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JAL-1842 remove redundant call to FeatureRenderer.featuresAdded()
[jalview.git]
/
src
/
jalview
/
schemes
/
CovariationColourScheme.java
diff --git
a/src/jalview/schemes/CovariationColourScheme.java
b/src/jalview/schemes/CovariationColourScheme.java
index
ee78317
..
dc7971b
100644
(file)
--- a/
src/jalview/schemes/CovariationColourScheme.java
+++ b/
src/jalview/schemes/CovariationColourScheme.java
@@
-20,10
+20,10
@@
*/
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 java.util.Hashtable;
import java.awt.Color;
import java.util.Hashtable;
@@
-37,9
+37,9
@@
import java.util.Map;
*/
public class CovariationColourScheme extends ResidueColourScheme
{
*/
public class CovariationColourScheme extends ResidueColourScheme
{
- public Hashtable helixcolorhash = new Hashtable();
+ public Map<String, Color> helixcolorhash = new Hashtable<>();
- public Hashtable positionsToHelix = new Hashtable();
+ public Map<Integer, String> positionsToHelix = new Hashtable<>();
int numHelix = 0;
int numHelix = 0;
@@
-50,8
+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]);
}
@@
-76,18
+76,19
@@
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());
}
}
for (int j = 0; j <= numHelix; j++)
{
}
}
for (int j = 0; j <= numHelix; j++)
{
- helixcolorhash.put(Integer.toString(j),
- jalview.util.ColorUtils.generateRandomColor(Color.white));
+ helixcolorhash.put(String.valueOf(j),
+ ColorUtils.generateRandomColor(Color.white));
}
}
}
}
@@
-124,12
+125,12
@@
public class CovariationColourScheme extends ResidueColourScheme
Color currentColour = Color.white;
String currentHelix = null;
// System.out.println(c + " " + j);
Color currentColour = Color.white;
String currentHelix = null;
// System.out.println(c + " " + j);
- currentHelix = (String) positionsToHelix.get(j);
+ currentHelix = positionsToHelix.get(j);
// System.out.println(positionsToHelix.get(j));
if (currentHelix != null)
{
// System.out.println(positionsToHelix.get(j));
if (currentHelix != null)
{
- currentColour = (Color) helixcolorhash.get(currentHelix);
+ currentColour = helixcolorhash.get(currentHelix);
}
// System.out.println(c + " " + j + " helix " + currentHelix + " " +
}
// System.out.println(c + " " + j + " helix " + currentHelix + " " +
@@
-148,4
+149,10
@@
public class CovariationColourScheme extends ResidueColourScheme
{
return "Covariation";
}
{
return "Covariation";
}
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}
}