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added description of alignment quality scores and separated
[jalview.git]
/
src
/
jalview
/
gui
/
AlignmentPanel.java
diff --git
a/src/jalview/gui/AlignmentPanel.java
b/src/jalview/gui/AlignmentPanel.java
index
f81e471
..
0acf425
100755
(executable)
--- a/
src/jalview/gui/AlignmentPanel.java
+++ b/
src/jalview/gui/AlignmentPanel.java
@@
-708,8
+708,7
@@
public class AlignmentPanel extends GAlignmentPanel
\r
// draw main sequence panel
\r
pg.translate(idWidth, 0);
\r
\r
// draw main sequence panel
\r
pg.translate(idWidth, 0);
\r
- seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
\r
- startRes, startSeq, 0);
\r
+ seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
\r
\r
if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
\r
{
\r
\r
if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
\r
{
\r
@@
-940,7
+939,7
@@
public class AlignmentPanel extends GAlignmentPanel
sy = s * av.charHeight + scaleHeight;
\r
\r
SequenceI seq = av.alignment.getSequenceAt(s);
\r
sy = s * av.charHeight + scaleHeight;
\r
\r
SequenceI seq = av.alignment.getSequenceAt(s);
\r
- java.util.Vector features = seq.getDatasetSequence().getSequenceFeatures();
\r
+ SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();
\r
SequenceGroup[] groups = av.alignment.findAllGroups(seq);
\r
for(res =0; res<alwidth; res++)
\r
{
\r
SequenceGroup[] groups = av.alignment.findAllGroups(seq);
\r
for(res =0; res<alwidth; res++)
\r
{
\r
@@
-987,33
+986,32
@@
public class AlignmentPanel extends GAlignmentPanel
+ " onMouseOver=\"toolTip('"
\r
+ alIndex + " " + triplet );
\r
}
\r
+ " onMouseOver=\"toolTip('"
\r
+ alIndex + " " + triplet );
\r
}
\r
- fSize = features.size();
\r
+ fSize = features.length;
\r
for (f = 0; f < fSize; f++)
\r
{
\r
for (f = 0; f < fSize; f++)
\r
{
\r
- SequenceFeature sf = (SequenceFeature) features.elementAt(f);
\r
\r
\r
- if ( (sf.getBegin() <= seq.findPosition(res)) &&
\r
- (sf.getEnd() >= seq.findPosition(res)))
\r
+ if ( (features[f].getBegin() <= seq.findPosition(res)) &&
\r
+ (features[f].getEnd() >= seq.findPosition(res)))
\r
{
\r
{
\r
- if (sf.getType().equals("disulfide bond"))
\r
+ if (features[f].getType().equals("disulfide bond"))
\r
{
\r
{
\r
- if (sf.getBegin() == seq.findPosition(res)
\r
- || sf.getEnd() == seq.findPosition(res))
\r
+ if (features[f].getBegin() == seq.findPosition(res)
\r
+ || features[f].getEnd() == seq.findPosition(res))
\r
{
\r
{
\r
- text.append("<br>disulfide bond " + sf.getBegin() + ":" +
\r
- sf.getEnd());
\r
+ text.append("<br>disulfide bond " + features[f].getBegin() + ":" +
\r
+ features[f].getEnd());
\r
}
\r
}
\r
else
\r
{
\r
text.append("<br>");
\r
}
\r
}
\r
else
\r
{
\r
text.append("<br>");
\r
- text.append(sf.getType());
\r
- if (sf.getDescription() != null && !sf.getType().equals(sf.getDescription()))
\r
- text.append(" " + sf.getDescription());
\r
+ text.append(features[f].getType());
\r
+ if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
\r
+ text.append(" " + features[f].getDescription());
\r
\r
\r
- if (sf.getStatus() != null && sf.getStatus().length()>0)
\r
+ if (features[f].getStatus() != null && features[f].getStatus().length()>0)
\r
{
\r
{
\r
- text.append(" (" + sf.getStatus() + ")");
\r
+ text.append(" (" + features[f].getStatus() + ")");
\r
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r