X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=b45fa6b45e051704d94ca6e18ac02a550de7d9c3;hb=a822fc744dcc06e6a8d2399218da0d0dfd56cf2b;hp=25a7a934a52b84f84ffb9322bd3c84a851dcf299;hpb=e6172518e085efc5703a2e0ce6675fe5f81ea253;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 25a7a93..b45fa6b 100755 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, 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 program 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 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program 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. + * 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. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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 . */ package jalview.appletgui; @@ -113,6 +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) @@ -148,12 +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.getShowunconserved()); - if (!ap.av.alignment.getGroups().contains(sg)) + displayNonconserved.setState(sg.getShowNonconserved()); + if (!ap.av.getAlignment().getGroups().contains(sg)) { groupMenu.remove(unGroupMenuItem); } @@ -181,13 +185,13 @@ 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 - DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq - .getDBRef(), new String[] - { target }); + DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs( + seq.getDBRef(), new String[] + { target }); // collect id string too String id = seq.getName(); String descr = seq.getDescription(); @@ -296,9 +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); + } } } @@ -447,6 +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(); @@ -493,9 +512,9 @@ 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); + ap.av.getGapCharacter()), + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); ap.alignFrame.addHistoryItem(editCommand); @@ -510,44 +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; @@ -569,7 +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); @@ -587,26 +570,25 @@ public class APopupMenu extends java.awt.PopupMenu implements return; } - - int rsize=0,gSize = sg.getSize(); - SequenceI[] rseqs,seqs = new SequenceI[gSize]; - SequenceFeature[] tfeatures,features = new SequenceFeature[gSize]; - + int rsize = 0, gSize = sg.getSize(); + SequenceI[] rseqs, seqs = new SequenceI[gSize]; + SequenceFeature[] tfeatures, features = new SequenceFeature[gSize]; + for (int i = 0; i < gSize; i++) { int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); - if (start<=end) + if (start <= end) { seqs[rsize] = sg.getSequenceAt(i); - features[rsize] = new SequenceFeature(null, null, null, start, end, - "Jalview"); + features[rsize] = new SequenceFeature(null, null, null, start, + end, "Jalview"); rsize++; } } rseqs = new SequenceI[rsize]; tfeatures = new SequenceFeature[rsize]; - System.arraycopy(seqs,0,rseqs, 0, rsize); + System.arraycopy(seqs, 0, rseqs, 0, rsize); System.arraycopy(features, 0, tfeatures, 0, rsize); features = tfeatures; seqs = rseqs; @@ -632,19 +614,22 @@ 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, + "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(), new Alignment(ap.av - .getSelectionAsNewSequence()), ap.av.showJVSuffix)); + cap.setText(new jalview.io.AppletFormatAdapter().formatSequences( + e.getActionCommand(), + new Alignment(ap.av.getSelectionAsNewSequence()), + ap.av.showJVSuffix)); } void editName() { - EditNameDialog dialog = new EditNameDialog(seq.getName(), seq - .getDescription(), " Sequence Name", + EditNameDialog dialog = new EditNameDialog(seq.getName(), + seq.getDescription(), " Sequence Name", "Sequence Description", ap.alignFrame, "Edit Sequence Name / Description", 500, 100, true); @@ -677,7 +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); } } @@ -713,10 +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); @@ -784,7 +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); @@ -797,6 +787,7 @@ public class APopupMenu extends java.awt.PopupMenu implements hideSeqs.addActionListener(this); repGroup.addActionListener(this); revealAll.addActionListener(this); + revealSeq.addActionListener(this); } void refresh() @@ -807,9 +798,9 @@ 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.getSequences(ap.av.getHiddenRepSequences()), + ap.av.getAlignment().getWidth()); refresh(); } @@ -871,9 +862,9 @@ 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()); @@ -901,9 +892,9 @@ 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(); } @@ -913,9 +904,9 @@ 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(); } @@ -937,16 +928,11 @@ public class APopupMenu extends java.awt.PopupMenu implements if (conservationMenuItem.getState()) { - Conservation c = new Conservation("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.cs.setConservation(Conservation.calculateConservation("Group", + 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(); } @@ -966,7 +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; @@ -975,7 +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); } @@ -994,7 +980,7 @@ public class APopupMenu extends java.awt.PopupMenu implements public void showNonconserved_itemStateChanged() { - getGroup().setShowunconserved(this.displayNonconserved.getState()); + getGroup().setShowNonconserved(this.displayNonconserved.getState()); refresh(); } @@ -1035,6 +1021,7 @@ public class APopupMenu extends java.awt.PopupMenu implements } ap.av.hideSequence(hseqs); + ap.av.sendSelection(); } }