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(JAL-978) refactored JABAWS2 service handle class to own package
[jalview.git]
/
src
/
jalview
/
renderer
/
AnnotationRenderer.java
diff --git
a/src/jalview/renderer/AnnotationRenderer.java
b/src/jalview/renderer/AnnotationRenderer.java
index
5c03881
..
d063c5b
100644
(file)
--- a/
src/jalview/renderer/AnnotationRenderer.java
+++ b/
src/jalview/renderer/AnnotationRenderer.java
@@
-163,7
+163,8
@@
public class AnnotationRenderer
{
if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
{
{
if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
{
- if (aa.groupRef != null && aa.groupRef.consensusData != null
+ // TODO implement group structure consensus
+ /* if (aa.groupRef != null && aa.groupRef.consensusData != null
&& aa.groupRef.isShowSequenceLogo())
{
//TODO check what happens for group selections
&& aa.groupRef.isShowSequenceLogo())
{
//TODO check what happens for group selections
@@
-171,11
+172,12
@@
public class AnnotationRenderer
aa.groupRef.consensusData[column], aa.groupRef
.getIgnoreGapsConsensus());
}
aa.groupRef.consensusData[column], aa.groupRef
.getIgnoreGapsConsensus());
}
+ */
// TODO extend annotation row to enable dynamic and static profile data
// to
// be stored
if (aa.groupRef == null && aa.sequenceRef == null
// TODO extend annotation row to enable dynamic and static profile data
// to
// be stored
if (aa.groupRef == null && aa.sequenceRef == null
- && av_renderProfile)
+ && av_renderProfile && hStrucConsensus!=null && hStrucConsensus.length>column)
{
return StructureFrequency.extractProfile(hStrucConsensus[column],
av_ignoreGapsConsensus);
{
return StructureFrequency.extractProfile(hStrucConsensus[column],
av_ignoreGapsConsensus);
@@
-201,6
+203,7
@@
public class AnnotationRenderer
// NOTES:
// AnnotationPanel needs to implement: ImageObserver, access to AlignViewport
updateFromAwtRenderPanel(annotPanel, av);
// NOTES:
// AnnotationPanel needs to implement: ImageObserver, access to AlignViewport
updateFromAwtRenderPanel(annotPanel, av);
+ fm = g.getFontMetrics();
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
int x = 0, y = 0;
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
int x = 0, y = 0;
@@
-344,7
+347,11
@@
public class AnnotationRenderer
}
}
}
}
}
}
-
+ if (!row.isValidStruc())
+ {
+ g.setColor(Color.orange);
+ g.fillRect((int)row.getInvalidStrucPos()*charWidth, y, charWidth, charHeight);
+ }
if (validCharWidth
&& validRes
&& row.annotations[column].displayCharacter != null
if (validCharWidth
&& validRes
&& row.annotations[column].displayCharacter != null
@@
-471,6
+478,15
@@
public class AnnotationRenderer
{
validEnd = true;
}
{
validEnd = true;
}
+ if ((row.annotations == null) || (row.annotations.length <= column)
+ || (row.annotations[column] == null))
+ {
+ validRes = false;
+ }
+ else
+ {
+ validRes = true;
+ }
// x ++;
// x ++;