActionListener(this); @@ -844,7 +916,7 @@ public class APopupMenu extends java.awt.PopupMenu implements seqMenu.add(pdb); } seqMenu.add(repGroup); - menu1.add(unGroupMenuItem); + menu1.add(editGroupName); menu1.add(colourMenu); menu1.add(showBoxes); menu1.add(showText); @@ -1028,6 +1100,12 @@ public class APopupMenu extends java.awt.PopupMenu implements ap.paintAlignment(true); } + void createGroupMenuItem_actionPerformed() + { + getGroup(); // implicitly create group + refresh(); + } + public void showColourText_itemStateChanged() { getGroup().setColourText(showColourText.getState());