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Correction for feature rendering
author
amwaterhouse
<Andrew Waterhouse>
Mon, 28 Nov 2005 17:15:06 +0000
(17:15 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Mon, 28 Nov 2005 17:15:06 +0000
(17:15 +0000)
src/jalview/io/HTMLOutput.java
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diff --git
a/src/jalview/io/HTMLOutput.java
b/src/jalview/io/HTMLOutput.java
index
00c7364
..
beb8829
100755
(executable)
--- a/
src/jalview/io/HTMLOutput.java
+++ b/
src/jalview/io/HTMLOutput.java
@@
-24,7
+24,6
@@
import java.awt.*;
\r
import jalview.datamodel.*;
\r
import jalview.gui.*;
\r
\r
import jalview.datamodel.*;
\r
import jalview.gui.*;
\r
-import jalview.schemes.*;
\r
\r
public class HTMLOutput
\r
{
\r
\r
public class HTMLOutput
\r
{
\r
@@
-141,10
+140,15
@@
public class HTMLOutput
\r
for (int res = 0; res < seq.getLength(); res++)
\r
{
\r
\r
for (int res = 0; res < seq.getLength(); res++)
\r
{
\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
\r
+ {
\r
+ color = sr.getResidueBoxColour(seq, res);
\r
\r
\r
- color = sr.findSequenceColour(Color.white, seq, res);
\r
+ color = fr.findFeatureColour(color, seq, res);
\r
+ }
\r
+ else
\r
+ color = Color.white;
\r
\r
\r
- color = fr.findFeatureColour(color, seq, res);
\r
\r
if (color.getRGB() < -1)
\r
{
\r
\r
if (color.getRGB() < -1)
\r
{
\r
@@
-235,9
+239,14
@@
public class HTMLOutput
\r
for (int res = startRes; res < endRes; res++)
\r
{
\r
\r
for (int res = startRes; res < endRes; res++)
\r
{
\r
- color = sr.findSequenceColour(Color.white, seq, res);
\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
\r
+ {
\r
+ color = sr.getResidueBoxColour(seq, res);
\r
\r
\r
- color = fr.findFeatureColour(color, seq, res);
\r
+ color = fr.findFeatureColour(color, seq, res);
\r
+ }
\r
+ else
\r
+ color = Color.white;
\r
\r
if (color.getRGB() < -1)
\r
{
\r
\r
if (color.getRGB() < -1)
\r
{
\r