StringBuffer keyboardNo2;
- java.net.URL linkImageURL;
-
private final SequenceAnnotationReport seqARep;
StringBuilder tooltipText = new StringBuilder();
*/
public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
{
- linkImageURL = getClass().getResource("/images/link.gif");
- seqARep = new SequenceAnnotationReport(linkImageURL.toString());
+ seqARep = new SequenceAnnotationReport(true);
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
void moveCursor(int dx, int dy)
{
- seqCanvas.cursorX += dx;
- seqCanvas.cursorY += dy;
-
+ moveCursor(dx, dy,false);
+ }
+ void moveCursor(int dx, int dy, boolean nextWord)
+ {
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
+ if (nextWord)
{
- int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
-
- if (!hidden.isVisible(seqCanvas.cursorX))
- {
- int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
- int[] region = hidden.getRegionWithEdgeAtRes(visx);
-
- if (region != null) // just in case
+ int maxHeight=av.getAlignment().getHeight();
+ SequenceI seqAtRow = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+ // look for next gap or residue
+ boolean isGap = Comparison.isGap(seqAtRow.getCharAt(seqCanvas.cursorX));
+ int p = seqCanvas.cursorX,lastP,r=seqCanvas.cursorY,lastR;
+ do
+ {
+ lastP = p;
+ lastR = r;
+ if (dy != 0)
{
- if (dx == 1)
+ r += dy;
+ if (r < 0)
{
- // moving right
- seqCanvas.cursorX = region[1] + 1;
+ r = 0;
}
- else if (dx == -1)
+ if (r >= maxHeight)
{
- // moving left
- seqCanvas.cursorX = region[0] - 1;
+ r = maxHeight - 1;
}
+ seqAtRow = av.getAlignment().getSequenceAt(r);
}
- seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
- }
+ p = nextVisible(hidden, maxWidth, p, dx);
+ } while ((dx != 0 ? p != lastP : r != lastR)
+ && isGap == Comparison.isGap(seqAtRow.getCharAt(p)));
+ seqCanvas.cursorX=p;
+ seqCanvas.cursorY=r;
+ } else {
+ int maxWidth = av.getAlignment().getWidth();
+ seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX, dx);
+ seqCanvas.cursorY += dy;
+ }
+ scrollToVisible(false);
+ }
- if (seqCanvas.cursorX >= maxWidth
- || !hidden.isVisible(seqCanvas.cursorX))
+ private int nextVisible(HiddenColumns hidden,int maxWidth, int original, int dx)
+ {
+ int newCursorX=original+dx;
+ if (av.hasHiddenColumns() && !hidden.isVisible(newCursorX))
+ {
+ int visx = hidden.absoluteToVisibleColumn(newCursorX - dx);
+ int[] region = hidden.getRegionWithEdgeAtRes(visx);
+
+ if (region != null) // just in case
{
- seqCanvas.cursorX = original;
+ if (dx == 1)
+ {
+ // moving right
+ newCursorX = region[1] + 1;
+ }
+ else if (dx == -1)
+ {
+ // moving left
+ newCursorX = region[0] - 1;
+ }
}
}
-
- scrollToVisible(false);
+ newCursorX = (newCursorX < 0) ? 0 : newCursorX;
+ if (newCursorX >= maxWidth
+ || !hidden.isVisible(newCursorX))
+ {
+ newCursorX = original;
+ }
+ return newCursorX;
}
-
/**
* Scroll to make the cursor visible in the viewport.
*
AlignFrame af = Desktop.getAlignFrameFor(complement);
FeatureRendererModel fr2 = af.getFeatureRenderer();
- int j = results.getSize();
+ List<SearchResultMatchI> matches = results.getResults();
+ int j = matches.size();
List<String> infos = new ArrayList<>();
for (int i = 0; i < j; i++)
{
- SearchResultMatchI match = results.getResults().get(i);
+ SearchResultMatchI match = matches.get(i);
int pos = match.getStart();
if (pos == match.getEnd())
{
{
List<SequenceFeature> features = ap.getFeatureRenderer()
.findFeaturesAtColumn(sequence, column + 1);
- unshownFeatures = seqARep.appendFeaturesLengthLimit(tooltipText, pos,
- features,
- this.ap.getSeqPanel().seqCanvas.fr, MAX_TOOLTIP_LENGTH);
+ unshownFeatures = seqARep.appendFeatures(tooltipText, pos,
+ features, this.ap.getSeqPanel().seqCanvas.fr,
+ MAX_TOOLTIP_LENGTH);
/*
* add features in CDS/protein complement at the corresponding
pos);
if (mf != null)
{
- unshownFeatures = seqARep.appendFeaturesLengthLimit(
- tooltipText, pos, mf, fr2,
- MAX_TOOLTIP_LENGTH);
+ unshownFeatures += seqARep.appendFeatures(tooltipText,
+ pos, mf, fr2, MAX_TOOLTIP_LENGTH);
}
}
}
{
char sequenceChar = sequence.getCharAt(column);
int pos = sequence.findPosition(column);
- setStatusMessage(sequence, seqIndex, sequenceChar, pos);
+ setStatusMessage(sequence.getName(), seqIndex, sequenceChar, pos);
return pos;
}
* Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
* </pre>
*
- * @param sequence
+ * @param seqName
* @param seqIndex
* sequence position in the alignment (1..)
* @param sequenceChar
* @param residuePos
* the sequence residue position (if not over a gap)
*/
- protected void setStatusMessage(SequenceI sequence, int seqIndex,
+ protected void setStatusMessage(String seqName, int seqIndex,
char sequenceChar, int residuePos)
{
StringBuilder text = new StringBuilder(32);
*/
String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
text.append("Sequence").append(seqno).append(" ID: ")
- .append(sequence.getName());
+ .append(seqName);
String residue = null;
{
return;
}
- SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+ SequenceI alignedSeq = al.getSequenceAt(sequenceIndex);
+ SequenceI ds = alignedSeq.getDatasetSequence();
for (SearchResultMatchI m : results.getResults())
{
SequenceI seq = m.getSequence();
if (seq == ds)
{
int start = m.getStart();
- setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
- start);
+ setStatusMessage(alignedSeq.getName(), sequenceIndex,
+ seq.getCharAt(start - 1), start);
return;
}
}