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JAL-1028 JAL-674 hooks to call external processing for peptide and nucleic acid seque...
author
jprocter
<jprocter@compbio.dundee.ac.uk>
Tue, 4 Dec 2012 10:47:44 +0000
(10:47 +0000)
committer
Jim Procter
<jprocter@compbio.dundee.ac.uk>
Wed, 13 Feb 2013 18:05:51 +0000
(18:05 +0000)
src/MCview/PDBfile.java
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diff --git
a/src/MCview/PDBfile.java
b/src/MCview/PDBfile.java
index
fb14a46
..
99d55b0
100755
(executable)
--- a/
src/MCview/PDBfile.java
+++ b/
src/MCview/PDBfile.java
@@
-60,7
+60,7
@@
public class PDBfile extends jalview.io.AlignFile
id = safeName(getDataName());
chains = new Vector();
id = safeName(getDataName());
chains = new Vector();
- ArrayList<SequenceI> rna=new ArrayList<SequenceI>();
+ ArrayList<SequenceI> rna=new ArrayList<SequenceI>(), prot=new ArrayList<SequenceI>();
PDBChain tmpchain;
String line = null;
boolean modelFlag = false;
PDBChain tmpchain;
String line = null;
boolean modelFlag = false;
@@
-178,6
+178,8
@@
public class PDBfile extends jalview.io.AlignFile
if(isRNA(chainseq)==true)
{
rna.add(chainseq);
if(isRNA(chainseq)==true)
{
rna.add(chainseq);
+ } else {
+ prot.add(chainseq);
}
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
}
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
@@
-201,6
+203,15
@@
public class PDBfile extends jalview.io.AlignFile
x.printStackTrace();
};
x.printStackTrace();
};
+ if (prot.size()>0)
+ try {
+ processPdbFileWithJmol(prot);
+ } catch (Exception x)
+ {
+ System.err.println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ };
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
@@
-214,7
+225,13
@@
public class PDBfile extends jalview.io.AlignFile
}
}
}
}
}
}
-
+ 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);
+ }
private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
// System.out.println("this is a PDB format and RNA sequence");
Annotate3D an3d = new Annotate3D();
private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
// System.out.println("this is a PDB format and RNA sequence");
Annotate3D an3d = new Annotate3D();