X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=6e3257d91018a7f32fea9561178338b8f058feb4;hb=8874aa9fd956f7bc248fe15a669a6d8d81d6891b;hp=487d1308872b97aca11fd30cb50b64ce39f883b1;hpb=3705d44c1e45abab9180067ed1e2862b9dea65d1;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java index 487d130..6e3257d 100755 --- a/src/jalview/appletgui/AnnotationLabels.java +++ b/src/jalview/appletgui/AnnotationLabels.java @@ -23,6 +23,7 @@ package jalview.appletgui; import jalview.analysis.AlignmentUtils; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.util.MessageManager; @@ -50,10 +51,9 @@ import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.util.Arrays; import java.util.Collections; -import java.util.Vector; -public class AnnotationLabels extends Panel implements ActionListener, - MouseListener, MouseMotionListener +public class AnnotationLabels extends Panel + implements ActionListener, MouseListener, MouseMotionListener { Image image; @@ -201,8 +201,9 @@ public class AnnotationLabels extends Panel implements ActionListener, ap.alignFrame); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle() - + " - " + aa[selectedRow].label, 500, 100); + jalview.bin.JalviewLite.addFrame(frame, + ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500, + 100); cap.setText(aa[selectedRow].toString()); } else if (evt.getActionCommand().equals(COPYCONS_SEQ)) @@ -225,13 +226,15 @@ public class AnnotationLabels extends Panel implements ActionListener, ap.annotationPanel.adjustPanelHeight(); setSize(getSize().width, ap.annotationPanel.getSize().height); ap.validate(); - ap.paintAlignment(true); + // TODO: only paint if we needed to + ap.paintAlignment(true, true); } boolean editLabelDescription(AlignmentAnnotation annotation) { - Checkbox padGaps = new Checkbox("Fill Empty Gaps With \"" - + ap.av.getGapCharacter() + "\"", annotation.padGaps); + Checkbox padGaps = new Checkbox( + "Fill Empty Gaps With \"" + ap.av.getGapCharacter() + "\"", + annotation.padGaps); EditNameDialog dialog = new EditNameDialog(annotation.label, annotation.description, " Annotation Label", @@ -320,8 +323,9 @@ public class AnnotationLabels extends Panel implements ActionListener, if (resizePanel) { - Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder - .getSize(), f = ap.seqPanelHolder.getSize(); + Dimension d = ap.annotationPanelHolder.getSize(), + e = ap.annotationSpaceFillerHolder.getSize(), + f = ap.seqPanelHolder.getSize(); int dif = evt.getY() - oldY; dif /= ap.av.getCharHeight(); @@ -331,15 +335,16 @@ public class AnnotationLabels extends Panel implements ActionListener, { ap.annotationPanel.setSize(d.width, d.height - dif); setSize(new Dimension(e.width, d.height - dif)); - ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width, - d.height - dif)); - ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height - - dif)); + ap.annotationSpaceFillerHolder + .setSize(new Dimension(e.width, d.height - dif)); + ap.annotationPanelHolder + .setSize(new Dimension(d.width, d.height - dif)); ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0, av.calcPanelHeight()); f.height += dif; ap.seqPanelHolder.setPreferredSize(f); - ap.setScrollValues(av.getStartRes(), av.getStartSeq()); + ap.setScrollValues(av.getRanges().getStartRes(), + av.getRanges().getStartSeq()); ap.validate(); // ap.paintAlignment(true); ap.addNotify(); @@ -450,7 +455,8 @@ public class AnnotationLabels extends Panel implements ActionListener, .getAlignmentAnnotation(); // DETECT RIGHT MOUSE BUTTON IN AWT - if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) + if ((evt.getModifiers() + & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) { PopupMenu popup = new PopupMenu( @@ -524,9 +530,10 @@ public class AnnotationLabels extends Panel implements ActionListener, popup.addSeparator(); final CheckboxMenuItem cbmi = new CheckboxMenuItem( MessageManager.getString("label.ignore_gaps_consensus"), - (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef - .getIgnoreGapsConsensus() : ap.av - .isIgnoreGapsConsensus()); + (aa[selectedRow].groupRef != null) + ? aa[selectedRow].groupRef + .getIgnoreGapsConsensus() + : ap.av.isIgnoreGapsConsensus()); final AlignmentAnnotation aaa = aa[selectedRow]; cbmi.addItemListener(new ItemListener() { @@ -542,7 +549,7 @@ public class AnnotationLabels extends Panel implements ActionListener, { ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); } - ap.paintAlignment(true); + ap.paintAlignment(true, true); } }); popup.add(cbmi); @@ -630,10 +637,10 @@ public class AnnotationLabels extends Panel implements ActionListener, // can be // updated. av.setShowConsensusHistogram(chist.getState()); - ap.alignFrame.showConsensusHistogram.setState(chist - .getState()); // TODO: implement - // ap.updateGUI()/alignFrame.updateGUI - // for applet + ap.alignFrame.showConsensusHistogram + .setState(chist.getState()); // TODO: implement + // ap.updateGUI()/alignFrame.updateGUI + // for applet ap.repaint(); // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); } @@ -679,11 +686,12 @@ public class AnnotationLabels extends Panel implements ActionListener, // can be // updated. av.setShowSequenceLogo(true); - ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO: - // implement - // ap.updateGUI()/alignFrame.updateGUI - // for - // applet + ap.alignFrame.normSequenceLogo + .setState(cprofn.getState()); // TODO: + // implement + // ap.updateGUI()/alignFrame.updateGUI + // for + // applet av.setNormaliseSequenceLogo(cprofn.getState()); ap.repaint(); // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); @@ -712,17 +720,51 @@ public class AnnotationLabels extends Panel implements ActionListener, // todo: make the ap scroll to the selection - not necessary, first // click highlights/scrolls, second selects ap.seqPanel.ap.idPanel.highlightSearchResults(null); - ap.av.setSelectionGroup(// new SequenceGroup( - aa[selectedRow].groupRef); // ); - ap.av.sendSelection(); - ap.paintAlignment(false); + // process modifiers + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null || sg == aa[selectedRow].groupRef + || !(jalview.util.Platform.isControlDown(evt) + || evt.isShiftDown())) + { + if (jalview.util.Platform.isControlDown(evt) + || evt.isShiftDown()) + { + // clone a new selection group from the associated group + ap.av.setSelectionGroup( + new SequenceGroup(aa[selectedRow].groupRef)); + } + else + { + // set selection to the associated group so it can be edited + ap.av.setSelectionGroup(aa[selectedRow].groupRef); + } + } + else + { + // modify current selection with associated group + int remainToAdd = aa[selectedRow].groupRef.getSize(); + for (SequenceI sgs : aa[selectedRow].groupRef.getSequences()) + { + if (jalview.util.Platform.isControlDown(evt)) + { + sg.addOrRemove(sgs, --remainToAdd == 0); + } + else + { + // notionally, we should also add intermediate sequences from + // last added sequence ? + sg.addSequence(sgs, --remainToAdd == 0); + } + } + } + ap.paintAlignment(false, false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + ap.av.sendSelection(); } else { - ap.seqPanel.ap.idPanel - .highlightSearchResults(aa[selectedRow].groupRef - .getSequences(null)); + ap.seqPanel.ap.idPanel.highlightSearchResults( + aa[selectedRow].groupRef.getSequences(null)); } return; } @@ -731,8 +773,8 @@ public class AnnotationLabels extends Panel implements ActionListener, if (evt.getClickCount() == 1) { ap.seqPanel.ap.idPanel - .highlightSearchResults(Arrays - .asList(new SequenceI[] { aa[selectedRow].sequenceRef })); + .highlightSearchResults(Arrays.asList(new SequenceI[] + { aa[selectedRow].sequenceRef })); } else if (evt.getClickCount() >= 2) { @@ -743,8 +785,8 @@ public class AnnotationLabels extends Panel implements ActionListener, // we make a copy rather than edit the current selection if no // modifiers pressed // see Enhancement JAL-1557 - if (!(jalview.util.Platform.isControlDown(evt) || evt - .isShiftDown())) + if (!(jalview.util.Platform.isControlDown(evt) + || evt.isShiftDown())) { sg = new SequenceGroup(sg); sg.clear(); @@ -772,7 +814,7 @@ public class AnnotationLabels extends Panel implements ActionListener, sg.addSequence(aa[selectedRow].sequenceRef, false); } ap.av.setSelectionGroup(sg); - ap.paintAlignment(false); + ap.paintAlignment(false, false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); ap.av.sendSelection(); } @@ -796,17 +838,13 @@ public class AnnotationLabels extends Panel implements ActionListener, return; } jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer(); - jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" - + sq.getStart() + "\t" + sq.getEnd() + "\t" - + sq.getSequenceAsString() + "\n"); + jalview.appletgui.AlignFrame.copiedSequences + .append(sq.getName() + "\t" + sq.getStart() + "\t" + sq.getEnd() + + "\t" + sq.getSequenceAsString() + "\n"); if (av.hasHiddenColumns()) { - jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector(); - for (int[] region : av.getColumnSelection().getHiddenColumns()) - { - jalview.appletgui.AlignFrame.copiedHiddenColumns - .addElement(new int[] { region[0], region[1] }); - } + jalview.appletgui.AlignFrame.copiedHiddenColumns = new HiddenColumns( + av.getAlignment().getHiddenColumns()); } }