X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=e27b9198f1cdae5692cccf81d3fca36dc0386399;hb=bad7a4b6634892d3174a940902e00704bf5007c1;hp=f92d67febe4d44e7c3b1c03fd0747e37c0a18a82;hpb=69bab27e77ceaca6d12e0de49f8fc62e01678f53;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index f92d67f..e27b919 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -326,17 +326,275 @@ public class AnnotationLabels extends JPanel implements MouseListener, return true; } - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ @Override public void mousePressed(MouseEvent evt) { getSelectedRow(evt.getY() - getScrollOffset()); oldY = evt.getY(); + if (!evt.isPopupTrigger()) + { + return; + } + evt.consume(); + // handle popup menu event + final AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + + JPopupMenu pop = new JPopupMenu( + MessageManager.getString("label.annotations")); + JMenuItem item = new JMenuItem(ADDNEW); + item.addActionListener(this); + pop.add(item); + if (selectedRow < 0) + { + if (hasHiddenRows) + { // let the user make everything visible again + item = new JMenuItem(SHOWALL); + item.addActionListener(this); + pop.add(item); + } + pop.show(this, evt.getX(), evt.getY()); + return; + } + item = new JMenuItem(EDITNAME); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(HIDE); + item.addActionListener(this); + pop.add(item); + // JAL-1264 hide all sequence-specific annotations of this type + if (selectedRow < aa.length) + { + if (aa[selectedRow].sequenceRef != null) + { + final String label = aa[selectedRow].label; + JMenuItem hideType = new JMenuItem(); + String text = MessageManager.getString("label.hide_all") + " " + + label; + hideType.setText(text); + hideType.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + AlignmentUtils.showOrHideSequenceAnnotations( + ap.av.getAlignment(), Collections.singleton(label), + null, false, false); + // for (AlignmentAnnotation ann : ap.av.getAlignment() + // .getAlignmentAnnotation()) + // { + // if (ann.sequenceRef != null && ann.label != null + // && ann.label.equals(label)) + // { + // ann.visible = false; + // } + // } + refresh(); + } + }); + pop.add(hideType); + } + } + item = new JMenuItem(DELETE); + item.addActionListener(this); + pop.add(item); + if (hasHiddenRows) + { + item = new JMenuItem(SHOWALL); + item.addActionListener(this); + pop.add(item); + } + item = new JMenuItem(OUTPUT_TEXT); + item.addActionListener(this); + pop.add(item); + // TODO: annotation object should be typed for autocalculated/derived + // property methods + if (selectedRow < aa.length) + { + final String label = aa[selectedRow].label; + if (!aa[selectedRow].autoCalculated) + { + if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) + { + // display formatting settings for this row. + pop.addSeparator(); + // av and sequencegroup need to implement same interface for + item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE, + aa[selectedRow].scaleColLabel); + item.addActionListener(this); + pop.add(item); + } + } + else if (label.indexOf("Consensus") > -1) + { + pop.addSeparator(); + // av and sequencegroup need to implement same interface for + final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( + MessageManager.getString("label.ignore_gaps_consensus"), + (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef + .getIgnoreGapsConsensus() : ap.av + .isIgnoreGapsConsensus()); + final AlignmentAnnotation aaa = aa[selectedRow]; + cbmi.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (aaa.groupRef != null) + { + // TODO: pass on reference to ap so the view can be updated. + aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); + ap.getAnnotationPanel().paint( + ap.getAnnotationPanel().getGraphics()); + } + else + { + ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); + } + } + }); + pop.add(cbmi); + // av and sequencegroup need to implement same interface for + if (aaa.groupRef != null) + { + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_group_histogram"), + aa[selectedRow].groupRef.isShowConsensusHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setShowConsensusHistogram(chist.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(chist); + final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( + MessageManager.getString("label.show_group_logo"), + aa[selectedRow].groupRef.isShowSequenceLogo()); + cprofl.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setshowSequenceLogo(cprofl.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cprofl); + final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( + MessageManager.getString("label.normalise_group_logo"), + aa[selectedRow].groupRef.isNormaliseSequenceLogo()); + cproflnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState()); + // automatically enable logo display if we're clicked + aaa.groupRef.setshowSequenceLogo(true); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cproflnorm); + } + else + { + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_histogram"), + av.isShowConsensusHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowConsensusHistogram(chist.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(chist); + final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( + MessageManager.getString("label.show_logo"), + av.isShowSequenceLogo()); + cprof.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowSequenceLogo(cprof.