X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=7b491e47e59ec10f8abdb2e39764bc66dff6bcb0;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=8290dcf1d14515177557e449132411fd582c755d;hpb=aaead18c6acb21da4d63f3ad9f454d9eb410152f;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 8290dcf..7b491e4 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -20,17 +20,6 @@ */ package jalview.gui; -import jalview.bin.Jalview; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.io.SequenceAnnotationReport; -import jalview.util.MessageManager; -import jalview.util.Platform; -import jalview.viewmodel.AlignmentViewport; -import jalview.viewmodel.ViewportRanges; - import java.awt.BorderLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; @@ -42,10 +31,22 @@ 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; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Sequence; +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; +import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; + /** * This panel hosts alignment sequence ids and responds to mouse clicks on them, * as well as highlighting ids matched by a search from the Find menu. @@ -64,8 +65,6 @@ public class IdPanel extends JPanel ScrollThread scrollThread = null; - String linkImageURL; - int offy; // int width; @@ -86,8 +85,7 @@ public class IdPanel extends JPanel this.av = av; alignPanel = parent; setIdCanvas(new IdCanvas(av)); - linkImageURL = getClass().getResource("/images/link.gif").toString(); - seqAnnotReport = new SequenceAnnotationReport(linkImageURL); + seqAnnotReport = new SequenceAnnotationReport(true); setLayout(new BorderLayout()); add(getIdCanvas(), BorderLayout.CENTER); addMouseListener(this); @@ -97,25 +95,45 @@ 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()) { - 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())); + /* + * 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 + { + 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()); + } } } @@ -130,7 +148,14 @@ 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) { @@ -201,7 +226,13 @@ 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); @@ -237,6 +268,7 @@ public class IdPanel extends JPanel if (scrollThread != null) { scrollThread.stopScrolling(); + scrollThread = null; } } @@ -281,14 +313,7 @@ public class IdPanel extends JPanel void startScrolling(boolean up) { scrollThread = new ScrollThread(up); - if (!Jalview.isJS()) - { - /* - * Java - run in a new thread - */ - scrollThread.start(); - } - else + if (Platform.isJS()) { /* * for JalviewJS using Swing Timer @@ -312,13 +337,22 @@ 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(); + } } /** @@ -342,9 +376,11 @@ 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; } @@ -353,7 +389,7 @@ public class IdPanel extends JPanel * (where isPopupTrigger() will answer true) * NB isRightMouseButton is also true for Cmd-click on Mac */ - if (SwingUtilities.isRightMouseButton(e) && !Platform.isAMac()) + if (Platform.isWinRightButton(e)) { return; } @@ -367,14 +403,13 @@ 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); @@ -387,30 +422,52 @@ 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; + } - /* - * build a new links menu based on the current links - * and any non-positional features - */ - List nlinks = Preferences.sequenceUrlLinks.getLinksForMenu(); - List features = sq.getFeatures().getNonPositionalFeatures(); - for (SequenceFeature sf : features) + Sequence sq = (Sequence) av.getAlignment().getSequenceAt(pos.seqIndex); + if (sq != null) { - if (sf.links != null) - { - for (String link : sf.links) - { - nlinks.add(link); - } - } + PopupMenu pop = new PopupMenu(alignPanel, sq, + Preferences.getGroupURLLinks()); + pop.show(this, e.getX(), e.getY()); } + } - PopupMenu pop = new PopupMenu(alignPanel, sq, features, - Preferences.getGroupURLLinks()); + /** + * 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()); } @@ -424,7 +481,7 @@ public class IdPanel extends JPanel lastid = seq; SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); - av.getSelectionGroup().addOrRemove(pickedSeq, true); + av.getSelectionGroup().addOrRemove(pickedSeq, false); } /** @@ -459,7 +516,7 @@ public class IdPanel extends JPanel for (int i = start; i <= end; i++) { av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), - i == end); + false); } } @@ -472,7 +529,11 @@ 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()); @@ -481,7 +542,7 @@ public class IdPanel extends JPanel if (e.isPopupTrigger()) // Windows reports this in mouseReleased { - showPopupMenu(e); + showPopupMenu(e, pos); } } @@ -495,7 +556,7 @@ public class IdPanel extends JPanel { getIdCanvas().setHighlighted(list); - if (list == null) + if (list == null || list.isEmpty()) { return; } @@ -539,7 +600,6 @@ public class IdPanel extends JPanel { this.up = up; setName("IdPanel$ScrollThread$" + String.valueOf(up)); - start(); } /**