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

[jalview.git] / src / jalview / io / AnnotationFile.java

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index c104fb2..eca27a7 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -34,8 +34,8 @@ 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;
@@ -1306,7 +1306,11 @@ public class AnnotationFile
       }
       else
       {
-        // assume 1:1 - so synthesise sequences to use to construct mapping ?
+        // assume 1:1 - so synthesise sequences to use to construct mapping
+        StructureFile pdbf = StructureSelectionManager
+                .getStructureSelectionManager().setMapping(false,
+                        new SequenceI[] { refSeq2.getDatasetSequence() },
+                        null, modelPath, modelProt);
         refSeq2.getDatasetSequence().addPDBId(modelpe);
         if (templateSeq == null && tPw != null)
         {
@@ -1804,9 +1808,9 @@ public class AnnotationFile
         else if (key.equalsIgnoreCase("consThreshold"))
         {
           sg.cs.setConservationInc(Integer.parseInt(value));
-          Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3, sg.getSequences(null),
-                  sg.getStartRes(), sg.getEndRes() + 1);
+          Conservation c = new Conservation("Group", 3,
+                  sg.getSequences(null), sg.getStartRes(),
+                  sg.getEndRes() + 1);
 
           c.calculate();
           c.verdict(false, 25); // TODO: refer to conservation percent threshold