X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=d11d7a182175a9c9494f04d892192fa59478f81b;hb=78f5bbe9330cbf3d686d1a5c411956e091c88541;hp=94eab765148b26d1cc0ad2f9dd3def0576122129;hpb=d0e1239635b38ef37d3cd35a6943dc0cd713d903;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 94eab76..d11d7a1 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -30,6 +30,7 @@ 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.MouseEvent; @@ -40,6 +41,7 @@ import java.awt.event.MouseWheelListener; import java.util.List; import javax.swing.JPanel; +import javax.swing.JPopupMenu; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; @@ -94,25 +96,27 @@ 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(); MousePos pos = sp.findMousePosition(e); - if (pos.annotationIndex != -1) + if (pos.isOverAnnotation()) { /* * mouse is over an annotation label in wrapped mode */ - AlignmentAnnotation annotation = av.getAlignment() - .getAlignmentAnnotation()[pos.annotationIndex]; + AlignmentAnnotation[] anns = av.getAlignment() + .getAlignmentAnnotation(); + AlignmentAnnotation annotation = anns[pos.annotationIndex]; setToolTipText(AnnotationLabels.getTooltip(annotation)); + alignPanel.alignFrame.setStatus( + AnnotationLabels.getStatusMessage(annotation, anns)); } else { @@ -121,10 +125,16 @@ public class IdPanel extends JPanel { 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, - sequence.getDisplayId(true) + " " + tip.toString())); + 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()); } } } @@ -141,7 +151,7 @@ public class IdPanel extends JPanel mouseDragging = true; MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); - if (pos.annotationIndex != -1) + if (pos.isOverAnnotation()) { // mouse is over annotation label in wrapped mode return; @@ -219,13 +229,12 @@ public class IdPanel extends JPanel } MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); - if (pos.annotationIndex != -1) + int seq = pos.seqIndex; + if (pos.isOverAnnotation() || seq < 0) { - // mouse is over annotation label in wrapped mode return; } - int seq = pos.seqIndex; String id = av.getAlignment().getSequenceAt(seq).getName(); String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id); @@ -253,7 +262,7 @@ public class IdPanel extends JPanel { if (scrollThread != null) { - scrollThread.running = false; + scrollThread.stopScrolling(); } } @@ -306,11 +315,6 @@ public class IdPanel extends JPanel } MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); - if (pos.annotationIndex != -1) - { - // mouse is over an annotation label in wrapped mode - return; - } if (e.isPopupTrigger()) // Mac reports this in mousePressed { @@ -358,14 +362,23 @@ public class IdPanel extends JPanel */ void showPopupMenu(MouseEvent e, MousePos pos) { + 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) @@ -373,6 +386,7 @@ public class IdPanel extends JPanel nlinks.addAll(sf.links); } } + } PopupMenu pop = new PopupMenu(alignPanel, sq, features, Preferences.getGroupURLLinks()); @@ -380,6 +394,38 @@ public class IdPanel extends JPanel } /** + * 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()); + } + + /** * Toggle whether the sequence is part of the current selection group. * * @param seq @@ -389,7 +435,7 @@ public class IdPanel extends JPanel lastid = seq; SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq); - av.getSelectionGroup().addOrRemove(pickedSeq, true); + av.getSelectionGroup().addOrRemove(pickedSeq, false); } /** @@ -424,7 +470,7 @@ public class IdPanel extends JPanel for (int i = start; i <= end; i++) { av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), - i == end); + false); } } @@ -439,14 +485,9 @@ public class IdPanel extends JPanel { if (scrollThread != null) { - scrollThread.running = false; + scrollThread.stopScrolling(); } MousePos pos = alignPanel.getSeqPanel().findMousePosition(e); - if (pos.annotationIndex != -1) - { - // mouse is over an annotation label in wrapped mode - return; - } mouseDragging = false; PaintRefresher.Refresh(this, av.getSequenceSetId()); @@ -469,7 +510,7 @@ public class IdPanel extends JPanel { getIdCanvas().setHighlighted(list); - if (list == null) + if (list == null || list.isEmpty()) { return; } @@ -494,24 +535,42 @@ public class IdPanel extends JPanel this.idCanvas = idCanvas; } - // this class allows scrolling off the bottom of the visible alignment + /** + * Performs scrolling of the visible alignment up or down, adding newly + * visible sequences to the current selection + */ class ScrollThread extends Thread { - boolean running = false; + private boolean running = false; - boolean up = true; + private boolean up; + /** + * Constructor for a thread that scrolls either up or down + * + * @param up + */ public ScrollThread(boolean up) { this.up = up; + setName("IdPanel$ScrollThread$" + String.valueOf(up)); start(); } + /** + * Sets a flag to stop the scrolling + */ public void stopScrolling() { running = false; } + /** + * Scrolls the alignment either up or down, one row at a time, adding newly + * visible sequences to the current selection. Speed is limited to a maximum + * of ten rows per second. The thread exits when the end of the alignment is + * reached or a flag is set to stop it. + */ @Override public void run() { @@ -519,29 +578,20 @@ public class IdPanel extends JPanel while (running) { - if (av.getRanges().scrollUp(up)) + ViewportRanges ranges = IdPanel.this.av.getRanges(); + if (ranges.scrollUp(up)) { - // scroll was ok, so add new sequence to selection - int seq = av.getRanges().getStartSeq(); - - if (!up) - { - seq = av.getRanges().getEndSeq(); - } - - if (seq < lastid) - { - selectSeqs(lastid - 1, seq); - } - else if (seq > lastid) - { - selectSeqs(lastid + 1, seq); - } - - lastid = seq; + int toSeq = up ? ranges.getStartSeq() : ranges.getEndSeq(); + int fromSeq = toSeq < lastid ? lastid - 1 : lastid + 1; + IdPanel.this.selectSeqs(fromSeq, toSeq); + + lastid = toSeq; } else { + /* + * scroll did nothing - reached limit of visible alignment + */ running = false; }