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cprof); + final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( + MessageManager.getString("label.normalise_logo"), + av.isNormaliseSequenceLogo()); + cprofnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowSequenceLogo(true); + av.setNormaliseSequenceLogo(cprofnorm.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cprofnorm); + } + final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); + consclipbrd.addActionListener(this); + pop.add(consclipbrd); + } + } + pop.show(this, evt.getX(), evt.getY()); + } /** @@ -503,379 +761,153 @@ public class AnnotationLabels extends JPanel implements MouseListener, // } // desc.append(""); // } - } - else - { - // begin the tooltip's html fragment - desc.append(""); - if (aa.hasScore()) - { - // TODO: limit precision of score to avoid noise from imprecise - // doubles - // (64.7 becomes 64.7+/some tiny value). - desc.append(" Score: " + aa.score); - } - } - if (desc.length() > 6) - { - desc.append(""); - this.setToolTipText(desc.toString()); - } - else - { - this.setToolTipText(null); - } - } - } - - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ - @Override - public void mouseClicked(MouseEvent evt) - { - final AlignmentAnnotation[] aa = ap.av.getAlignment() - .getAlignmentAnnotation(); - if (SwingUtilities.isLeftMouseButton(evt)) - { - if (selectedRow > -1 && selectedRow < aa.length) - { - if (aa[selectedRow].groupRef != null) - { - if (evt.getClickCount() >= 2) - { - // todo: make the ap scroll to the selection - not necessary, first - // click highlights/scrolls, second selects - ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); - ap.av.setSelectionGroup(// new SequenceGroup( - aa[selectedRow].groupRef); // ); - ap.paintAlignment(false); - PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); - ap.av.sendSelection(); - } - else - { - ap.getSeqPanel().ap.getIdPanel().highlightSearchResults( - aa[selectedRow].groupRef.getSequences(null)); - } - return; - } - else if (aa[selectedRow].sequenceRef != null) - { - if (evt.getClickCount() == 1) - { - ap.getSeqPanel().ap - .getIdPanel() - .highlightSearchResults( - Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef })); - } - else if (evt.getClickCount() >= 2) - { - ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); - 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.av.sendSelection(); - ap.paintAlignment(false); - PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); - } - - } - } - } - if (!evt.isPopupTrigger()) - { - return; - } - - JPopupMenu pop = new JPopupMenu( - MessageManager.getString("label.annotations")); - JMenuItem item = new JMenuItem(ADDNEW); - item.addActionListener(this); - pop.add(item); - if (selectedRow < 0) - { - if (hasHiddenRows) - { // let the user make everything visible again - item = new JMenuItem(SHOWALL); - item.addActionListener(this); - pop.add(item); - } - pop.show(this, evt.getX(), evt.getY()); - return; - } - item = new JMenuItem(EDITNAME); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(HIDE); - item.addActionListener(this); - pop.add(item); - // JAL-1264 hide all sequence-specific annotations of this type - if (selectedRow < aa.length) - { - if (aa[selectedRow].sequenceRef != null) - { - final String label = aa[selectedRow].label; - JMenuItem hideType = new JMenuItem(); - String text = MessageManager.getString("label.hide_all") + " " - + label; - hideType.setText(text); - hideType.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - AlignmentUtils.showOrHideSequenceAnnotations( - ap.av.getAlignment(), Collections.singleton(label), - null, false, false); - // for (AlignmentAnnotation ann : ap.av.getAlignment() - // .getAlignmentAnnotation()) - // { - // if (ann.sequenceRef != null && ann.label != null - // && ann.label.equals(label)) - // { - // ann.visible = false; - // } - // } - refresh(); - } - }); - pop.add(hideType); - } - } - item = new JMenuItem(DELETE); - item.addActionListener(this); - pop.add(item); - if (hasHiddenRows) - { - item = new JMenuItem(SHOWALL); - item.addActionListener(this); - pop.add(item); - } - item = new JMenuItem(OUTPUT_TEXT); - item.addActionListener(this); - pop.add(item); - // TODO: annotation object should be typed for autocalculated/derived - // property methods - if (selectedRow < aa.length) - { - final String label = aa[selectedRow].label; - if (!aa[selectedRow].autoCalculated) + } + else { - if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) + // begin the tooltip's html fragment + desc.append(""); + if (aa.hasScore()) { - // display formatting settings for this row. - pop.addSeparator(); - // av and sequencegroup need to implement same interface for - item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE, - aa[selectedRow].scaleColLabel); - item.addActionListener(this); - pop.add(item); + // TODO: limit precision of score to avoid noise from imprecise + // doubles + // (64.7 becomes 64.7+/some tiny value). + desc.append(" Score: " + aa.score); } } - else if (label.indexOf("Consensus") > -1) + if (desc.length() > 6) { - pop.addSeparator(); - // av and sequencegroup need to implement same interface for - final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( - MessageManager.getString("label.ignore_gaps_consensus"), - (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef - .getIgnoreGapsConsensus() : ap.av - .isIgnoreGapsConsensus()); - final AlignmentAnnotation aaa = aa[selectedRow]; - cbmi.addActionListener(new ActionListener() + desc.append(""); + this.setToolTipText(desc.toString()); + } + else + { + this.setToolTipText(null); + } + } + } + + @Override + public void mouseClicked(MouseEvent evt) + { + final AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + if (!evt.isPopupTrigger() && SwingUtilities.isLeftMouseButton(evt)) + { + if (selectedRow > -1 && selectedRow < aa.length) + { + if (aa[selectedRow].groupRef != null) { - @Override - public void actionPerformed(ActionEvent e) + if (evt.getClickCount() >= 2) { - if (aaa.groupRef != null) + // todo: make the ap scroll to the selection - not necessary, first + // click highlights/scrolls, second selects + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); + // process modifiers + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null + || sg == aa[selectedRow].groupRef + || !