From: tcofoegbu Date: Tue, 26 Apr 2016 16:42:45 +0000 (+0100) Subject: merge X-Git-Tag: Release_2_10_0~247 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=743a0473c959092ec7c80bdb8169a541d33657cd;hp=a425013582780002a90b7b5acf2ee063b847784d;p=jalview.git merge --- diff --git a/build.xml b/build.xml index 00fdf04..57cd9d2 100755 --- a/build.xml +++ b/build.xml @@ -421,13 +421,11 @@ + - - - + - diff --git a/lib/castor-1.1-cycle-xml.jar b/lib/castor-1.1-cycle-xml.jar index 1cfc700..5070435 100644 Binary files a/lib/castor-1.1-cycle-xml.jar and b/lib/castor-1.1-cycle-xml.jar differ diff --git a/lib/min-jabaws-client-2.1.0.jar b/lib/min-jabaws-client-2.1.0.jar index 7ad030a..ea5a1f4 100644 Binary files a/lib/min-jabaws-client-2.1.0.jar and b/lib/min-jabaws-client-2.1.0.jar differ diff --git a/lib/quaqua-filechooser-only-8.0.jar b/lib/quaqua-filechooser-only-8.0.jar index 429fe77..182e0da 100644 Binary files a/lib/quaqua-filechooser-only-8.0.jar and b/lib/quaqua-filechooser-only-8.0.jar differ diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 8fe3bca..1eeda98 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -51,7 +51,6 @@ import java.util.Map; import java.util.Vector; import javax.swing.UIManager; -import javax.swing.UnsupportedLookAndFeelException; /** * Main class for Jalview Application
@@ -68,6 +67,7 @@ public class Jalview // grab all the rights we can the JVM Policy.setPolicy(new Policy() { + @Override public PermissionCollection getPermissions(CodeSource codesource) { Permissions perms = new Permissions(); @@ -75,6 +75,7 @@ public class Jalview return (perms); } + @Override public void refresh() { } @@ -178,7 +179,7 @@ public class Jalview } catch (Exception ex) { } - if (new Platform().isAMac()) + if (Platform.isAMac()) { System.setProperty("com.apple.mrj.application.apple.menu.about.name", "Jalview"); @@ -187,10 +188,10 @@ public class Jalview { UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager .getLookAndFeel()); - } catch (UnsupportedLookAndFeelException e) + } catch (Throwable e) { - // TODO Auto-generated catch block - e.printStackTrace(); + System.err.println("Failed to set QuaQua look and feel: " + + e.toString()); } } @@ -729,6 +730,7 @@ public class Jalview + "\n\n(you can enable or disable usage tracking in the preferences)", new Runnable() { + @Override public void run() { Cache.log @@ -738,6 +740,7 @@ public class Jalview } }, new Runnable() { + @Override public void run() { Cache.log.debug("Not enabling Google Tracking."); @@ -1040,6 +1043,7 @@ public class Jalview class rnabuttonlistener implements ActionListener { + @Override public void actionPerformed(ActionEvent arg0) { System.out.println("Good idea ! "); @@ -1049,6 +1053,7 @@ class rnabuttonlistener implements ActionListener class pbuttonlistener implements ActionListener { + @Override public void actionPerformed(ActionEvent arg0) { @@ -1169,6 +1174,7 @@ class FeatureFetcher new Thread(new Runnable() { + @Override public void run() { synchronized (us) diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index f92d67f..68df498 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -326,418 +326,136 @@ 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(); - } - - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ - @Override - public void mouseReleased(MouseEvent evt) - { - int start = selectedRow; - getSelectedRow(evt.getY() - getScrollOffset()); - int end = selectedRow; - - if (start != end) - { - // Swap these annotations - AlignmentAnnotation startAA = ap.av.getAlignment() - .getAlignmentAnnotation()[start]; - if (end == -1) - { - end = ap.av.getAlignment().getAlignmentAnnotation().length - 1; - } - AlignmentAnnotation endAA = ap.av.getAlignment() - .getAlignmentAnnotation()[end]; - - ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; - ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; - } - - resizePanel = false; - dragEvent = null; - repaint(); - ap.getAnnotationPanel().repaint(); - } - - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ - @Override - public void mouseEntered(MouseEvent evt) - { - if (evt.getY() < 10) + if (!evt.isPopupTrigger()) { - resizePanel = true; - repaint(); + return; } - } + evt.consume(); + // handle popup menu event + final AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ - @Override - public void mouseExited(MouseEvent evt) - { - if (dragEvent == null) + JPopupMenu pop = new JPopupMenu( + MessageManager.getString("label.annotations")); + JMenuItem item = new JMenuItem(ADDNEW); + item.addActionListener(this); + pop.add(item); + if (selectedRow < 0) { - resizePanel = false; - repaint(); + 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; } - } - - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ - @Override - public void mouseDragged(MouseEvent evt) - { - dragEvent = evt; - - if (resizePanel) + 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) { - Dimension d = ap.annotationScroller.getPreferredSize(); - int dif = evt.getY() - oldY; - - dif /= ap.av.getCharHeight(); - dif *= ap.av.getCharHeight(); - - if ((d.height - dif) > 20) + if (aa[selectedRow].sequenceRef != null) { - ap.annotationScroller.setPreferredSize(new Dimension(d.width, - d.height - dif)); - d = ap.annotationSpaceFillerHolder.getPreferredSize(); - ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension( - d.width, d.height - dif)); - ap.paintAlignment(true); + 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); } - - ap.addNotify(); } - else + item = new JMenuItem(DELETE); + item.addActionListener(this); + pop.add(item); + if (hasHiddenRows) { - repaint(); + item = new JMenuItem(SHOWALL); + item.addActionListener(this); + pop.add(item); } - } - - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ - @Override - public void mouseMoved(MouseEvent evt) - { - resizePanel = evt.getY() < 10; - - getSelectedRow(evt.getY() - getScrollOffset()); - - if (selectedRow > -1 - && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow) + 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) { - AlignmentAnnotation aa = ap.av.getAlignment() - .getAlignmentAnnotation()[selectedRow]; - - StringBuffer desc = new StringBuffer(); - if (aa.description != null - && !aa.description.equals("New description")) + final String label = aa[selectedRow].label; + if (!aa[selectedRow].autoCalculated) { - // TODO: we could refactor and merge this code with the code in - // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature - // tooltips - desc.append(aa.getDescription(true).trim()); - // check to see if the description is an html fragment. - if (desc.length() < 6 - || (desc.substring(0, 6).toLowerCase().indexOf("") < 0)) + if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) { - // clean the description ready for embedding in html - desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc) - .replaceAll("<")); - desc.insert(0, ""); + // 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 + } + 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() { - // remove terminating html if any - int i = desc.substring(desc.length() - 7).toLowerCase() - .lastIndexOf(""); - if (i > -1) + @Override + public void actionPerformed(ActionEvent e) { - desc.setLength(desc.length() - 7 + i); + 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); + } } - } - if (aa.hasScore()) - { - desc.append("
"); - } - // if (aa.hasProperties()) - // { - // desc.append(""); - // for (String prop : aa.getProperties()) - // { - // desc.append(""); - // } - // desc.append("
" + prop + "" - // + aa.getProperty(prop) + "
"); - // } - } - 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) - { - 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) + }); + 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"), @@ -876,6 +594,282 @@ public class AnnotationLabels extends JPanel implements MouseListener, } } pop.show(this, evt.getX(), evt.getY()); + + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void mouseReleased(MouseEvent evt) + { + int start = selectedRow; + getSelectedRow(evt.getY() - getScrollOffset()); + int end = selectedRow; + + if (start != end) + { + // Swap these annotations + AlignmentAnnotation startAA = ap.av.getAlignment() + .getAlignmentAnnotation()[start]; + if (end == -1) + { + end = ap.av.getAlignment().getAlignmentAnnotation().length - 1; + } + AlignmentAnnotation endAA = ap.av.getAlignment() + .getAlignmentAnnotation()[end]; + + ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; + ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; + } + + resizePanel = false; + dragEvent = null; + repaint(); + ap.getAnnotationPanel().repaint(); + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void mouseEntered(MouseEvent evt) + { + if (evt.getY() < 10) + { + resizePanel = true; + repaint(); + } + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void mouseExited(MouseEvent evt) + { + if (dragEvent == null) + { + resizePanel = false; + repaint(); + } + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void mouseDragged(MouseEvent evt) + { + dragEvent = evt; + + if (resizePanel) + { + Dimension d = ap.annotationScroller.getPreferredSize(); + int dif = evt.getY() - oldY; + + dif /= ap.av.getCharHeight(); + dif *= ap.av.getCharHeight(); + + if ((d.height - dif) > 20) + { + ap.annotationScroller.setPreferredSize(new Dimension(d.width, + d.height - dif)); + d = ap.annotationSpaceFillerHolder.getPreferredSize(); + ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension( + d.width, d.height - dif)); + ap.paintAlignment(true); + } + + ap.addNotify(); + } + else + { + repaint(); + } + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void mouseMoved(MouseEvent evt) + { + resizePanel = evt.getY() < 10; + + getSelectedRow(evt.getY() - getScrollOffset()); + + if (selectedRow > -1 + && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow) + { + AlignmentAnnotation aa = ap.av.getAlignment() + .getAlignmentAnnotation()[selectedRow]; + + StringBuffer desc = new StringBuffer(); + if (aa.description != null + && !aa.description.equals("New description")) + { + // TODO: we could refactor and merge this code with the code in + // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature + // tooltips + desc.append(aa.getDescription(true).trim()); + // check to see if the description is an html fragment. + if (desc.length() < 6 + || (desc.substring(0, 6).toLowerCase().indexOf("") < 0)) + { + // clean the description ready for embedding in html + desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc) + .replaceAll("<")); + desc.insert(0, ""); + } + else + { + // remove terminating html if any + int i = desc.substring(desc.length() - 7).toLowerCase() + .lastIndexOf(""); + if (i > -1) + { + desc.setLength(desc.length() - 7 + i); + } + } + if (aa.hasScore()) + { + desc.append("
"); + } + // if (aa.hasProperties()) + // { + // desc.append(""); + // for (String prop : aa.getProperties()) + // { + // desc.append(""); + // } + // desc.append("
" + prop + "" + // + aa.getProperty(prop) + "
"); + // } + } + 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); + } + } + } + + @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) + { + 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()); + } + + } + } + return; + } } /** diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index e247793..c84505b 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -191,8 +191,10 @@ public class IdPanel extends JPanel implements MouseListener, * Ignore single click. Ignore 'left' click followed by 'right' click (user * selects a row then its pop-up menu). */ - if (e.getClickCount() < 2 || e.isPopupTrigger()) + if (e.getClickCount() < 2 || SwingUtilities.isRightMouseButton(e)) { + // reinstate isRightMouseButton check to ignore mouse-related popup events + // note - this does nothing on default MacBookPro force-trackpad config! return; }