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Merge branch 'develop' into bug/JAL-2323disulfideOverview
[jalview.git]
/
src
/
jalview
/
renderer
/
AnnotationRenderer.java
diff --git
a/src/jalview/renderer/AnnotationRenderer.java
b/src/jalview/renderer/AnnotationRenderer.java
index
d7ae950
..
a0e530c
100644
(file)
--- a/
src/jalview/renderer/AnnotationRenderer.java
+++ b/
src/jalview/renderer/AnnotationRenderer.java
@@
-28,7
+28,7
@@
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.ProfileI;
+import jalview.datamodel.ProfilesI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.util.Platform;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.util.Platform;
@@
-74,7
+74,7
@@
public class AnnotationRenderer
private ColumnSelection columnSelection;
private ColumnSelection columnSelection;
- private ProfileI[] hconsensus;
+ private ProfilesI hconsensus;
private Hashtable[] complementConsensus;
private Hashtable[] complementConsensus;
@@
-352,7
+352,7
@@
public class AnnotationRenderer
{
// TODO? group consensus for cDNA complement
return AAFrequency.extractProfile(
{
// TODO? group consensus for cDNA complement
return AAFrequency.extractProfile(
- aa.groupRef.consensusData[column],
+ aa.groupRef.consensusData.get(column),
aa.groupRef.getIgnoreGapsConsensus());
}
// TODO extend annotation row to enable dynamic and static profile data to
aa.groupRef.getIgnoreGapsConsensus());
}
// TODO extend annotation row to enable dynamic and static profile data to
@@
-366,7
+366,8
@@
public class AnnotationRenderer
}
else
{
}
else
{
- return AAFrequency.extractProfile(hconsensus[column],
+ return AAFrequency.extractProfile(
+hconsensus.get(column),
av_ignoreGapsConsensus);
}
}
av_ignoreGapsConsensus);
}
}