X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=e12c39704b4d282c6314581fa4a329ce2993af94;hb=65173997db7b8fff0aa6db0fd2fa8435a820c364;hp=06568ca55946caa8d594a1297151e2fd825f9c48;hpb=4c6cd08af580ff73cfce39bec34ae4658a4b4b34;p=jalview.git
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 06568ca..e12c397 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -201,6 +201,7 @@ public class SeqPanel extends JPanel implements MouseListener,
int res = 0;
int x = evt.getX();
+ int startRes = av.getRanges().getStartRes();
if (av.getWrapAlignment())
{
@@ -215,7 +216,7 @@ public class SeqPanel extends JPanel implements MouseListener,
int y = evt.getY();
y -= hgap;
- x -= seqCanvas.LABEL_WEST;
+ x = Math.max(0, x - seqCanvas.labelWidthWest);
int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
if (cwidth < 1)
@@ -224,10 +225,11 @@ public class SeqPanel extends JPanel implements MouseListener,
}
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
{
@@ -237,7 +239,7 @@ public class SeqPanel extends JPanel implements MouseListener,
// 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
@@ -406,8 +408,7 @@ public class SeqPanel extends JPanel implements MouseListener,
}
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);
@@ -682,6 +683,8 @@ public class SeqPanel extends JPanel implements MouseListener,
}
lastSearchResults = results;
+ boolean wasScrolled = false;
+
if (av.isFollowHighlight())
{
// don't allow highlight of protein/cDNA to also scroll a complementary
@@ -689,14 +692,19 @@ public class SeqPanel extends JPanel implements MouseListener,
// over residue to change abruptly, causing highlighted residue in panel 2
// to change, causing a scroll in panel 1 etc)
ap.setToScrollComplementPanel(false);
- if (ap.scrollToPosition(results, false))
+ wasScrolled = ap.scrollToPosition(results, false);
+ if (wasScrolled)
{
seqCanvas.revalidate();
}
ap.setToScrollComplementPanel(true);
}
- setStatusMessage(results);
- seqCanvas.highlightSearchResults(results);
+
+ boolean noFastPaint = wasScrolled && av.getWrapAlignment();
+ if (seqCanvas.highlightSearchResults(results, noFastPaint))
+ {
+ setStatusMessage(results);
+ }
}
@Override
@@ -869,19 +877,48 @@ public class SeqPanel extends JPanel implements MouseListener,
* aligned sequence object
* @param column
* alignment column
- * @param seq
+ * @param seqIndex
* index of sequence in alignment
* @return sequence position of residue at column, or adjacent residue if at a
* gap
*/
- int setStatusMessage(SequenceI sequence, final int column, int seq)
+ int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
+ {
+ char sequenceChar = sequence.getCharAt(column);
+ int pos = sequence.findPosition(column);
+ setStatusMessage(sequence, seqIndex, sequenceChar, pos);
+
+ return pos;
+ }
+
+ /**
+ * Builds the status message for the current cursor location and writes it to
+ * the status bar, for example
+ *
+ *
+ * Sequence 3 ID: FER1_SOLLC
+ * Sequence 5 ID: FER1_PEA Residue: THR (4)
+ * Sequence 5 ID: FER1_PEA Residue: B (3)
+ * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
+ *
+ *
+ * @param sequence
+ * @param seqIndex
+ * sequence position in the alignment (1..)
+ * @param sequenceChar
+ * the character under the cursor
+ * @param residuePos
+ * the sequence residue position (if not over a gap)
+ */
+ protected void setStatusMessage(SequenceI sequence, int seqIndex,
+ char sequenceChar, int residuePos)
{
StringBuilder text = new StringBuilder(32);
/*
* Sequence number (if known), and sequence name.
*/
- String seqno = seq == -1 ? "" : " " + (seq + 1);
+ String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
text.append("Sequence").append(seqno).append(" ID: ")
.append(sequence.getName());
@@ -890,13 +927,12 @@ public class SeqPanel extends JPanel implements MouseListener,
/*
* Try to translate the display character to residue name (null for gap).
*/
- final String displayChar = String.valueOf(sequence.getCharAt(column));
- boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
- int pos = sequence.findPosition(column);
+ boolean isGapped = Comparison.isGap(sequenceChar);
if (!isGapped)
{
boolean nucleotide = av.getAlignment().isNucleotide();
+ String displayChar = String.valueOf(sequenceChar);
if (nucleotide)
{
residue = ResidueProperties.nucleotideName.get(displayChar);
@@ -910,11 +946,9 @@ public class SeqPanel extends JPanel implements MouseListener,
text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
.append(": ").append(residue == null ? displayChar : residue);
- text.append(" (").append(Integer.toString(pos)).append(")");
+ text.append(" (").append(Integer.toString(residuePos)).append(")");
}
ap.alignFrame.statusBar.setText(text.toString());
-
- return pos;
}
/**
@@ -942,12 +976,9 @@ public class SeqPanel extends JPanel implements MouseListener,
if (seq == ds)
{
- /*
- * Convert position in sequence (base 1) to sequence character array
- * index (base 0)
- */
- int start = m.getStart() - m.getSequence().getStart();
- setStatusMessage(seq, start, sequenceIndex);
+ int start = m.getStart();
+ setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
+ start);
return;
}
}
@@ -1570,7 +1601,7 @@ public class SeqPanel extends JPanel implements MouseListener,
SearchResultsI highlight = new SearchResults();
highlight.addResult(sequence, features.get(0).getBegin(), features
.get(0).getEnd());
- seqCanvas.highlightSearchResults(highlight);
+ seqCanvas.highlightSearchResults(highlight, false);
/*
* open the Amend Features dialog; clear highlighting afterwards,
@@ -1579,7 +1610,8 @@ public class SeqPanel extends JPanel implements MouseListener,
List seqs = Collections.singletonList(sequence);
seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
ap);
- seqCanvas.highlightSearchResults(null);
+ av.setSearchResults(null); // clear highlighting
+ seqCanvas.repaint(); // draw new/amended features
}
}
}
@@ -1595,7 +1627,7 @@ public class SeqPanel extends JPanel implements MouseListener,
av.getRanges().scrollRight(true);
}
- else
+ else if (!av.getWrapAlignment())
{
av.getRanges().scrollUp(false);
}
@@ -1606,7 +1638,7 @@ public class SeqPanel extends JPanel implements MouseListener,
{
av.getRanges().scrollRight(false);
}
- else
+ else if (!av.getWrapAlignment())
{
av.getRanges().scrollUp(true);
}
@@ -2125,8 +2157,7 @@ public class SeqPanel extends JPanel implements MouseListener,
if (copycolsel
&& av.hasHiddenColumns()
- && (av.getAlignment().getHiddenColumns() == null || av
- .getAlignment().getHiddenColumns().getHiddenRegions() == null))
+ && (av.getAlignment().getHiddenColumns() == null))
{
System.err.println("Bad things");
}