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No score colour scheme, group colours saved if conservation applied
author
amwaterhouse
<Andrew Waterhouse>
Wed, 17 Aug 2005 09:08:50 +0000
(09:08 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Wed, 17 Aug 2005 09:08:50 +0000
(09:08 +0000)
src/jalview/gui/Jalview2XML.java
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diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
5d94c3c
..
a449d7f
100755
(executable)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-297,29
+297,35
@@
public class Jalview2XML
\r
if (sg.cs instanceof ConservationColourScheme)
\r
{
\r
\r
if (sg.cs instanceof ConservationColourScheme)
\r
{
\r
- groups[i].setConsThreshold(((ConservationColourScheme) sg.cs).inc);
\r
- }
\r
+ ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
\r
+ groups[i].setConsThreshold(ccs.inc);
\r
+
\r
+ if (ccs.cs instanceof jalview.schemes.UserColourScheme)
\r
+ {
\r
+ groups[i].setColour(SetUserColourScheme(ccs.cs, userColours,
\r
+ jms));
\r
+ }
\r
\r
\r
- if (sg.cs instanceof ResidueColourScheme)
\r
- {
\r
- groups[i].setPidThreshold(((ResidueColourScheme) sg.cs).getThreshold());
\r
- }
\r
- else if (sg.cs instanceof ScoreColourScheme)
\r
- {
\r
- groups[i].setPidThreshold(((ScoreColourScheme) sg.cs).getThreshold());
\r
}
\r
\r
}
\r
\r
- if (sg.cs instanceof jalview.schemes.UserColourScheme)
\r
+ else if (sg.cs instanceof jalview.schemes.UserColourScheme)
\r
{
\r
groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
\r
jms));
\r
}
\r
else
\r
{
\r
{
\r
groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
\r
jms));
\r
}
\r
else
\r
{
\r
- groups[i].setColour(ColourSchemeProperty.getColourName(
\r
- sg.cs));
\r
+ groups[i].setColour(ColourSchemeProperty.getColourName(
\r
+ sg.cs));
\r
+ }
\r
+
\r
+ if (sg.cs instanceof ResidueColourScheme)
\r
+ {
\r
+ groups[i].setPidThreshold(((ResidueColourScheme) sg.cs).getThreshold());
\r
}
\r
\r
}
\r
\r
+
\r
+
\r
groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
\r
groups[i].setDisplayBoxes(sg.getDisplayBoxes());
\r
groups[i].setDisplayText(sg.getDisplayText());
\r
groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
\r
groups[i].setDisplayBoxes(sg.getDisplayBoxes());
\r
groups[i].setDisplayText(sg.getDisplayText());
\r
@@
-361,17
+367,16
@@
public class Jalview2XML
\r
if (cs instanceof ConservationColourScheme)
\r
{
\r
\r
if (cs instanceof ConservationColourScheme)
\r
{
\r
- view.setConsThreshold(((ConservationColourScheme) cs).inc);
\r
+ ConservationColourScheme ccs = (ConservationColourScheme)cs;
\r
+ view.setConsThreshold(ccs.inc);
\r
+ if(ccs.cs instanceof jalview.schemes.UserColourScheme)
\r
+ view.setBgColour(SetUserColourScheme(ccs.cs, userColours, jms));
\r
}
\r
\r
if (cs instanceof ResidueColourScheme)
\r
{
\r
view.setPidThreshold(((ResidueColourScheme) cs).getThreshold());
\r
}
\r
}
\r
\r
if (cs instanceof ResidueColourScheme)
\r
{
\r
view.setPidThreshold(((ResidueColourScheme) cs).getThreshold());
\r
}
\r
- else if (cs instanceof ScoreColourScheme)
\r
- {
\r
- view.setPidThreshold(((ScoreColourScheme) cs).getThreshold());
\r
- }
\r
\r
view.setConservationSelected(av.getConservationSelected());
\r
view.setPidSelected(av.getAbovePIDThreshold());
\r
\r
view.setConservationSelected(av.getConservationSelected());
\r
view.setPidSelected(av.getAbovePIDThreshold());
\r
@@
-634,10
+639,6
@@
public class Jalview2XML
{
\r
((ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold(), true);
\r
}
\r
{
\r
((ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold(), true);
\r
}
\r
- else if (cs instanceof ScoreColourScheme)
\r
- {
\r
- ((ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold(), true);
\r
- }
\r
}
\r
\r
Vector seqs = new Vector();
\r
}
\r
\r
Vector seqs = new Vector();
\r
@@
-734,10
+735,6
@@
public class Jalview2XML
{
\r
((ResidueColourScheme) cs).setThreshold(view.getPidThreshold(), true);
\r
}
\r
{
\r
((ResidueColourScheme) cs).setThreshold(view.getPidThreshold(), true);
\r
}
\r
- else if (cs instanceof ScoreColourScheme)
\r
- {
\r
- ((ScoreColourScheme) cs).setThreshold(view.getPidThreshold(), true);
\r
- }
\r
\r
if(cs!=null)
\r
cs.setConsensus(af.viewport.vconsensus);
\r
\r
if(cs!=null)
\r
cs.setConsensus(af.viewport.vconsensus);
\r