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[jalview.git]
/
src
/
jalview
/
gui
/
SequenceRenderer.java
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
8d7755c
..
6c7fb37
100755
(executable)
--- a/
src/jalview/gui/SequenceRenderer.java
+++ b/
src/jalview/gui/SequenceRenderer.java
@@
-104,7
+104,7
@@
public class SequenceRenderer
{
\r
if (cs != null)
\r
{
\r
{
\r
if (cs != null)
\r
{
\r
- resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
\r
+ resBoxColour = cs.findColour(seq.getCharAt(i), i);
\r
}
\r
else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
\r
{
\r
}
\r
else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
\r
{
\r
@@
-236,12
+236,12
@@
public class SequenceRenderer
&& !av.getColourText()
\r
&& av.thresholdTextColour==0)
\r
{
\r
&& !av.getColourText()
\r
&& av.thresholdTextColour==0)
\r
{
\r
- if(av.renderGaps)
\r
- graphics.drawString(seq.getSequence(start, end + 1), 0, y1);
\r
- else
\r
+ if (av.renderGaps)
\r
+ graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
\r
+ else
\r
{
\r
char gap = av.getGapCharacter();
\r
{
\r
char gap = av.getGapCharacter();
\r
- graphics.drawString( seq.getSequence(start, end+1).replace(gap, ' '), 0, y1);
\r
+ graphics.drawString( seq.getSequenceAsString(start, end+1).replace(gap, ' '), 0, y1);
\r
}
\r
}
\r
else
\r
}
\r
}
\r
else
\r
@@
-387,7
+387,7
@@
public class SequenceRenderer
{
\r
if (i < seq.getLength())
\r
{
\r
{
\r
if (i < seq.getLength())
\r
{
\r
- s = seq.getSequence().charAt(i);
\r
+ s = seq.getCharAt(i);
\r
}
\r
\r
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
\r
}
\r
\r
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
\r