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JAL-3949 fixed failing commandlinetests due to more output and line count limit
[jalview.git]
/
src
/
jalview
/
schemes
/
RNAInteractionColourScheme.java
diff --git
a/src/jalview/schemes/RNAInteractionColourScheme.java
b/src/jalview/schemes/RNAInteractionColourScheme.java
index
f4c831a
..
8610417
100644
(file)
--- a/
src/jalview/schemes/RNAInteractionColourScheme.java
+++ b/
src/jalview/schemes/RNAInteractionColourScheme.java
@@
-20,12
+20,11
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import java.awt.Color;
import jalview.datamodel.SequenceI;
import java.awt.Color;
-import java.util.Map;
public class RNAInteractionColourScheme extends ResidueColourScheme
{
public class RNAInteractionColourScheme extends ResidueColourScheme
{
@@
-45,25
+44,12
@@
public class RNAInteractionColourScheme extends ResidueColourScheme
public Color findColour(char c, int j, SequenceI seq)
{
// FIXME this is just a copy of NucleotideColourScheme
public Color findColour(char c, int j, SequenceI seq)
{
// FIXME this is just a copy of NucleotideColourScheme
- Color currentColour;
- if ((threshold == 0) || aboveThreshold(c, j))
+ Color currentColour = Color.white;
+ try
{
{
- try
- {
- currentColour = colors[ResidueProperties.nucleotideIndex[c]];
- } catch (Exception ex)
- {
- return Color.white;
- }
- }
- else
- {
- return Color.white;
- }
-
- if (conservationColouring)
+ currentColour = colors[ResidueProperties.nucleotideIndex[c]];
+ } catch (Exception ex)
{
{
- currentColour = applyConservation(currentColour, j);
}
return currentColour;
}
return currentColour;
@@
-86,8
+72,8
@@
public class RNAInteractionColourScheme extends ResidueColourScheme
* be coloured
*/
@Override
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new RNAInteractionColourScheme();
}
{
return new RNAInteractionColourScheme();
}