X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=58c7703f65e3c356f6d7a4d009a77eb964176e06;hb=3b4233b78bba3c53c98fc9b9166b267e5b744411;hp=17bc65f71e41379f5f8fe3a24953de715502b8a9;hpb=b65330720abd1329eac5fddbed9516b8302abe52;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java old mode 100755 new mode 100644 index 17bc65f..58c7703 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -1,19 +1,22 @@ /* - * 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; @@ -26,8 +29,10 @@ import jalview.analysis.*; import jalview.commands.*; import jalview.datamodel.*; import jalview.schemes.*; +import jalview.util.MessageManager; import jalview.util.UrlLink; import jalview.io.AppletFormatAdapter; +import jalview.io.SequenceAnnotationReport; public class APopupMenu extends java.awt.PopupMenu implements ActionListener, ItemListener @@ -68,6 +73,8 @@ 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 +87,21 @@ 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 +113,32 @@ 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 editSequence = new MenuItem( + MessageManager.getString("label.edit_sequence")); - MenuItem sequenceFeature = new MenuItem("Create Sequence Feature"); + MenuItem sequenceDetails = new MenuItem( + MessageManager.getString("label.sequence_details") + "..."); - MenuItem editSequence = new MenuItem("Edit Sequence"); + MenuItem selSeqDetails = new MenuItem( + MessageManager.getString("label.sequence_details") + "..."); 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 +174,23 @@ 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.alignment.getGroups().contains(sg)) + 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 +201,7 @@ 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 +215,7 @@ 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 @@ -293,25 +323,31 @@ public class APopupMenu extends java.awt.PopupMenu implements if (seq != null) { seqMenu.setLabel(seq.getName()); - repGroup.setLabel("Represent Group with " + seq.getName()); + repGroup.setLabel(MessageManager.formatMessage( + "label.represent_group_with", new String[] + { seq.getName() })); } else { remove(seqMenu); } - if (!ap.av.hasHiddenRows) + if (!ap.av.hasHiddenRows()) { remove(revealAll); remove(revealSeq); - } else { - final int index = ap.av.alignment.findIndex(seq); + } + 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 +482,23 @@ public class APopupMenu extends java.awt.PopupMenu implements unGroupMenuItem_actionPerformed(); } + else if (source == createGroupMenuItem) + { + createGroupMenuItem_actionPerformed(); + } + else if (source == sequenceName) { editName(); } + else if (source == sequenceDetails) + { + showSequenceDetails(); + } + else if (source == selSeqDetails) + { + showSequenceSelectionDetails(); + } else if (source == pdb) { addPDB(); @@ -513,8 +562,9 @@ public class APopupMenu extends java.awt.PopupMenu implements EditCommand editCommand = new EditCommand("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); @@ -529,44 +579,8 @@ public class APopupMenu extends java.awt.PopupMenu implements Vector regions = new Vector(); if (sg != null) { - int start = sg.getStartRes(); - int end = sg.getEndRes() + 1; - - do - { - if (ap.av.hasHiddenColumns) - { - if (start == 0) - { - start = ap.av.colSel.adjustForHiddenColumns(start); - } - - end = ap.av.colSel.getHiddenBoundaryRight(start); - if (start == end) - { - end = sg.getEndRes() + 1; - } - if (end > sg.getEndRes()) - { - end = sg.getEndRes() + 1; - } - } - - regions.addElement(new int[] - { start, end }); - - if (ap.av.hasHiddenColumns) - { - start = ap.av.colSel.adjustForHiddenColumns(end); - start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1; - } - } while (end < sg.getEndRes()); - - int[][] startEnd = new int[regions.size()][2]; - for (int i = 0; i < regions.size(); i++) - { - startEnd[i] = (int[]) regions.elementAt(i); - } + int[][] startEnd = ap.av.getVisibleRegionBoundaries( + sg.getStartRes(), sg.getEndRes() + 1); String description; int caseChange; @@ -588,8 +602,8 @@ public class APopupMenu extends java.awt.PopupMenu implements } ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, - sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, - caseChange); + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); @@ -650,14 +664,60 @@ 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)); + + } + + 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.minmax + : 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() @@ -692,57 +752,71 @@ public class APopupMenu extends java.awt.PopupMenu implements 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); @@ -805,12 +879,14 @@ public class APopupMenu extends java.awt.PopupMenu implements toLower.addActionListener(this); editMenu.add(toggleCase); seqMenu.add(sequenceName); + // 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); @@ -832,9 +908,7 @@ public class APopupMenu extends java.awt.PopupMenu implements 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(); } @@ -896,9 +970,8 @@ public class APopupMenu extends java.awt.PopupMenu implements if (abovePIDColour.getState()) { - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), 0, - ap.av.alignment.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()); @@ -926,9 +999,8 @@ public class APopupMenu extends java.awt.PopupMenu implements { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), 0, - ap.av.alignment.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); refresh(); } @@ -938,9 +1010,8 @@ public class APopupMenu extends java.awt.PopupMenu implements sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), 0, - ap.av.alignment.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); refresh(); } @@ -963,10 +1034,9 @@ public class APopupMenu extends java.awt.PopupMenu implements { sg.cs.setConservation(Conservation.calculateConservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(ap.av.hiddenRepSequences), 0, - ap.av.alignment.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(); } @@ -986,7 +1056,7 @@ public class APopupMenu extends java.awt.PopupMenu implements // 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; @@ -995,11 +1065,17 @@ public class APopupMenu extends java.awt.PopupMenu implements void unGroupMenuItem_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); - ap.av.alignment.deleteGroup(sg); + ap.av.getAlignment().deleteGroup(sg); ap.av.setSelectionGroup(null); ap.paintAlignment(true); } + void createGroupMenuItem_actionPerformed() + { + getGroup(); // implicitly create group + refresh(); + } + public void showColourText_itemStateChanged() { getGroup().setColourText(showColourText.getState());