X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=dadf25a55e7eb8759fad7176d0adec91ff4910ed;hb=7a5cac232c59bba9964ec32ecdd787b8028cde48;hp=d34c6538993bb25f8c3d07b5e2673f26f6187f11;hpb=26b115b0a77d521da92a06572d9b7819c2d0d49a;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index d34c653..dadf25a 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -20,10 +20,12 @@ */ package jalview.gui; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.gui.SeqPanel.MousePos; import jalview.io.SequenceAnnotationReport; import jalview.util.MessageManager; import jalview.util.Platform; @@ -41,6 +43,7 @@ import java.awt.event.MouseWheelListener; import java.util.List; import javax.swing.JPanel; +import javax.swing.JPopupMenu; import javax.swing.SwingUtilities; import javax.swing.Timer; import javax.swing.ToolTipManager; @@ -96,25 +99,46 @@ public class IdPanel extends JPanel } /** - * Respond to mouse movement by constructing tooltip text for the sequence id - * under the mouse. + * Responds to mouse movement by setting tooltip text for the sequence id + * under the mouse (or possibly annotation label, when in wrapped mode) * * @param e - * DOCUMENT ME! */ @Override public void mouseMoved(MouseEvent e) { SeqPanel sp = alignPanel.getSeqPanel(); - int seq = Math.max(0, sp.findSeq(e)); - if (seq > -1 && seq < av.getAlignment().getHeight()) + MousePos pos = sp.findMousePosition(e); + if (pos.isOverAnnotation()) + { + /* + * mouse is over an annotation label in wrapped mode + */ + AlignmentAnnotation[] anns = av.getAlignment() + .getAlignmentAnnotation(); + AlignmentAnnotation annotation = anns[pos.annotationIndex]; + setToolTipText(AnnotationLabels.getTooltip(annotation)); + alignPanel.alignFrame.setStatus( + AnnotationLabels.getStatusMessage(annotation, anns)); + } + else { - SequenceI sequence = av.getAlignment().getSequenceAt(seq); - StringBuilder tip = new StringBuilder(64); - seqAnnotReport.createTooltipAnnotationReport(tip, sequence, - av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr); - setToolTipText(JvSwingUtils.wrapTooltip(true, - sequence.getDisplayId(true) + " " + tip.toString())); + int seq = Math.max(0, pos.seqIndex); + if (seq < av.getAlignment().getHeight()) + { + SequenceI sequence = av.getAlignment().getSequenceAt(seq); + StringBuilder tip = new StringBuilder(64); + tip.append(sequence.getDisplayId(true)).append(" "); + seqAnnotReport.createTooltipAnnotationReport(tip, sequence, + av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr); + setToolTipText(JvSwingUtils.wrapTooltip(true, tip.toString())); + + StringBuilder text = new StringBuilder(); + text.append("Sequence ").append(String.valueOf(seq + 1)) + .append(" ID: ") + .append(sequence.getName()); + alignPanel.alignFrame.setStatus(text.toString()); + } } } @@ -129,7 +153,14 @@ public class IdPanel extends JPanel { mouseDragging = true; - int seq = Math.max(0, alignPanel.getSeqPanel().findSeq(e)); + MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); + if (pos.isOverAnnotation()) + { + // mouse is over annotation label in wrapped mode + return; + } + + int seq = Math.max(0, pos.seqIndex); if (seq < lastid) { @@ -200,7 +231,13 @@ public class IdPanel extends JPanel return; } - int seq = alignPanel.getSeqPanel().findSeq(e); + MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); + int seq = pos.seqIndex; + if (pos.isOverAnnotation() || seq < 0) + { + return; + } + String id = av.getAlignment().getSequenceAt(seq).getName(); String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id); @@ -209,7 +246,7 @@ public class IdPanel extends JPanel jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), JvOptionPane.WARNING_MESSAGE); @@ -236,6 +273,7 @@ public class IdPanel extends JPanel if (scrollThread != null) { scrollThread.stopScrolling(); + scrollThread = null; } } @@ -280,14 +318,7 @@ public class IdPanel extends JPanel void startScrolling(boolean up) { scrollThread = new ScrollThread(up); - if (!Platform.isJS()) - { - /* - * Java - run in a new thread - */ - scrollThread.start(); - } - else + if (Platform.isJS()) { /* * for