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JAL-654_dssp formatting and javadoc
author
Jim Procter
<j.procter@dundee.ac.uk>
Mon, 6 Oct 2014 11:11:11 +0000
(12:11 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Mon, 6 Oct 2014 11:11:11 +0000
(12:11 +0100)
src/MCview/PDBfile.java
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diff --git
a/src/MCview/PDBfile.java
b/src/MCview/PDBfile.java
index
3dd567e
..
7f5c427
100755
(executable)
--- a/
src/MCview/PDBfile.java
+++ b/
src/MCview/PDBfile.java
@@
-241,7
+241,9
@@
public class PDBfile extends jalview.io.AlignFile
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
- throw new IOException(MessageManager.getString("exception.outofmemory_loading_pdb_file"));
+ throw new IOException(
+ MessageManager
+ .getString("exception.outofmemory_loading_pdb_file"));
} catch (NumberFormatException ex)
{
if (line != null)
} catch (NumberFormatException ex)
{
if (line != null)
@@
-305,6
+307,14
@@
public class PDBfile extends jalview.io.AlignFile
;
}
;
}
+ /**
+ * matches ochains against al and populates seqs with the best match between
+ * each ochain and the set in al
+ *
+ * @param ochains
+ * @param al
+ * @param dnaOrProtein
+ */
private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains,
AlignmentI al, String dnaOrProtein)
{
private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains,
AlignmentI al, String dnaOrProtein)
{