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 3025907..0a0504e 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -20,6 +20,12 @@
  */
 package jalview.io;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.util.List;
+import java.util.Vector;
+
 import jalview.analysis.AlignSeq;
 import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.Alignment;
@@ -31,14 +37,8 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
 import jalview.structure.StructureImportSettings;
-
-import java.awt.Color;
-import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.util.List;
-import java.util.Vector;
-
-import MCview.PDBChain;
+import jalview.structure.StructureImportSettings.TFType;
+import mc_view.PDBChain;
 
 public abstract class StructureFile extends AlignFile
 {
@@ -68,10 +68,30 @@ public abstract class StructureFile extends AlignFile
 
   private boolean pdbIdAvailable;
 
-  public StructureFile(String inFile, DataSourceType sourceType)
+  private StructureImportSettings.TFType temperatureFactorType = TFType.DEFAULT;
+
+  public void setTemperatureFactorType(StructureImportSettings.TFType t)
+  {
+    this.temperatureFactorType = t;
+  }
+
+  public StructureImportSettings.TFType getTemperatureFactorType()
+  {
+    return temperatureFactorType;
+  }
+
+  public StructureFile(Object inFile, DataSourceType sourceType)
           throws IOException
   {
-    super(inFile, sourceType);
+    this(inFile, sourceType, null);
+  }
+
+  public StructureFile(Object inFile, DataSourceType sourceType,
+          StructureImportSettings.TFType tempfacType) throws IOException
+  {
+    super(false, inFile, sourceType);
+    this.setTemperatureFactorType(tempfacType);
+    doParse();
   }
 
   public StructureFile(FileParse fp) throws IOException
@@ -95,10 +115,11 @@ public abstract class StructureFile extends AlignFile
             .isProcessSecondaryStructure();
     this.externalSecondaryStructure = StructureImportSettings
             .isExternalSecondaryStructure();
-
+    this.temperatureFactorType = StructureImportSettings
+            .getTemperatureFactorType();
   }
 
-  public StructureFile(boolean parseImmediately, String dataObject,
+  public StructureFile(boolean parseImmediately, Object dataObject,
           DataSourceType sourceType) throws IOException
   {
     super(parseImmediately, dataObject, sourceType);
@@ -119,6 +140,7 @@ public abstract class StructureFile extends AlignFile
     pdbSequence.setName(getId() + "|" + pdbSequence.getName());
     PDBEntry entry = new PDBEntry();
     entry.setId(getId());
+    entry.setFakedPDBId(!isPPDBIdAvailable());
     entry.setType(getStructureFileType());
     if (chain.id != null)
     {
@@ -318,6 +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));
@@ -342,7 +366,14 @@ public abstract class StructureFile extends AlignFile
     StructureImportSettings.setShowSeqFeatures(true);
   }
 
-  public PDBChain findChain(String id) throws Exception
+  /**
+   * Answers the first PDBChain found matching the given id, or null if none is
+   * found
+   * 
+   * @param id
+   * @return
+   */
+  public PDBChain findChain(String id)
   {
     for (PDBChain chain : getChains())
     {
@@ -351,7 +382,7 @@ public abstract class StructureFile extends AlignFile
         return chain;
       }
     }
-    throw new Exception("PDB chain not Found!");
+    return null;
   }
 
   public void makeResidueList()