JAL-629 need to delay call to AlignFile.parse() if StructureFile needs to configure...

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

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 7ecbc2d..0a0504e 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -89,8 +89,9 @@ public abstract class StructureFile extends AlignFile
   public StructureFile(Object inFile, DataSourceType sourceType,
           StructureImportSettings.TFType tempfacType) throws IOException
   {
-    super(inFile, sourceType);
+    super(false, inFile, sourceType);
     this.setTemperatureFactorType(tempfacType);
+    doParse();
   }
 
   public StructureFile(FileParse fp) throws IOException
@@ -339,6 +340,8 @@ public abstract class StructureFile extends AlignFile
                 .setProcessSecondaryStructure(predictSecondaryStructure);
         StructureImportSettings
                 .setExternalSecondaryStructure(externalSecondaryStructure);
+        StructureImportSettings
+                .setTemperatureFactorType(temperatureFactorType);
         Object jmf = constructor.newInstance(args);
         AlignmentI al = new Alignment((SequenceI[]) cl
                 .getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf));