X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=85a2fbe1a3cd55b4ffef0ef498a3240470ba3571;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=7dcd3ac96b4694f82f1c4e5c34659f91bff4da82;hpb=276594c533ac5346dab8b49d14efae9b49aac5c9;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java index 7dcd3ac..85a2fbe 100755 --- a/src/jalview/appletgui/AnnotationLabels.java +++ b/src/jalview/appletgui/AnnotationLabels.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. @@ -455,7 +455,7 @@ public class AnnotationLabels extends Panel implements ActionListener, { popup.addSeparator(); final CheckboxMenuItem cbmi = new CheckboxMenuItem( - "Ignore Gaps In Consensus", + MessageManager.getString("label.ignore_gaps_consensus"), (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef .getIgnoreGapsConsensus() : ap.av .getIgnoreGapsConsensus()); @@ -480,7 +480,7 @@ public class AnnotationLabels extends Panel implements ActionListener, if (aaa.groupRef != null) { final CheckboxMenuItem chist = new CheckboxMenuItem( - "Show Group Histogram", + MessageManager.getString("label.show_group_histogram"), aa[selectedRow].groupRef.isShowConsensusHistogram()); chist.addItemListener(new ItemListener() { @@ -499,7 +499,7 @@ public class AnnotationLabels extends Panel implements ActionListener, }); popup.add(chist); final CheckboxMenuItem cprofl = new CheckboxMenuItem( - "Show Group Logo", + MessageManager.getString("label.show_group_logo"), aa[selectedRow].groupRef.isShowSequenceLogo()); cprofl.addItemListener(new ItemListener() { @@ -519,7 +519,7 @@ public class AnnotationLabels extends Panel implements ActionListener, popup.add(cprofl); final CheckboxMenuItem cprofn = new CheckboxMenuItem( - "Normalise Group Logo", + MessageManager.getString("label.normalise_group_logo"), aa[selectedRow].groupRef.isNormaliseSequenceLogo()); cprofn.addItemListener(new ItemListener() { @@ -542,7 +542,7 @@ public class AnnotationLabels extends Panel implements ActionListener, else { final CheckboxMenuItem chist = new CheckboxMenuItem( - "Show Histogram", av.isShowConsensusHistogram()); + MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram()); chist.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent e) @@ -564,7 +564,7 @@ public class AnnotationLabels extends Panel implements ActionListener, }); popup.add(chist); final CheckboxMenuItem cprof = new CheckboxMenuItem( - "Show Logo", av.isShowSequenceLogo()); + MessageManager.getString("label.show_logo"), av.isShowSequenceLogo()); cprof.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent e) @@ -587,7 +587,7 @@ public class AnnotationLabels extends Panel implements ActionListener, }); popup.add(cprof); final CheckboxMenuItem cprofn = new CheckboxMenuItem( - "Normalise Logo", av.isNormaliseSequenceLogo()); + MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo()); cprofn.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent e) @@ -648,17 +648,40 @@ public class AnnotationLabels extends Panel implements ActionListener, } else if (aa[selectedRow].sequenceRef != null) { - Vector sr = new Vector(); - sr.addElement(aa[selectedRow].sequenceRef); if (evt.getClickCount() == 1) { - ap.seqPanel.ap.idPanel.highlightSearchResults(sr); + ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays + .asList(new SequenceI[] + { aa[selectedRow].sequenceRef })); } else if (evt.getClickCount() >= 2) { ap.seqPanel.ap.idPanel.highlightSearchResults(null); - SequenceGroup sg = new SequenceGroup(); - sg.addSequence(aa[selectedRow].sequenceRef, false); + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg!=null) + { + // we make a copy rather than edit the current selection if no modifiers pressed + // see Enhancement JAL-1557 + if (!(evt.isControlDown() || evt.isShiftDown())) + { + sg = new SequenceGroup(sg); + sg.clear(); + sg.addSequence(aa[selectedRow].sequenceRef, false); + } else { + if (evt.isControlDown()) + { + sg.addOrRemove(aa[selectedRow].sequenceRef, true); + } else { + // notionally, we should also add intermediate sequences from last added sequence ? + sg.addSequence(aa[selectedRow].sequenceRef, true); + } + } + } else { + sg = new SequenceGroup(); + sg.setStartRes(0); + sg.setEndRes(ap.av.getAlignment().getWidth()-1); + sg.addSequence(aa[selectedRow].sequenceRef, false); + } ap.av.setSelectionGroup(sg); ap.paintAlignment(false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());