X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=3b37b62972d4179c2b193036e3835cac41928e04;hb=4663ab6ec8142df859d031bff618d78809e22082;hp=7a99a20ff4a9a522182b56eb470a91ed11a49767;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java old mode 100755 new mode 100644 index 7a99a20..3b37b62 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -1,33 +1,62 @@ /* - * 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 2.8.2) + * 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.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 @@ -68,6 +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(); @@ -80,17 +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(); @@ -102,21 +137,34 @@ 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( + MessageManager.getString("label.create_sequence_feature")); - MenuItem sequenceFeature = new MenuItem("Create Sequence Feature"); + MenuItem editSequence = new MenuItem( + MessageManager.getString("label.edit_sequence")); - MenuItem editSequence = new MenuItem("Edit Sequence"); + MenuItem sequenceDetails = new MenuItem( + MessageManager.getString("label.sequence_details") + "..."); + MenuItem selSeqDetails = new MenuItem( + MessageManager.getString("label.sequence_details") + "..."); + + MenuItem makeReferenceSeq = new MenuItem(); + Sequence seq; MenuItem revealAll = new MenuItem(); MenuItem revealSeq = new MenuItem(); + /** * index of sequence to be revealed */ - int revealSeq_index=-1; + int revealSeq_index = -1; + Menu menu1 = new Menu(); public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links) @@ -152,15 +200,23 @@ public class APopupMenu extends java.awt.PopupMenu implements if (sg != null && sg.getSize() > 0) { - editGroupName.setLabel("Name: "+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 @@ -171,7 +227,7 @@ 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++) { @@ -185,7 +241,7 @@ public class APopupMenu extends java.awt.PopupMenu implements final String target = urlLink.getTarget(); // link.substring(0, // link.indexOf("|")); final String label = urlLink.getLabel(); - if (seq!=null && urlLink.isDynamic()) + if (seq != null && urlLink.isDynamic()) { // collect matching db-refs @@ -293,7 +349,20 @@ public class APopupMenu extends java.awt.PopupMenu implements if (seq != null) { seqMenu.setLabel(seq.getName()); - repGroup.setLabel("Represent Group with " + seq.getName()); + if (seq == ap.av.getAlignment().getSeqrep()) + { + makeReferenceSeq.setLabel(MessageManager + .getString("action.unmark_as_reference"));// Unmark + // representative"); + } + else + { + makeReferenceSeq.setLabel(MessageManager + .getString("action.set_as_reference")); // ); + } + repGroup.setLabel(MessageManager.formatMessage( + "label.represent_group_with", new String[] + { seq.getName() })); } else { @@ -304,14 +373,18 @@ public class APopupMenu extends java.awt.PopupMenu implements { remove(revealAll); remove(revealSeq); - } else { + } + else + { final int index = ap.av.getAlignment().findIndex(seq); if (ap.av.adjustForHiddenSeqs(index) - ap.av.adjustForHiddenSeqs(index - 1) > 1) { - revealSeq_index=index; - } else { + revealSeq_index = index; + } + else + { remove(revealSeq); } } @@ -446,10 +519,27 @@ public class APopupMenu extends java.awt.PopupMenu implements unGroupMenuItem_actionPerformed(); } + else if (source == createGroupMenuItem) + { + createGroupMenuItem_actionPerformed(); + } + else if (source == sequenceName) { editName(); } + else if (source == makeReferenceSeq) + { + makeReferenceSeq_actionPerformed(); + } + else if (source == sequenceDetails) + { + showSequenceDetails(); + } + else if (source == selSeqDetails) + { + showSequenceSelectionDetails(); + } else if (source == pdb) { addPDB(); @@ -500,7 +590,9 @@ 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, @@ -510,11 +602,12 @@ 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, ap.av.getAlignment()); + sg.getStartRes(), sg.getEndRes() + 1, + ap.av.getAlignment()); ap.alignFrame.addHistoryItem(editCommand); @@ -529,9 +622,8 @@ public class APopupMenu extends java.awt.PopupMenu implements Vector regions = new Vector(); if (sg != null) { - // TODO test change case behaves identically in JvLite - int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(), - sg.getEndRes() + 1); + int[][] startEnd = ap.av.getVisibleRegionBoundaries( + sg.getStartRes(), sg.getEndRes() + 1); String description; int caseChange; @@ -553,8 +645,8 @@ public class APopupMenu extends java.awt.PopupMenu implements } ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, - sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd, - caseChange); + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); @@ -598,7 +690,7 @@ 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); } } @@ -615,16 +707,59 @@ 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); - // JBPNote: getSelectionAsNewSequence behaviour has changed - this method now returns a full copy of sequence data + 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.getShowJVSuffix(), ap.av, true)); + + } + protected void showSequenceSelectionDetails() + { + createSequenceDetailsReport(ap.av.getSequenceSelection()); + } + + protected void showSequenceDetails() + { + createSequenceDetailsReport(new SequenceI[] + { seq }); + } + + public void createSequenceDetailsReport(SequenceI[] sequences) + { + + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame); + + StringBuffer contents = new StringBuffer(); + for (SequenceI seq : sequences) + { + contents.append(MessageManager.formatMessage( + "label.annotation_for_displayid", new String[] + { seq.getDisplayId(true) })); + new SequenceAnnotationReport(null) + .createSequenceAnnotationReport( + contents, + seq, + true, + true, + false, + (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax() + : null); + contents.append("

