From 7277d3d8dcfd5f39fe220165e1ea87be62daa25c Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 6 Oct 2014 12:11:11 +0100 Subject: [PATCH] JAL-654_dssp formatting and javadoc --- src/MCview/PDBfile.java | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 3dd567e..7f5c427 100755 --- 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"); - 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) @@ -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 ochains, AlignmentI al, String dnaOrProtein) { -- 1.7.10.2