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JAL-3081 sort annotations by order read from project after reloading
[jalview.git]
/
src
/
jalview
/
schemes
/
CovariationColourScheme.java
diff --git
a/src/jalview/schemes/CovariationColourScheme.java
b/src/jalview/schemes/CovariationColourScheme.java
index
3637ce3
..
dc7971b
100644
(file)
--- a/
src/jalview/schemes/CovariationColourScheme.java
+++ b/
src/jalview/schemes/CovariationColourScheme.java
@@
-20,10
+20,9
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceI;
import jalview.util.ColorUtils;
import java.awt.Color;
import jalview.util.ColorUtils;
import java.awt.Color;
@@
-38,9
+37,9
@@
import java.util.Map;
*/
public class CovariationColourScheme extends ResidueColourScheme
{
*/
public class CovariationColourScheme extends ResidueColourScheme
{
- public Map<String, Color> helixcolorhash = new Hashtable<String, Color>();
+ public Map<String, Color> helixcolorhash = new Hashtable<>();
- public Map<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
+ public Map<Integer, String> positionsToHelix = new Hashtable<>();
int numHelix = 0;
int numHelix = 0;
@@
-51,8
+50,8
@@
public class CovariationColourScheme 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 CovariationColourScheme(coll.getAlignmentAnnotation()[0]);
}
{
return new CovariationColourScheme(coll.getAlignmentAnnotation()[0]);
}
@@
-77,10
+76,11
@@
public class CovariationColourScheme extends ResidueColourScheme
positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
this.annotation._rnasecstr[x].getFeatureGroup());
positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
this.annotation._rnasecstr[x].getFeatureGroup());
- if (Integer.parseInt(this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
+ if (Integer.parseInt(
+ this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
{
{
- numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
- .getFeatureGroup());
+ numHelix = Integer
+ .parseInt(this.annotation._rnasecstr[x].getFeatureGroup());
}
}
}
}
@@
-149,4
+149,10
@@
public class CovariationColourScheme extends ResidueColourScheme
{
return "Covariation";
}
{
return "Covariation";
}
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}
}