"); + } + Frame frame = new Frame(); + frame.add(cap); + 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() })); } void editName() @@ -649,67 +784,85 @@ 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 { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); - cap.setText("Paste your PDB file here."); + cap.setText(MessageManager.getString("label.paste_pdb_file")); cap.setPDBImport(seq); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file for sequence "+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("Group"); - groupMenu.setLabel("Selection"); + groupMenu.setLabel(MessageManager.getString("label.selection")); sequenceFeature.addActionListener(this); editGroupName.addActionListener(this); - unGroupMenuItem.setLabel("Remove Group"); + unGroupMenuItem.setLabel(MessageManager + .getString("action.remove_group")); unGroupMenuItem.addActionListener(this); - nucleotideMenuItem.setLabel("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("Group Colour"); - showBoxes.setLabel("Boxes"); + colourMenu.setLabel(MessageManager.getString("label.group_colour")); + showBoxes.setLabel(MessageManager.getString("action.boxes")); showBoxes.setState(true); showBoxes.addItemListener(this); sequenceName.addActionListener(this); - displayNonconserved.setLabel("Show Nonconserved"); + sequenceDetails.addActionListener(this); + selSeqDetails.addActionListener(this); + displayNonconserved.setLabel(MessageManager + .getString("label.show_non_conversed")); displayNonconserved.setState(false); displayNonconserved.addItemListener(this); - showText.setLabel("Text"); + showText.setLabel(MessageManager.getString("action.text")); showText.addItemListener(this); - showColourText.setLabel("Colour Text"); + showColourText.setLabel(MessageManager.getString("label.colour_text")); showColourText.addItemListener(this); - outputmenu.setLabel("Output to Textbox..."); - seqMenu.setLabel("Sequence"); - pdb.setLabel("View PDB Structure"); - hideSeqs.setLabel("Hide Sequences"); - repGroup.setLabel("Represent Group with"); - revealAll.setLabel("Reveal All"); - revealSeq.setLabel("Reveal Sequences"); - menu1.setLabel("Group"); + outputmenu.setLabel(MessageManager.getString("label.out_to_textbox")); + seqMenu.setLabel(MessageManager.getString("label.sequence")); + pdb.setLabel(MessageManager.getString("label.view_pdb_structure")); + hideSeqs.setLabel(MessageManager.getString("action.hide_sequences")); + 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") + ":"); add(groupMenu); this.add(seqMenu); this.add(hideSeqs); this.add(revealSeq); this.add(revealAll); - groupMenu.add(editGroupName); + // groupMenu.add(selSeqDetails); groupMenu.add(editMenu); groupMenu.add(outputmenu); groupMenu.add(sequenceFeature); + groupMenu.add(createGroupMenuItem); + groupMenu.add(unGroupMenuItem); groupMenu.add(menu1); colourMenu.add(noColourmenuItem); @@ -729,34 +882,34 @@ 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); @@ -772,12 +925,15 @@ public class APopupMenu extends java.awt.PopupMenu implements toLower.addActionListener(this); editMenu.add(toggleCase); seqMenu.add(sequenceName); + seqMenu.add(makeReferenceSeq); + // seqMenu.add(sequenceDetails); + if (!ap.av.applet.useXtrnalSviewer) { seqMenu.add(pdb); } seqMenu.add(repGroup); - menu1.add(unGroupMenuItem); + menu1.add(editGroupName); menu1.add(colourMenu); menu1.add(showBoxes); menu1.add(showText); @@ -789,6 +945,7 @@ public class APopupMenu extends java.awt.PopupMenu implements repGroup.addActionListener(this); revealAll.addActionListener(this); revealSeq.addActionListener(this); + makeReferenceSeq.addActionListener(this); } void refresh() @@ -799,9 +956,7 @@ public class APopupMenu extends java.awt.PopupMenu implements protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme( - sg.getSequences(ap.av.getHiddenRepSequences()), - ap.av.getAlignment().getWidth()); + sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); refresh(); } @@ -863,13 +1018,12 @@ public class APopupMenu extends java.awt.PopupMenu implements if (abovePIDColour.getState()) { - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), 0, - ap.av.getAlignment().getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); - sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus()); SliderPanel.showPIDSlider(); @@ -877,7 +1031,7 @@ public class APopupMenu extends java.awt.PopupMenu implements else // remove PIDColouring { - sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); + sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); } refresh(); @@ -893,9 +1047,8 @@ public class APopupMenu extends java.awt.PopupMenu implements { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), 0, - ap.av.getAlignment().getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); refresh(); } @@ -905,9 +1058,8 @@ public class APopupMenu extends java.awt.PopupMenu implements sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), 0, - ap.av.getAlignment().getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); refresh(); } @@ -930,10 +1082,9 @@ public class APopupMenu extends java.awt.PopupMenu implements { sg.cs.setConservation(Conservation.calculateConservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(ap.av.getHiddenRepSequences()), 0, - ap.av.getAlignment().getWidth(), - false, ap.av.getConsPercGaps(),false)); + ResidueProperties.propHash, 3, sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment() + .getWidth(), false, ap.av.getConsPercGaps(), false)); SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); SliderPanel.showConservationSlider(); } @@ -967,6 +1118,12 @@ 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()); @@ -978,6 +1135,28 @@ public class APopupMenu extends java.awt.PopupMenu implements getGroup().setDisplayText(showText.getState()); refresh(); } + public void makeReferenceSeq_actionPerformed() + { + if (!ap.av.getAlignment().hasSeqrep()) + { + // initialise the display flags so the user sees something happen + ap.av.setDisplayReferenceSeq(true); + ap.av.setColourByReferenceSeq(true); + ap.av.getAlignment().setSeqrep(seq); + } + else + { + if (ap.av.getAlignment().getSeqrep() == seq) + { + ap.av.getAlignment().setSeqrep(null); + } + else + { + ap.av.getAlignment().setSeqrep(seq); + } + } + refresh(); + } public void showNonconserved_itemStateChanged() {