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adds annotation for display (with flag to set alignmentAnnotation as hidden initially)
author
jprocter
<Jim Procter>
Fri, 20 Apr 2007 14:06:19 +0000
(14:06 +0000)
committer
jprocter
<Jim Procter>
Fri, 20 Apr 2007 14:06:19 +0000
(14:06 +0000)
src/MCview/PDBfile.java
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diff --git
a/src/MCview/PDBfile.java
b/src/MCview/PDBfile.java
index
6fdd978
..
227bcf7
100755
(executable)
--- a/
src/MCview/PDBfile.java
+++ b/
src/MCview/PDBfile.java
@@
-31,6
+31,10
@@
public class PDBfile
public Vector chains;
public String id;
public Vector chains;
public String id;
+ /**
+ * set to true to add chain alignment annotation as visible annotation.
+ */
+ boolean VisibleChainAnnotation=false;
public PDBfile(String inFile, String inType)
throws IOException
{
public PDBfile(String inFile, String inType)
throws IOException
{
@@
-128,7
+132,17
@@
public class PDBfile
entry.setFile(inFile.getAbsolutePath());
}
dataset.addPDBId(entry);
entry.setFile(inFile.getAbsolutePath());
}
dataset.addPDBId(entry);
- getSeqs().addElement(dataset.deriveSequence()); // PDBChain objects maintain reference to dataset
+ SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects maintain reference to dataset
+ seqs.addElement(chainseq);
+ AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
+ if (chainannot!=null)
+ {
+ for (int ai=0; ai<chainannot.length; ai++)
+ {
+ chainannot[ai].visible=VisibleChainAnnotation;
+ annotations.addElement(chainannot[ai]);
+ }
+ }
}
}
catch (OutOfMemoryError er)
}
}
catch (OutOfMemoryError er)