From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 11 Oct 2016 08:37:28 +0000 (+0100)
Subject: Merge branch 'releases/Release_2_10_Branch' into develop
X-Git-Tag: Release_2_10_0b1~3^2~15^2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dbd2c7a3bee8879f3f5af8c3959af22cce0b4085;hp=-c;p=jalview.git

Merge branch 'releases/Release_2_10_Branch' into develop
---

dbd2c7a3bee8879f3f5af8c3959af22cce0b4085
diff --combined src/jalview/ext/jmol/JmolParser.java
index c73657f,ca45d7b..5866d51
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@@ -124,12 -124,11 +124,11 @@@ public class JmolParser extends Structu
        try
        {
          /*
-          * params -o (output to sysout) -i (no info logging, less verbose)
-          * -n (nodisplay) -x (exit when finished)
+          * params -o (output to sysout) -n (nodisplay) -x (exit when finished)
           * see http://wiki.jmol.org/index.php/Jmol_Application
           */
          viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
-                 null, "-x -o -n -i", this);
+                 null, "-x -o -n", this);
          // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
          viewer.setBooleanProperty("defaultStructureDSSP", true);
        } catch (ClassCastException x)
@@@ -151,15 -150,7 +150,15 @@@
        List<SequenceI> prot = new ArrayList<SequenceI>();
        PDBChain tmpchain;
        String pdbId = (String) ms.getInfo(0, "title");
 -      setId(pdbId);
 +
 +      if (pdbId == null)
 +      {
 +        setId(safeName(getDataName()));
 +      }
 +      else
 +      {
 +        setId(pdbId);
 +      }
        List<Atom> significantAtoms = convertSignificantAtoms(ms);
        for (Atom tmpatom : significantAtoms)
        {
@@@ -174,7 -165,7 +173,7 @@@
            tmpchain.atoms.addElement(tmpatom);
          } catch (Exception e)
          {
 -          tmpchain = new PDBChain(pdbId, tmpatom.chain);
 +          tmpchain = new PDBChain(getId(), tmpatom.chain);
            getChains().add(tmpchain);
            tmpchain.atoms.addElement(tmpatom);
          }
@@@ -185,6 -176,10 +184,6 @@@
        makeResidueList();
        makeCaBondList();
  
 -      if (getId() == null)
 -      {
 -        setId(safeName(getDataName()));
 -      }
        for (PDBChain chain : getChains())
        {
          SequenceI chainseq = postProcessChain(chain);