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JAL-2432 percentage checkbox follows threshold value field
[jalview.git]
/
src
/
jalview
/
appletgui
/
AnnotationColourChooser.java
diff --git
a/src/jalview/appletgui/AnnotationColourChooser.java
b/src/jalview/appletgui/AnnotationColourChooser.java
index
d4a21b2
..
f516bc9
100644
(file)
--- a/
src/jalview/appletgui/AnnotationColourChooser.java
+++ b/
src/jalview/appletgui/AnnotationColourChooser.java
@@
-20,6
+20,12
@@
*/
package jalview.appletgui;
*/
package jalview.appletgui;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+
import java.awt.BorderLayout;
import java.awt.Button;
import java.awt.Checkbox;
import java.awt.BorderLayout;
import java.awt.Button;
import java.awt.Checkbox;
@@
-44,12
+50,6
@@
import java.util.HashMap;
import java.util.Map;
import java.util.Vector;
import java.util.Map;
import java.util.Vector;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.SequenceGroup;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
public class AnnotationColourChooser extends Panel implements
ActionListener, AdjustmentListener, ItemListener, MouseListener
{
public class AnnotationColourChooser extends Panel implements
ActionListener, AdjustmentListener, ItemListener, MouseListener
{
@@
-88,10
+88,7
@@
public class AnnotationColourChooser extends Panel implements
oldgroupColours = new HashMap<SequenceGroup, ColourSchemeI>();
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
oldgroupColours = new HashMap<SequenceGroup, ColourSchemeI>();
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- if (sg.cs != null)
- {
- oldgroupColours.put(sg, sg.cs);
- }
+ oldgroupColours.put(sg, sg.getColourScheme());
}
}
this.av = av;
}
}
this.av = av;
@@
-519,8
+516,6
@@
public class AnnotationColourChooser extends Panel implements
AnnotationColourGradient acg = null;
if (currentColours.getState())
{
AnnotationColourGradient acg = null;
if (currentColours.getState())
{
- acg = new AnnotationColourGradient(currentAnnotation,
- av.getGlobalColourScheme(), aboveThreshold);
}
else
{
}
else
{
@@
-544,21
+539,21
@@
public class AnnotationColourChooser extends Panel implements
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- if (sg.cs == null)
+ if (sg.getColourScheme() == null)
{
continue;
}
if (currentColours.getState())
{
{
continue;
}
if (currentColours.getState())
{
- sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
- aboveThreshold);
+ sg.setColourScheme(new AnnotationColourGradient(
+ currentAnnotation, sg.getColourScheme(), aboveThreshold));
}
else
{
}
else
{
- sg.cs = new AnnotationColourGradient(currentAnnotation,
- minColour.getBackground(), maxColour.getBackground(),
- aboveThreshold);
+ sg.setColourScheme(new AnnotationColourGradient(
+ currentAnnotation, minColour.getBackground(), maxColour
+ .getBackground(), aboveThreshold));
}
}
}
}
}
}
@@
-575,11
+570,10
@@
public class AnnotationColourChooser extends Panel implements
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- sg.cs = oldgroupColours.get(sg);
+ sg.setColourScheme(oldgroupColours.get(sg));
}
}
ap.paintAlignment(true);
}
}
ap.paintAlignment(true);
-
}
@Override
}
@Override