}
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultMatchI#getSequence()
- */
@Override
public SequenceI getSequence()
{
return sequence;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultMatchI#getStart()
- */
@Override
public int getStart()
{
return start;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultMatchI#getEnd()
- */
@Override
public int getEnd()
{
return (sequence == m.getSequence() && start == m.getStart()
&& end == m.getEnd());
}
+
+ @Override
+ public boolean contains(SequenceI seq, int from, int to)
+ {
+ return (sequence == seq && start <= from && end >= to);
+ }
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#addResult(jalview.datamodel.SequenceI, int, int)
- */
@Override
public SearchResultMatchI addResult(SequenceI seq, int start, int end)
{
Match m = new Match(seq, start, end);
- matches.add(m);
+ if (!matches.contains(m))
+ {
+ matches.add(m);
+ }
return m;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#involvesSequence(jalview.datamodel.SequenceI)
- */
@Override
public boolean involvesSequence(SequenceI sequence)
{
return false;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResults(jalview.datamodel.SequenceI, int, int)
- */
@Override
public int[] getResults(SequenceI sequence, int start, int end)
{
{
int count = 0;
BitSet mask = new BitSet();
+ int startRes = sqcol.getStartRes();
+ int endRes = sqcol.getEndRes();
+
for (SequenceI s : sqcol.getSequences())
{
- int[] cols = getResults(s, sqcol.getStartRes(), sqcol.getEndRes());
+ int[] cols = getResults(s, startRes, endRes);
if (cols != null)
{
for (int pair = 0; pair < cols.length; pair += 2)
return count;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getSize()
- */
@Override
public int getSize()
{
return matches.size();
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#isEmpty()
- */
@Override
public boolean isEmpty()
{
return matches.isEmpty();
}
- /* (non-Javadoc)
- * @see jalview.datamodel.SearchResultsI#getResults()
- */
@Override
public List<SearchResultMatchI> getResults()
{
*/
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;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import java.awt.BorderLayout;
import java.awt.event.MouseEvent;
import java.util.List;
import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
}
/**
- * 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());
+ }
}
}
{
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)
{
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);
{
if (scrollThread != null)
{
- scrollThread.running = false;
+ scrollThread.stopScrolling();
}
}
return;
}
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
+
if (e.isPopupTrigger()) // Mac reports this in mousePressed
{
- showPopupMenu(e);
+ showPopupMenu(e, pos);
return;
}
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);
*
* @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<SequenceFeature> features = null;
+ if (sq != null)
+ {
List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
- List<SequenceFeature> 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());
}
/**
+ * 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
lastid = seq;
SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
- av.getSelectionGroup().addOrRemove(pickedSeq, true);
+ av.getSelectionGroup().addOrRemove(pickedSeq, false);
}
/**
for (int i = start; i <= end; i++)
{
av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
- i == end);
+ false);
}
}
{
if (scrollThread != null)
{
- scrollThread.running = false;
+ scrollThread.stopScrolling();
}
+ MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
mouseDragging = false;
PaintRefresher.Refresh(this, av.getSequenceSetId());
if (e.isPopupTrigger()) // Windows reports this in mouseReleased
{
- showPopupMenu(e);
+ showPopupMenu(e, pos);
}
}
{
getIdCanvas().setHighlighted(list);
- if (list == null)
+ if (list == null || list.isEmpty())
{
return;
}
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()
{
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;
}
git://source.jalview.org / jalview.git / commitdiff