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ensure lastSeq is refreshed if new feature added
[jalview.git]
/
src
/
jalview
/
io
/
AnnotationFile.java
diff --git
a/src/jalview/io/AnnotationFile.java
b/src/jalview/io/AnnotationFile.java
index
801a9ab
..
04861a2
100755
(executable)
--- a/
src/jalview/io/AnnotationFile.java
+++ b/
src/jalview/io/AnnotationFile.java
@@
-287,7
+287,7
@@
public class AnnotationFile
\r
if(refSeq!=null)
\r
{
\r
\r
if(refSeq!=null)
\r
{
\r
- annotation.createSequenceMapping(refSeq, refSeqIndex);
\r
+ annotation.createSequenceMapping(refSeq, refSeqIndex, false);
\r
refSeq.addAlignmentAnnotation(annotation);
\r
}
\r
\r
refSeq.addAlignmentAnnotation(annotation);
\r
}
\r
\r
@@
-333,7
+333,8
@@
public class AnnotationFile
// Either this character represents a helix or sheet
\r
// or an integer which can be displayed
\r
ss = token.charAt(0);
\r
// Either this character represents a helix or sheet
\r
// or an integer which can be displayed
\r
ss = token.charAt(0);
\r
- displayChar = "";
\r
+ if(displayChar.equals(token.substring(0,1)))
\r
+ displayChar = "";
\r
}
\r
else if(desc.length()<1)
\r
desc = token;
\r
}
\r
else if(desc.length()<1)
\r
desc = token;
\r
@@
-355,7
+356,7
@@
public class AnnotationFile
for(int j=0; j<annotations.length; j++)
\r
{
\r
if(annotations[j]!=null)
\r
for(int j=0; j<annotations.length; j++)
\r
{
\r
if(annotations[j]!=null)
\r
- annotations[j].colour = ucs.findColour("A");
\r
+ annotations[j].colour = ucs.findColour('A');
\r
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r
@@
-413,7
+414,7
@@
public class AnnotationFile
if(st.hasMoreTokens())
\r
{
\r
UserColourScheme ucs = new UserColourScheme(st.nextToken());
\r
if(st.hasMoreTokens())
\r
{
\r
UserColourScheme ucs = new UserColourScheme(st.nextToken());
\r
- colour = ucs.findColour("A");
\r
+ colour = ucs.findColour('A');
\r
}
\r
\r
annotation.setThreshold(new GraphLine(value, label, colour));
\r
}
\r
\r
annotation.setThreshold(new GraphLine(value, label, colour));
\r