X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=b45fa6b45e051704d94ca6e18ac02a550de7d9c3;hb=b4877bc99e12cf4465e43e090e19277c3139ce77;hp=5288fe4862f4bc090b3f6c2455a9758467ed711c;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 5288fe4..b45fa6b 100755 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -112,6 +112,11 @@ public class APopupMenu extends java.awt.PopupMenu implements MenuItem revealAll = new MenuItem(); + MenuItem revealSeq = new MenuItem(); + /** + * index of sequence to be revealed + */ + int revealSeq_index=-1; Menu menu1 = new Menu(); public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links) @@ -147,12 +152,12 @@ public class APopupMenu extends java.awt.PopupMenu implements if (sg != null && sg.getSize() > 0) { - editGroupName.setLabel(sg.getName()); + editGroupName.setLabel("Name: "+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)) { groupMenu.remove(unGroupMenuItem); } @@ -180,7 +185,7 @@ public class APopupMenu extends java.awt.PopupMenu implements final String target = urlLink.getTarget(); // link.substring(0, // link.indexOf("|")); final String label = urlLink.getLabel(); - if (urlLink.isDynamic()) + if (seq!=null && urlLink.isDynamic()) { // collect matching db-refs @@ -295,9 +300,20 @@ public class APopupMenu extends java.awt.PopupMenu implements remove(seqMenu); } - if (!ap.av.hasHiddenRows) + if (!ap.av.hasHiddenRows()) { remove(revealAll); + remove(revealSeq); + } else { + final int index = ap.av.getAlignment().findIndex(seq); + + if (ap.av.adjustForHiddenSeqs(index) + - ap.av.adjustForHiddenSeqs(index - 1) > 1) + { + revealSeq_index=index; + } else { + remove(revealSeq); + } } } @@ -446,6 +462,10 @@ public class APopupMenu extends java.awt.PopupMenu implements { hideSequences(true); } + else if (source == revealSeq) + { + ap.av.showSequence(revealSeq_index); + } else if (source == revealAll) { ap.av.showAllHiddenSeqs(); @@ -493,8 +513,8 @@ 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); @@ -509,44 +529,8 @@ 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; @@ -568,7 +552,7 @@ public class APopupMenu extends java.awt.PopupMenu implements } ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, - sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); @@ -632,6 +616,8 @@ public class APopupMenu extends java.awt.PopupMenu implements 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 + // TODO consider using getSequenceSelection instead here cap.setText(new jalview.io.AppletFormatAdapter().formatSequences( e.getActionCommand(), @@ -676,7 +662,7 @@ public class APopupMenu extends java.awt.PopupMenu implements cap.setPDBImport(seq); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300); + jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file for sequence "+seq.getName(), 400, 300); } } @@ -712,10 +698,12 @@ public class APopupMenu extends java.awt.PopupMenu implements hideSeqs.setLabel("Hide Sequences"); repGroup.setLabel("Represent Group with"); revealAll.setLabel("Reveal All"); + revealSeq.setLabel("Reveal Sequences"); menu1.setLabel("Group"); add(groupMenu); this.add(seqMenu); this.add(hideSeqs); + this.add(revealSeq); this.add(revealAll); groupMenu.add(editGroupName); groupMenu.add(editMenu); @@ -783,7 +771,10 @@ public class APopupMenu extends java.awt.PopupMenu implements toLower.addActionListener(this); editMenu.add(toggleCase); seqMenu.add(sequenceName); - seqMenu.add(pdb); + if (!ap.av.applet.useXtrnalSviewer) + { + seqMenu.add(pdb); + } seqMenu.add(repGroup); menu1.add(unGroupMenuItem); menu1.add(colourMenu); @@ -796,6 +787,7 @@ public class APopupMenu extends java.awt.PopupMenu implements hideSeqs.addActionListener(this); repGroup.addActionListener(this); revealAll.addActionListener(this); + revealSeq.addActionListener(this); } void refresh() @@ -807,8 +799,8 @@ public class APopupMenu extends java.awt.PopupMenu implements { SequenceGroup sg = getGroup(); sg.cs = new ClustalxColourScheme( - sg.getSequences(ap.av.hiddenRepSequences), - ap.av.alignment.getWidth()); + sg.getSequences(ap.av.getHiddenRepSequences()), + ap.av.getAlignment().getWidth()); refresh(); } @@ -871,8 +863,8 @@ 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.getSequences(ap.av.getHiddenRepSequences()), 0, + ap.av.getAlignment().getWidth())); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); @@ -901,8 +893,8 @@ 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.getSequences(ap.av.getHiddenRepSequences()), 0, + ap.av.getAlignment().getWidth())); refresh(); } @@ -913,8 +905,8 @@ 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.getSequences(ap.av.getHiddenRepSequences()), 0, + ap.av.getAlignment().getWidth())); refresh(); } @@ -936,16 +928,11 @@ public class APopupMenu extends java.awt.PopupMenu implements if (conservationMenuItem.getState()) { - Conservation c = new Conservation("Group", + sg.cs.setConservation(Conservation.calculateConservation("Group", ResidueProperties.propHash, 3, - sg.getSequences(ap.av.hiddenRepSequences), 0, - ap.av.alignment.getWidth()); - - c.calculate(); - c.verdict(false, ap.av.ConsPercGaps); - - sg.cs.setConservation(c); - + sg.getSequences(ap.av.getHiddenRepSequences()), 0, + ap.av.getAlignment().getWidth(), + false, ap.av.getConsPercGaps(),false)); SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); SliderPanel.showConservationSlider(); } @@ -965,7 +952,7 @@ 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; @@ -974,7 +961,7 @@ 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); } @@ -1034,6 +1021,7 @@ public class APopupMenu extends java.awt.PopupMenu implements } ap.av.hideSequence(hseqs); + ap.av.sendSelection(); } }