git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2533 update javadoc
[jalview.git]
/
src
/
jalview
/
gui
/
SequenceRenderer.java
diff --git
a/src/jalview/gui/SequenceRenderer.java
b/src/jalview/gui/SequenceRenderer.java
index
764ef3f
..
91c3f0f
100755
(executable)
--- a/
src/jalview/gui/SequenceRenderer.java
+++ b/
src/jalview/gui/SequenceRenderer.java
@@
-53,14
+53,13
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
boolean forOverview = false;
/**
boolean forOverview = false;
/**
- * Creates a new SequenceRenderer object.
+ * Creates a new SequenceRenderer object
*
*
- * @param av
- * DOCUMENT ME!
+ * @param viewport
*/
*/
- public SequenceRenderer(AlignViewport av)
+ public SequenceRenderer(AlignViewport viewport)
{
{
- this.av = av;
+ this.av = viewport;
}
/**
}
/**
@@
-83,8
+82,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
this.renderGaps = renderGaps;
}
this.renderGaps = renderGaps;
}
- @Override
- public Color getResidueBoxColour(SequenceI seq, int i)
+ protected Color getResidueBoxColour(SequenceI seq, int i)
{
// rate limiting step when rendering overview for lots of groups
allGroups = av.getAlignment().findAllGroups(seq);
{
// rate limiting step when rendering overview for lots of groups
allGroups = av.getAlignment().findAllGroups(seq);
@@
-118,8
+116,6
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
public Color getResidueColour(final SequenceI seq, int position,
FeatureColourFinder finder)
{
public Color getResidueColour(final SequenceI seq, int position,
FeatureColourFinder finder)
{
- // TODO replace 8 or so code duplications with calls to this method
- // (refactored as needed)
Color col = getResidueBoxColour(seq, position);
if (finder != null)
Color col = getResidueBoxColour(seq, position);
if (finder != null)
@@
-141,7
+137,7
@@
public class SequenceRenderer implements jalview.api.SequenceRenderer
*/
void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
*/
void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
- if (shader != null)
+ if (shader.getColourScheme() != null)
{
resBoxColour = shader.findColour(seq.getCharAt(i),
i, seq);
{
resBoxColour = shader.findColour(seq.getCharAt(i),
i, seq);