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JAL-674 commented out annotate3d calling code for Jmol external processing routine
author
jprocter
<jprocter@compbio.dundee.ac.uk>
Tue, 4 Dec 2012 10:48:53 +0000
(10:48 +0000)
committer
jprocter
<jprocter@compbio.dundee.ac.uk>
Tue, 4 Dec 2012 10:48:53 +0000
(10:48 +0000)
src/MCview/PDBfile.java
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diff --git
a/src/MCview/PDBfile.java
b/src/MCview/PDBfile.java
index
8a826a1
..
6a61f6a
100755
(executable)
--- a/
src/MCview/PDBfile.java
+++ b/
src/MCview/PDBfile.java
@@
-235,10
+235,8
@@
public class PDBfile extends jalview.io.AlignFile
}
private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
{
}
private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
{
-// System.out.println("this is a PDB format and RNA sequence");
- Annotate3D an3d = new Annotate3D();
- AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
- replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+ // process prot sequence with Jmol to get annotated alignment.
+ // replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
}
private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
// System.out.println("this is a PDB format and RNA sequence");
}
private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
// System.out.println("this is a PDB format and RNA sequence");