(jalview.util.Platform.isControlDown(evt) || evt + .isShiftDown())) { - // TODO: pass on reference to ap so the view can be updated. - aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); - ap.getAnnotationPanel().paint( - ap.getAnnotationPanel().getGraphics()); + 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 { - ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); + // 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); + PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + ap.av.sendSelection(); } - }); - pop.add(cbmi); - // av and sequencegroup need to implement same interface for - if (aaa.groupRef != null) - { - final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - MessageManager.getString("label.show_group_histogram"), - aa[selectedRow].groupRef.isShowConsensusHistogram()); - chist.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - aaa.groupRef.setShowConsensusHistogram(chist.getState()); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); - } - }); - pop.add(chist); - final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( - MessageManager.getString("label.show_group_logo"), - aa[selectedRow].groupRef.isShowSequenceLogo()); - cprofl.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - aaa.groupRef.setshowSequenceLogo(cprofl.getState()); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); - } - }); - pop.add(cprofl); - final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( - MessageManager.getString("label.normalise_group_logo"), - aa[selectedRow].groupRef.isNormaliseSequenceLogo()); - cproflnorm.addActionListener(new ActionListener() + else { - @Override - public void actionPerformed(ActionEvent e) - { - - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState()); - // automatically enable logo display if we're clicked - aaa.groupRef.setshowSequenceLogo(true); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); - } - }); - pop.add(cproflnorm); + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults( + aa[selectedRow].groupRef.getSequences(null)); + } + return; } - else + else if (aa[selectedRow].sequenceRef != null) { - final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - MessageManager.getString("label.show_histogram"), - av.isShowConsensusHistogram()); - chist.addActionListener(new ActionListener() + if (evt.getClickCount() == 1) { - @Override - public void actionPerformed(ActionEvent e) - { - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - av.setShowConsensusHistogram(chist.getState()); - ap.alignFrame.setMenusForViewport(); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); - } - }); - pop.add(chist); - final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( - MessageManager.getString("label.show_logo"), - av.isShowSequenceLogo()); - cprof.addActionListener(new ActionListener() + ap.getSeqPanel().ap + .getIdPanel() + .highlightSearchResults( + Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef })); + } + else if (evt.getClickCount() >= 2) { - @Override - public void actionPerformed(ActionEvent e) + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg != null) { - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - av.setShowSequenceLogo(cprof.getState()); - ap.alignFrame.setMenusForViewport(); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + // 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())) + { + sg = new SequenceGroup(sg); + sg.clear(); + sg.addSequence(aa[selectedRow].sequenceRef, false); + } + else + { + if (jalview.util.Platform.isControlDown(evt)) + { + sg.addOrRemove(aa[selectedRow].sequenceRef, true); + } + else + { + // notionally, we should also add intermediate sequences from + // last added sequence ? + sg.addSequence(aa[selectedRow].sequenceRef, true); + } + } } - }); - pop.add(cprof); - final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( - MessageManager.getString("label.normalise_logo"), - av.isNormaliseSequenceLogo()); - cprofnorm.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) + else { - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - av.setShowSequenceLogo(true); - av.setNormaliseSequenceLogo(cprofnorm.getState()); - ap.alignFrame.setMenusForViewport(); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + sg = new SequenceGroup(); + sg.setStartRes(0); + sg.setEndRes(ap.av.getAlignment().getWidth() - 1); + sg.addSequence(aa[selectedRow].sequenceRef, false); } - }); - pop.add(cprofnorm); + ap.av.setSelectionGroup(sg); + ap.paintAlignment(false); + PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + ap.av.sendSelection(); + } + } - final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); - consclipbrd.addActionListener(this); - pop.add(consclipbrd); } + return; } - pop.show(this, evt.getX(), evt.getY()); } /**