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JAL-2089 Merge branch releases/Release_2_10_Branch to master
[jalview.git]
/
src
/
jalview
/
io
/
SequenceAnnotationReport.java
diff --git
a/src/jalview/io/SequenceAnnotationReport.java
b/src/jalview/io/SequenceAnnotationReport.java
index
676404b
..
dd0664b
100644
(file)
--- a/
src/jalview/io/SequenceAnnotationReport.java
+++ b/
src/jalview/io/SequenceAnnotationReport.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-23,6
+23,7
@@
package jalview.io;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.io.gff.GffConstants;
import jalview.util.DBRefUtils;
import jalview.util.UrlLink;
import jalview.util.DBRefUtils;
import jalview.util.UrlLink;
@@
-140,8
+141,7
@@
public class SequenceAnnotationReport
}
else
{
}
else
{
- if (tmpString.indexOf("<") > -1
- || tmpString.indexOf(">") > -1)
+ if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
{
// The description does not specify html is to
// be used, so we must remove < > symbols
{
// The description does not specify html is to
// be used, so we must remove < > symbols
@@
-166,8
+166,7
@@
public class SequenceAnnotationReport
.getType());
if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
{
.getType());
if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
{
- sb.append(" Score=").append(
- String.valueOf(feature.getScore()));
+ sb.append(" Score=").append(String.valueOf(feature.getScore()));
}
}
String status = (String) feature.getValue("status");
}
}
String status = (String) feature.getValue("status");
@@
-175,6
+174,12
@@
public class SequenceAnnotationReport
{
sb.append("; (").append(status).append(")");
}
{
sb.append("; (").append(status).append(")");
}
+ String clinSig = (String) feature
+ .getValue(GffConstants.CLINICAL_SIGNIFICANCE);
+ if (clinSig != null)
+ {
+ sb.append("; ").append(clinSig);
+ }
}
}
appendLinks(sb, feature);
}
}
appendLinks(sb, feature);
@@
-305,8
+310,7
@@
public class SequenceAnnotationReport
String unq = urls[u] + "|" + urls[u + 1];
if (!uniques.contains(unq))
{
String unq = urls[u] + "|" + urls[u + 1];
if (!uniques.contains(unq))
{
- result.add(new String[] { target, label, urls[u],
- urls[u + 1] });
+ result.add(new String[] { target, label, urls[u], urls[u + 1] });
uniques.add(unq);
}
}
uniques.add(unq);
}
}
@@
-324,8
+328,7
@@
public class SequenceAnnotationReport
String unq = urls[u] + "|" + urls[u + 1];
if (!uniques.contains(unq))
{
String unq = urls[u] + "|" + urls[u + 1];
if (!uniques.contains(unq))
{
- result.add(new String[] { target, label, urls[u],
- urls[u + 1] });
+ result.add(new String[] { target, label, urls[u], urls[u + 1] });
uniques.add(unq);
}
}
uniques.add(unq);
}
}
@@
-342,8
+345,7
@@
public class SequenceAnnotationReport
String unq = urls[u] + "|" + urls[u + 1];
if (!uniques.contains(unq))
{
String unq = urls[u] + "|" + urls[u + 1];
if (!uniques.contains(unq))
{
- result.add(new String[] { target, label, urls[u],
- urls[u + 1] });
+ result.add(new String[] { target, label, urls[u], urls[u + 1] });
uniques.add(unq);
}
}
uniques.add(unq);
}
}