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Merge branch 'develop' into features/JAL-2094_colourInterface
[jalview.git]
/
src
/
jalview
/
viewmodel
/
seqfeatures
/
FeatureRendererModel.java
diff --git
a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index
d813fe2
..
9733081
100644
(file)
--- a/
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/
src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@
-27,8
+27,10
@@
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureRenderer;
+import jalview.schemes.Colour;
import jalview.schemes.FeatureColour;
import jalview.schemes.UserColourScheme;
import jalview.schemes.FeatureColour;
import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
import java.awt.Color;
import java.beans.PropertyChangeListener;
import java.awt.Color;
import java.beans.PropertyChangeListener;
@@
-65,6
+67,12
@@
public abstract class FeatureRendererModel implements
protected AlignViewportI av;
protected AlignViewportI av;
+ /*
+ * map holds per feature type, {{min, max}, {min, max}} feature score
+ * values for positional and non-positional features respectively
+ */
+ private Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
+
@Override
public AlignViewportI getViewport()
{
@Override
public AlignViewportI getViewport()
{
@@
-191,8
+199,6
@@
public abstract class FeatureRendererModel implements
renderOrder = neworder;
}
renderOrder = neworder;
}
- protected Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
-
public Map<String, float[][]> getMinMax()
{
return minmax;
public Map<String, float[][]> getMinMax()
{
return minmax;
@@
-539,7
+545,7
@@
public abstract class FeatureRendererModel implements
if (fc == null)
{
Color col = UserColourScheme.createColourFromName(featureType);
if (fc == null)
{
Color col = UserColourScheme.createColourFromName(featureType);
- fc = new FeatureColour(col);
+ fc = new FeatureColour(new Colour(col));
featureColours.put(featureType, fc);
}
return fc;
featureColours.put(featureType, fc);
}
return fc;
@@
-555,7
+561,7
@@
public abstract class FeatureRendererModel implements
public Color getColour(SequenceFeature feature)
{
FeatureColourI fc = getFeatureStyle(feature.getType());
public Color getColour(SequenceFeature feature)
{
FeatureColourI fc = getFeatureStyle(feature.getType());
- return fc.getColor(feature);
+ return ColorUtils.getColor(fc.getColor(feature));
}
protected boolean showFeature(SequenceFeature sequenceFeature)
}
protected boolean showFeature(SequenceFeature sequenceFeature)
@@
-759,9
+765,6
@@
public abstract class FeatureRendererModel implements
return renderOrder != null;
}
return renderOrder != null;
}
- /**
- * Returns feature types in ordering of rendering, where last means on top
- */
public List<String> getRenderOrder()
{
if (renderOrder == null)
public List<String> getRenderOrder()
{
if (renderOrder == null)
@@
-811,7
+814,7
@@
public abstract class FeatureRendererModel implements
* @return list of groups
*/
@Override
* @return list of groups
*/
@Override
- public List getGroups(boolean visible)
+ public List<String> getGroups(boolean visible)
{
if (featureGroups != null)
{
{
if (featureGroups != null)
{
@@
-882,10
+885,6
@@
public abstract class FeatureRendererModel implements
return av.getFeaturesDisplayed();
}
return av.getFeaturesDisplayed();
}
- /**
- * Returns a (possibly empty) list of visible feature types, in render order
- * (last is on top)
- */
@Override
public List<String> getDisplayedFeatureTypes()
{
@Override
public List<String> getDisplayedFeatureTypes()
{