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7131594
)
FeatureSettings bug fixed
author
amwaterhouse
<Andrew Waterhouse>
Fri, 24 Mar 2006 15:35:10 +0000
(15:35 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Fri, 24 Mar 2006 15:35:10 +0000
(15:35 +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
7e2d1dd
..
893846c
100755
(executable)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-472,8
+472,9
@@
public class Jalview2XML
setting.setColour(
\r
af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB()
\r
);
\r
setting.setColour(
\r
af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB()
\r
);
\r
+
\r
setting.setDisplay(
\r
setting.setDisplay(
\r
- av.featuresDisplayed.contains(type)
\r
+ av.featuresDisplayed.containsKey(type)
\r
);
\r
\r
fs.addSetting(setting);
\r
);
\r
\r
fs.addSetting(setting);
\r
@@
-679,12
+680,12
@@
public class Jalview2XML
Features[] features = JSEQ[i].getFeatures();
\r
for (int f = 0; f < features.length; f++)
\r
{
\r
Features[] features = JSEQ[i].getFeatures();
\r
for (int f = 0; f < features.length; f++)
\r
{
\r
- //features[f].getBegin()
\r
jalview.datamodel.SequenceFeature sf
\r
= new jalview.datamodel.SequenceFeature(features[f].getType(),
\r
features[f].getDescription(), features[f].getStatus(),
\r
jalview.datamodel.SequenceFeature sf
\r
= new jalview.datamodel.SequenceFeature(features[f].getType(),
\r
features[f].getDescription(), features[f].getStatus(),
\r
- features[f].getBegin(), features[f].getEnd());
\r
- sf.setFeatureGroup(features[f].getFeatureGroup());
\r
+ features[f].getBegin(), features[f].getEnd(),
\r
+ features[f].getFeatureGroup());
\r
+
\r
al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
\r
}
\r
}
\r
al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
\r
}
\r
}
\r
@@
-701,7
+702,8
@@
public class Jalview2XML
\r
}
\r
}
\r
\r
}
\r
}
\r
- /////////////////////////////////
\r
+
\r
+ /////////////////////////////////
\r
//////////////////////////////////
\r
//LOAD ANNOTATIONS
\r
if (vamsasSet.getAnnotation() != null)
\r
//////////////////////////////////
\r
//LOAD ANNOTATIONS
\r
if (vamsasSet.getAnnotation() != null)
\r
@@
-739,6
+741,7
@@
public class Jalview2XML
}
\r
}
\r
\r
}
\r
}
\r
\r
+
\r
/////////////////////////////////
\r
// LOAD VIEWPORT
\r
Viewport[] views = jms.getViewport();
\r
/////////////////////////////////
\r
// LOAD VIEWPORT
\r
Viewport[] views = jms.getViewport();
\r
@@
-805,6
+808,7
@@
public class Jalview2XML
}
\r
\r
\r
}
\r
\r
\r
+
\r
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
\r
view.getHeight());
\r
af.viewport.setStartRes(view.getStartRes());
\r
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
\r
view.getHeight());
\r
af.viewport.setStartRes(view.getStartRes());
\r
@@
-889,20
+893,24
@@
public class Jalview2XML
if(jms.getFeatureSettings()!=null)
\r
{
\r
af.viewport.featuresDisplayed = new Hashtable();
\r
if(jms.getFeatureSettings()!=null)
\r
{
\r
af.viewport.featuresDisplayed = new Hashtable();
\r
- // af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)
\r
- // jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();
\r
+ String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
\r
for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
\r
{
\r
Setting setting = jms.getFeatureSettings().getSetting(fs);
\r
\r
af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
\r
new java.awt.Color(setting.getColour()));
\r
for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
\r
{
\r
Setting setting = jms.getFeatureSettings().getSetting(fs);
\r
\r
af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
\r
new java.awt.Color(setting.getColour()));
\r
+
\r
+ renderOrder[fs] = setting.getType();
\r
+
\r
if(setting.getDisplay())
\r
af.viewport.featuresDisplayed.put(
\r
setting.getType(), new Integer(setting.getColour()));
\r
}
\r
if(setting.getDisplay())
\r
af.viewport.featuresDisplayed.put(
\r
setting.getType(), new Integer(setting.getColour()));
\r
}
\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
\r
}
\r
\r
}
\r
\r
+
\r
Desktop.addInternalFrame(af, view.getTitle(),
\r
view.getWidth(), view.getHeight());
\r
\r
Desktop.addInternalFrame(af, view.getTitle(),
\r
view.getWidth(), view.getHeight());
\r
\r