JAL-629 Tidy up tests and replaced methods before merge to develop

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

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index fb416db..6ec0298 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -70,7 +70,7 @@ public abstract class StructureFile extends AlignFile
 
   private boolean pdbIdAvailable;
 
-  private StructureImportSettings.TFType temperatureFactorType = TFType.DEFAULT;
+  private TFType temperatureFactorType = TFType.DEFAULT;
 
   private String paeMatrix = null;
 
@@ -91,12 +91,12 @@ public abstract class StructureFile extends AlignFile
     return paeMatrix != null;
   }
 
-  public void setTemperatureFactorType(StructureImportSettings.TFType t)
+  public void setTemperatureFactorType(TFType t)
   {
     this.temperatureFactorType = t;
   }
 
-  public StructureImportSettings.TFType getTemperatureFactorType()
+  public TFType getTemperatureFactorType()
   {
     return temperatureFactorType;
   }
@@ -118,7 +118,7 @@ public abstract class StructureFile extends AlignFile
   }
 
   public StructureFile(Object inFile, DataSourceType sourceType,
-          StructureImportSettings.TFType tempfacType) throws IOException
+          TFType tempfacType) throws IOException
   {
     super(false, inFile, sourceType);
     this.setTemperatureFactorType(tempfacType);
@@ -359,54 +359,6 @@ public abstract class StructureFile extends AlignFile
     }
   }
 
-  @SuppressWarnings({ "unchecked", "rawtypes" })
-  private void NOTprocessWithJmolParser(List<SequenceI> prot)
-          throws Exception
-  {
-    try
-    {
-
-      Class cl = Class.forName("jalview.ext.jmol.JmolParser");
-      if (cl != null)
-      {
-        final Constructor constructor = cl
-                .getConstructor(new Class[]
-                { FileParse.class });
-        final Object[] args = new Object[] {
-            new FileParse(getDataName(), dataSourceType) };
-
-        StructureImportSettings.setShowSeqFeatures(false);
-        StructureImportSettings.setVisibleChainAnnotation(false);
-        StructureImportSettings
-                .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));
-        cl.getMethod("addAnnotations", new Class[] { AlignmentI.class })
-                .invoke(jmf, al);
-        for (SequenceI sq : al.getSequences())
-        {
-          if (sq.getDatasetSequence() != null)
-          {
-            sq.getDatasetSequence().getAllPDBEntries().clear();
-          }
-          else
-          {
-            sq.getAllPDBEntries().clear();
-          }
-        }
-        replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
-      }
-    } catch (ClassNotFoundException q)
-    {
-    }
-    StructureImportSettings.setShowSeqFeatures(true);
-  }
-
   private void processWithJmolParser(List<SequenceI> prot,
           boolean doXferSettings) throws MalformedURLException, IOException
   {