From: Jim Procter 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;