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Status is now in otherData of feature
author
amwaterhouse
<Andrew Waterhouse>
Wed, 14 Jun 2006 10:17:45 +0000
(10:17 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Wed, 14 Jun 2006 10:17:45 +0000
(10:17 +0000)
src/jalview/appletgui/SeqPanel.java
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src/jalview/datamodel/SequenceFeature.java
patch
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src/jalview/gui/AlignmentPanel.java
patch
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src/jalview/gui/Jalview2XML.java
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src/jalview/gui/SeqPanel.java
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diff --git
a/src/jalview/appletgui/SeqPanel.java
b/src/jalview/appletgui/SeqPanel.java
index
4b7a45e
..
5ff10ce
100755
(executable)
--- a/
src/jalview/appletgui/SeqPanel.java
+++ b/
src/jalview/appletgui/SeqPanel.java
@@
-551,9
+551,9
@@
public class SeqPanel
if (sf.getDescription() != null)
\r
featureText.append(" " + sf.getDescription());
\r
\r
if (sf.getDescription() != null)
\r
featureText.append(" " + sf.getDescription());
\r
\r
- if (sf.getStatus() != null && sf.getStatus().length() > 0)
\r
+ if (sf.getValue("status") != null )
\r
{
\r
{
\r
- featureText.append(" (" + sf.getStatus() + ")");
\r
+ featureText.append(" (" + sf.getValue("status") + ")");
\r
}
\r
featureText.append("\n");
\r
\r
}
\r
featureText.append("\n");
\r
\r
diff --git
a/src/jalview/datamodel/SequenceFeature.java
b/src/jalview/datamodel/SequenceFeature.java
index
b054ea1
..
3d8744f
100755
(executable)
--- a/
src/jalview/datamodel/SequenceFeature.java
+++ b/
src/jalview/datamodel/SequenceFeature.java
@@
-33,7
+33,6
@@
public class SequenceFeature
public float score;
\r
public String type;
\r
public String description;
\r
public float score;
\r
public String type;
\r
public String description;
\r
- public String status;
\r
Hashtable otherDetails;
\r
public java.util.Vector links;
\r
\r
Hashtable otherDetails;
\r
public java.util.Vector links;
\r
\r
@@
-52,11
+51,14
@@
public class SequenceFeature
{
\r
this.type = type;
\r
this.description = desc;
\r
{
\r
this.type = type;
\r
this.description = desc;
\r
- this.status = status;
\r
+ if(status!=null)
\r
+ setValue("status", status);
\r
+
\r
this.begin = begin;
\r
this.end = end;
\r
this.featureGroup = featureGroup;
\r
}
\r
this.begin = begin;
\r
this.end = end;
\r
this.featureGroup = featureGroup;
\r
}
\r
+
\r
public SequenceFeature(String type,
\r
String desc,
\r
int begin, int end,
\r
public SequenceFeature(String type,
\r
String desc,
\r
int begin, int end,
\r
@@
-65,7
+67,6
@@
public class SequenceFeature
{
\r
this.type = type;
\r
this.description = desc;
\r
{
\r
this.type = type;
\r
this.description = desc;
\r
- this.status = status;
\r
this.begin = begin;
\r
this.end = end;
\r
this.score = score;
\r
this.begin = begin;
\r
this.end = end;
\r
this.score = score;
\r
@@
-79,8
+80,8
@@
public class SequenceFeature
return false;
\r
\r
\r
return false;
\r
\r
\r
- if(!(type+description+status).equals
\r
- (sf.type+sf.description+sf.status))
\r
+ if(!(type+description).equals
\r
+ (sf.type+sf.description))
\r
return false;
\r
\r
return true;
\r
return false;
\r
\r
return true;
\r
@@
-147,21
+148,6
@@
public class SequenceFeature
description = desc;
\r
}
\r
\r
description = desc;
\r
}
\r
\r
- /**
\r
- * DOCUMENT ME!
\r
- *
\r
- * @return DOCUMENT ME!
\r
- */
\r
- public String getStatus()
\r
- {
\r
- return status;
\r
- }
\r
-
\r
- public void setStatus(String status)
\r
- {
\r
- this.status = status;
\r
- }
\r
-
\r
public String getFeatureGroup()
\r
{
\r
return featureGroup;
\r
public String getFeatureGroup()
\r
{
\r
return featureGroup;
\r
diff --git
a/src/jalview/gui/AlignmentPanel.java
b/src/jalview/gui/AlignmentPanel.java
index
20ed37d
..
4a7a05d
100755
(executable)
--- a/
src/jalview/gui/AlignmentPanel.java
+++ b/
src/jalview/gui/AlignmentPanel.java
@@
-1171,9
+1171,9
@@
public class AlignmentPanel extends GAlignmentPanel
if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
\r
text.append(" " + features[f].getDescription());
\r
\r
if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
\r
text.append(" " + features[f].getDescription());
\r
\r
- if (features[f].getStatus() != null && features[f].getStatus().length()>0)
\r
+ if (features[f].getValue("status") != null )
\r
{
\r
{
\r
- text.append(" (" + features[f].getStatus() + ")");
\r
+ text.append(" (" + features[f].getValue("status") + ")");
\r
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r
diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
8ac5e8c
..
f79a158
100755
(executable)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-210,7
+210,6
@@
public class Jalview2XML
features.setBegin(sf[index].getBegin());
\r
features.setEnd(sf[index].getEnd());
\r
features.setDescription(sf[index].getDescription());
\r
features.setBegin(sf[index].getBegin());
\r
features.setEnd(sf[index].getEnd());
\r
features.setDescription(sf[index].getDescription());
\r
- features.setStatus(sf[index].getStatus());
\r
features.setType(sf[index].getType());
\r
features.setFeatureGroup(sf[index].getFeatureGroup());
\r
jseq.addFeatures(features);
\r
features.setType(sf[index].getType());
\r
features.setFeatureGroup(sf[index].getFeatureGroup());
\r
jseq.addFeatures(features);
\r
diff --git
a/src/jalview/gui/SeqPanel.java
b/src/jalview/gui/SeqPanel.java
index
79d55fd
..
d457593
100755
(executable)
--- a/
src/jalview/gui/SeqPanel.java
+++ b/
src/jalview/gui/SeqPanel.java
@@
-569,9
+569,9
@@
public class SeqPanel extends JPanel implements MouseListener,
&& !features[i].description.equals(features[i].getType()))
\r
sbuffer.append("; " + features[i].getDescription());
\r
\r
&& !features[i].description.equals(features[i].getType()))
\r
sbuffer.append("; " + features[i].getDescription());
\r
\r
- if (features[i].getStatus() != null && features[i].getStatus().length()>0)
\r
+ if (features[i].getValue("status") != null)
\r
{
\r
{
\r
- sbuffer.append("; (" + features[i].getStatus() + ")");
\r
+ sbuffer.append("; (" + features[i].getValue("status") + ")");
\r
}
\r
if (features[i].links != null)
\r
sbuffer.append(" <img src=\"" + linkImageURL + "\">");
\r
}
\r
if (features[i].links != null)
\r
sbuffer.append(" <img src=\"" + linkImageURL + "\">");
\r