JalviewJS using Swing Timer @@ -311,13 +342,22 @@ public class IdPanel extends JPanel { if (scrollThread == null) { - // finished and nulled itself + // IdPanel.stopScrolling called t.stop(); } } }); t.start(); } + else + /** + * Java only + * + * @j2sIgnore + */ + { + scrollThread.start(); + } } /** @@ -341,9 +381,11 @@ public class IdPanel extends JPanel return; } + MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); + if (e.isPopupTrigger()) // Mac reports this in mousePressed { - showPopupMenu(e); + showPopupMenu(e, pos); return; } @@ -366,14 +408,13 @@ public class IdPanel extends JPanel av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1); } - int seq = alignPanel.getSeqPanel().findSeq(e); if (e.isShiftDown() && (lastid != -1)) { - selectSeqs(lastid, seq); + selectSeqs(lastid, pos.seqIndex); } else { - selectSeq(seq); + selectSeq(pos.seqIndex); } av.isSelectionGroupChanged(true); @@ -386,30 +427,69 @@ public class IdPanel extends JPanel * * @param e */ - void showPopupMenu(MouseEvent e) + void showPopupMenu(MouseEvent e, MousePos pos) { - int seq2 = alignPanel.getSeqPanel().findSeq(e); - Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2); + if (pos.isOverAnnotation()) + { + showAnnotationMenu(e, pos); + return; + } + + Sequence sq = (Sequence) av.getAlignment().getSequenceAt(pos.seqIndex); /* * build a new links menu based on the current links * and any non-positional features */ + List features = null; + if (sq != null) + { List nlinks = Preferences.sequenceUrlLinks.getLinksForMenu(); - List features = sq.getFeatures().getNonPositionalFeatures(); + features = sq.getFeatures().getNonPositionalFeatures(); for (SequenceFeature sf : features) { if (sf.links != null) { - for (String link : sf.links) - { - nlinks.add(link); - } + nlinks.addAll(sf.links); } } + } PopupMenu pop = new PopupMenu(alignPanel, sq, features, - Preferences.getGroupURLLinks()); + Preferences.getGroupURLLinks() // empty list; not implemented + ); + pop.show(this, e.getX(), e.getY()); + } + + /** + * On right mouse click on a Consensus annotation label, shows a limited popup + * menu, with options to configure the consensus calculation and rendering. + * + * @param e + * @param pos + * @see AnnotationLabels#showPopupMenu(MouseEvent) + */ + void showAnnotationMenu(MouseEvent e, MousePos pos) + { + if (pos.annotationIndex == -1) + { + return; + } + AlignmentAnnotation[] anns = this.av.getAlignment() + .getAlignmentAnnotation(); + if (anns == null || pos.annotationIndex >= anns.length) + { + return; + } + AlignmentAnnotation ann = anns[pos.annotationIndex]; + if (!ann.label.contains("Consensus")) + { + return; + } + + JPopupMenu pop = new JPopupMenu( + MessageManager.getString("label.annotations")); + AnnotationLabels.addConsensusMenuOptions(this.alignPanel, ann, pop); pop.show(this, e.getX(), e.getY()); } @@ -423,7 +503,7 @@ public class IdPanel extends JPanel lastid = seq; SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); - av.getSelectionGroup().addOrRemove(pickedSeq, true); + av.getSelectionGroup().addOrRemove(pickedSeq, false); } /** @@ -458,7 +538,7 @@ public class IdPanel extends JPanel for (int i = start; i <= end; i++) { av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), - i == end); + false); } } @@ -471,7 +551,11 @@ public class IdPanel extends JPanel @Override public void mouseReleased(MouseEvent e) { - stopScrolling(); + if (scrollThread != null) + { + stopScrolling(); + } + MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); mouseDragging = false; PaintRefresher.Refresh(this, av.getSequenceSetId()); @@ -480,7 +564,7 @@ public class IdPanel extends JPanel if (e.isPopupTrigger()) // Windows reports this in mouseReleased { - showPopupMenu(e); + showPopupMenu(e, pos); } } @@ -494,7 +578,7 @@ public class IdPanel extends JPanel { getIdCanvas().setHighlighted(list); - if (list == null) + if (list == null || list.isEmpty()) { return; } @@ -538,7 +622,6 @@ public class IdPanel extends JPanel { this.up = up; setName("IdPanel$ScrollThread$" + String.valueOf(up)); - start(); } /**