git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2388 Comment typo
[jalview.git]
/
src
/
jalview
/
appletgui
/
UserDefinedColours.java
diff --git
a/src/jalview/appletgui/UserDefinedColours.java
b/src/jalview/appletgui/UserDefinedColours.java
index
88098a9
..
95e36b5
100644
(file)
--- a/
src/jalview/appletgui/UserDefinedColours.java
+++ b/
src/jalview/appletgui/UserDefinedColours.java
@@
-22,6
+22,7
@@
package jalview.appletgui;
import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceGroup;
import jalview.api.FeatureColourI;
import jalview.datamodel.SequenceGroup;
+import jalview.renderer.ResidueShader;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.FeatureColour;
import jalview.schemes.ResidueProperties;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.FeatureColour;
import jalview.schemes.ResidueProperties;
@@
-93,7
+94,7
@@
public class UserDefinedColours extends Panel implements ActionListener,
if (seqGroup != null)
{
if (seqGroup != null)
{
- oldColourScheme = seqGroup.cs;
+ oldColourScheme = seqGroup.getColourScheme();
}
else
{
}
else
{
@@
-407,14
+408,9
@@
public class UserDefinedColours extends Panel implements ActionListener,
{
final Button button = new Button();
Color col = Color.white;
{
final Button button = new Button();
Color col = Color.white;
- if (oldColourScheme != null)
+ if (oldColourScheme != null && oldColourScheme.isSimple())
{
{
- try
- {
- col = oldColourScheme.findColour(aa.charAt(0), -1, null);
- } catch (Exception ex)
- {
- }
+ col = oldColourScheme.findColour(aa.charAt(0), 0, null, null, 0f);
}
button.setBackground(col);
oldColours.addElement(col);
}
button.setBackground(col);
oldColours.addElement(col);
@@
-501,20
+497,24
@@
public class UserDefinedColours extends Panel implements ActionListener,
}
UserColourScheme ucs = new UserColourScheme(newColours);
}
UserColourScheme ucs = new UserColourScheme(newColours);
- if (ap != null)
- {
- ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
- }
+ // if (ap != null)
+ // {
+ // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ // }
if (ap != null)
{
if (seqGroup != null)
{
if (ap != null)
{
if (seqGroup != null)
{
- seqGroup.cs = ucs;
+ seqGroup.cs = new ResidueShader(ucs);
+ seqGroup.getGroupColourScheme().setThreshold(0,
+ ap.av.isIgnoreGapsConsensus());
}
else
{
ap.av.setGlobalColourScheme(ucs);
}
else
{
ap.av.setGlobalColourScheme(ucs);
+ ap.av.getResidueShading().setThreshold(0,
+ ap.av.isIgnoreGapsConsensus());
}
ap.seqPanel.seqCanvas.img = null;
ap.paintAlignment(true);
}
ap.seqPanel.seqCanvas.img = null;
ap.paintAlignment(true);
@@
-592,7
+592,7
@@
public class UserDefinedColours extends Panel implements ActionListener,
{
if (seqGroup != null)
{
{
if (seqGroup != null)
{
- seqGroup.cs = ucs;
+ seqGroup.cs = new ResidueShader(ucs);
}
else
{
}
else
{