import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
+import java.util.ListIterator;
import javax.swing.JPanel;
import javax.swing.SwingUtilities;
int res = 0;
int x = evt.getX();
+ int startRes = av.getRanges().getStartRes();
if (av.getWrapAlignment())
{
int y = evt.getY();
y -= hgap;
- x -= seqCanvas.LABEL_WEST;
+ x = Math.max(0, x - seqCanvas.LABEL_WEST);
int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
if (cwidth < 1)
}
wrappedBlock = y / cHeight;
- wrappedBlock += av.getRanges().getStartRes() / cwidth;
-
- res = wrappedBlock * cwidth + x / av.getCharWidth();
-
+ wrappedBlock += startRes / cwidth;
+ // allow for wrapped view scrolled right (possible from Overview)
+ int startOffset = startRes % cwidth;
+ res = wrappedBlock * cwidth
+ + Math.min(cwidth - 1, startOffset + x / av.getCharWidth());
}
else
{
// right-hand gutter
x = seqCanvas.getX() + seqCanvas.getWidth();
}
- res = (x / av.getCharWidth()) + av.getRanges().getStartRes();
+ res = (x / av.getCharWidth()) + startRes;
if (res > av.getRanges().getEndRes())
{
// moused off right
}
else
{
- av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY,
- av);
+ av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY);
}
setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
seqCanvas.cursorX, seqCanvas.cursorY);
@Override
public void mouseReleased(MouseEvent evt)
{
+ boolean didDrag = mouseDragging; // did we come here after a drag
mouseDragging = false;
mouseWheelPressed = false;
if (!editingSeqs)
{
- doMouseReleasedDefineMode(evt);
+ doMouseReleasedDefineMode(evt, didDrag);
return;
}
/*
* set status bar message, returning residue position in sequence
*/
+ boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
final int pos = setStatusMessage(sequence, column, seq);
- if (ssm != null && pos > -1)
+ if (ssm != null && !isGapped)
{
mouseOverSequence(sequence, column, pos);
}
}
}
- if (av.isShowSequenceFeatures() && pos != -1)
+ /*
+ * add any features at the position to the tooltip; if over a gap, only
+ * add features that straddle the gap (pos may be the residue before or
+ * after the gap)
+ */
+ if (av.isShowSequenceFeatures())
{
List<SequenceFeature> features = ap.getFeatureRenderer()
.findFeaturesAtRes(sequence.getDatasetSequence(), pos);
+ if (isGapped)
+ {
+ removeAdjacentFeatures(features, column + 1, sequence);
+ }
seqARep.appendFeatures(tooltipText, pos, features,
this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
}
}
+ /**
+ * Removes from the list of features any that start after, or end before, the
+ * given column position. This allows us to retain only those features
+ * adjacent to a gapped position that straddle the position. Contact features
+ * that 'straddle' the position are also removed, since they are not 'at' the
+ * position.
+ *
+ * @param features
+ * @param column
+ * alignment column (1..)
+ * @param sequence
+ */
+ protected void removeAdjacentFeatures(List<SequenceFeature> features,
+ final int column, SequenceI sequence)
+ {
+ // TODO should this be an AlignViewController method (and reused by applet)?
+ ListIterator<SequenceFeature> it = features.listIterator();
+ while (it.hasNext())
+ {
+ SequenceFeature sf = it.next();
+ if (sf.isContactFeature()
+ || sequence.findIndex(sf.getBegin()) > column
+ || sequence.findIndex(sf.getEnd()) < column)
+ {
+ it.remove();
+ }
+ }
+ }
+
private Point lastp = null;
/*
/**
* Sets the status message in alignment panel, showing the sequence number
- * (index) and id, residue and residue position for the given sequence and
- * column position. Returns the calculated residue position in the sequence,
- * or -1 for a gapped column position.
+ * (index) and id, and residue and residue position if not at a gap, for the
+ * given sequence and column position. Returns the residue position returned
+ * by Sequence.findPosition. Note this may be for the nearest adjacent residue
+ * if at a gapped position.
*
* @param sequence
* aligned sequence object
* alignment column
* @param seq
* index of sequence in alignment
- * @return position of column in sequence or -1 if at a gap
+ * @return sequence position of residue at column, or adjacent residue if at a
+ * gap
*/
int setStatusMessage(SequenceI sequence, final int column, int seq)
{
.append(sequence.getName());
String residue = null;
+
/*
* Try to translate the display character to residue name (null for gap).
*/
final String displayChar = String.valueOf(sequence.getCharAt(column));
- if (av.getAlignment().isNucleotide())
+ boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
+ int pos = sequence.findPosition(column);
+
+ if (!isGapped)
{
- residue = ResidueProperties.nucleotideName.get(displayChar);
- if (residue != null)
+ boolean nucleotide = av.getAlignment().isNucleotide();
+ if (nucleotide)
{
- text.append(" Nucleotide: ").append(residue);
+ residue = ResidueProperties.nucleotideName.get(displayChar);
}
- }
- else
- {
- residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
- .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet
- .get(displayChar));
- if (residue != null)
+ else
{
- text.append(" Residue: ").append(residue);
+ residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
+ .equals(displayChar) ? "STOP"
+ : ResidueProperties.aa2Triplet.get(displayChar));
}
- }
+ text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
+ .append(": ").append(residue == null ? displayChar : residue);
- int pos = -1;
- if (residue != null)
- {
- pos = sequence.findPosition(column);
text.append(" (").append(Integer.toString(pos)).append(")");
}
ap.alignFrame.statusBar.setText(text.toString());
+
return pos;
}
av.setSelectionGroup(null);
}
+ int column = findColumn(evt);
+ boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
+
+ /*
+ * find features at the position (if not gapped), or straddling
+ * the position (if at a gap)
+ */
List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
.findFeaturesAtRes(sequence.getDatasetSequence(),
- sequence.findPosition(findColumn(evt)));
+ sequence.findPosition(column));
+ if (isGapped)
+ {
+ removeAdjacentFeatures(features, column, sequence);
+ }
if (!features.isEmpty())
{
List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
.findFeaturesAtRes(sequence.getDatasetSequence(),
sequence.findPosition(res));
- List<String> links = new ArrayList<String>();
+ List<String> links = new ArrayList<>();
for (SequenceFeature sf : allFeatures)
{
if (sf.links != null)
}
/**
- * DOCUMENT ME!
+ * Update the display after mouse up on a selection or group
*
* @param evt
- * DOCUMENT ME!
+ * mouse released event details
+ * @param afterDrag
+ * true if this event is happening after a mouse drag (rather than a
+ * mouse down)
*/
- public void doMouseReleasedDefineMode(MouseEvent evt)
+ public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
{
if (stretchGroup == null)
{
// always do this - annotation has own state
// but defer colourscheme update until hidden sequences are passed in
boolean vischange = stretchGroup.recalcConservation(true);
- needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
+ needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
+ && afterDrag;
if (stretchGroup.cs != null)
{
stretchGroup.cs.alignmentChanged(stretchGroup,
ap.getCalculationDialog().validateCalcTypes();
}
- // process further ?
- if (!av.followSelection)
- {
- return;
- }
+ return;
+ }
+
+ // process further ?
+ if (!av.followSelection)
+ {
+ return;
}
/*
if (copycolsel
&& av.hasHiddenColumns()
- && (av.getAlignment().getHiddenColumns() == null || av
- .getAlignment().getHiddenColumns().getHiddenRegions() == null))
+ && (av.getAlignment().getHiddenColumns() == null))
{
System.err.println("Bad things");
}
git://source.jalview.org / jalview.git / blobdiff