X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=acdae460bd1286bc89af012c1723e3b9985ef638;hb=e4d3bc400c467cf2547a1c99e9c73ab19fddd015;hp=9b14901641663c9804f6f7c1e3e6bcad04bc0829;hpb=3c1b3076db1b85fc726b2e67a3b7b708211758be;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 9b14901..acdae46 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. * @@ -157,7 +157,7 @@ public class APopupMenu extends java.awt.PopupMenu implements 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); } @@ -169,7 +169,7 @@ public class APopupMenu extends java.awt.PopupMenu implements remove(groupMenu); } - if (seq!=null && links != null && links.size() > 0) + if (links != null && links.size() > 0) { Menu linkMenu = new Menu("Link"); String link; @@ -300,12 +300,12 @@ 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.alignment.findIndex(seq); + final int index = ap.av.getAlignment().findIndex(seq); if (ap.av.adjustForHiddenSeqs(index) - ap.av.adjustForHiddenSeqs(index - 1) > 1) @@ -513,8 +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); @@ -529,44 +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; @@ -588,7 +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); @@ -652,6 +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(), @@ -833,8 +799,7 @@ 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,ap.av.getHiddenRepSequences()); refresh(); } @@ -897,8 +862,8 @@ 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()); @@ -927,8 +892,8 @@ 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(); } @@ -939,8 +904,8 @@ 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(); } @@ -962,16 +927,11 @@ 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(); } @@ -991,7 +951,7 @@ 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; @@ -1000,7 +960,7 @@ 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); }