From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 19 Jan 2017 17:08:41 +0000 (+0000)
Subject: Merge branch 'spike/JAL-2040_JAL-2137_phyre2' into features/JAL-2040_JAL-2137_phyre2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3e98c1348b037f0972367245a524f182029a9686;p=jalview.git

Merge branch 'spike/JAL-2040_JAL-2137_phyre2' into features/JAL-2040_JAL-2137_phyre2
---

3e98c1348b037f0972367245a524f182029a9686
diff --cc src/jalview/ext/jmol/JmolParser.java
index b2ba256,438b403..45e72d7
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@@ -186,6 -170,13 +186,14 @@@ public class JmolParser extends Structu
        makeResidueList();
        makeCaBondList();
  
+       if (getId() == null)
+       {
+         // always use resource name, not the hardwired file
+         // Does the value of ID get used ? Behaviour needs to be
+         // documented and tested
+         setId(getDataName());
+       }
++
        for (PDBChain chain : getChains())
        {
          SequenceI chainseq = postProcessChain(chain);
diff --cc src/jalview/io/AnnotationFile.java
index 34fdabe,3bb41c4..eca27a7
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@@ -32,10 -34,14 +34,13 @@@ import jalview.datamodel.SequenceGroup
  import jalview.datamodel.SequenceI;
  import jalview.schemes.ColourSchemeI;
  import jalview.schemes.ColourSchemeProperty;
 -import jalview.schemes.ResidueProperties;
  import jalview.schemes.UserColourScheme;
+ import jalview.structure.StructureSelectionManager;
  
  import java.io.BufferedReader;
+ import java.io.File;
  import java.io.FileReader;
+ import java.io.IOException;
  import java.io.InputStreamReader;
  import java.io.StringReader;
  import java.net.URL;