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JAL-674 parser flag to control secondary structure processing
author
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 10 Oct 2014 15:22:24 +0000
(16:22 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 10 Oct 2014 15:22:24 +0000
(16:22 +0100)
src/MCview/PDBfile.java
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diff --git
a/src/MCview/PDBfile.java
b/src/MCview/PDBfile.java
index
7f5c427
..
bc58c9a
100755
(executable)
--- a/
src/MCview/PDBfile.java
+++ b/
src/MCview/PDBfile.java
@@
-42,6
+42,7
@@
public class PDBfile extends jalview.io.AlignFile
boolean VisibleChainAnnotation = false;
public PDBfile(String inFile, String inType) throws IOException
boolean VisibleChainAnnotation = false;
public PDBfile(String inFile, String inType) throws IOException
+ boolean processSecondaryStructure=true;
{
super(inFile, inType);
}
{
super(inFile, inType);
}
@@
-202,6
+203,8
@@
public class PDBfile extends jalview.io.AlignFile
}
}
}
}
}
}
+ if (processSecondaryStructure)
+ {
if (rna.size() > 0)
try
{
if (rna.size() > 0)
try
{
@@
-225,19
+228,7
@@
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");