JAL-2136 JAL-2137 Improved STRUCTMODEL annotation syntax to reinstated fasta file...

[jalview.git] / src / jalview / gui / StructureChooser.java

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 66fe431..a3f739a 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -907,11 +907,15 @@ public class StructureChooser extends GStructureChooser implements
             String templateId = getPhyreResultTable().getValueAt(row,
                     templateColIndex).toString();
             String structureFile = phyre2ResultDirectory + templateId;
+            String fastaMapping = phyre2ResultDirectory
+                    + templateId.replaceAll(".pdb", ".fasta");
+            // System.out.println("structure file >>>>> " + structureFile);
+            // System.out.println("fasta mapping  >>>>> " + fastaMapping);
             pdbEntriesToView[count++] = new AssociateStructureFileWithSeq()
                     .associateStructureWithSeq(structureFile,
                             DataSourceType.FILE, selectedSequence, true,
                             Desktop.instance);
-            ssm.registerPhyre2Template(structureFile);
+            ssm.registerPhyre2Template(structureFile, fastaMapping);
           }
 
           final StructureSelectionManager ssm = ap