Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 61a9b48..d39ab38 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -35,7 +35,6 @@ import jalview.structure.StructureImportSettings;
 import java.awt.Color;
 import java.io.IOException;
 import java.lang.reflect.Constructor;
-import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
@@ -46,6 +45,11 @@ public abstract class StructureFile extends AlignFile
 
   private String id;
 
+  public enum StructureFileType
+  {
+    PDB, MMCIF, MMTF
+  };
+
   private PDBEntry.Type dbRefType;
 
   /**
@@ -68,9 +72,12 @@ public abstract class StructureFile extends AlignFile
 
   private Vector<PDBChain> chains;
 
-  public StructureFile(String inFile, String type) throws IOException
+  private boolean pdbIdAvailable;
+
+  public StructureFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public StructureFile(FileParse fp) throws IOException
@@ -98,9 +105,9 @@ public abstract class StructureFile extends AlignFile
   }
 
   public StructureFile(boolean parseImmediately, String dataObject,
-          String type) throws IOException
+          DataSourceType sourceType) throws IOException
   {
-    super(parseImmediately, dataObject, type);
+    super(parseImmediately, dataObject, sourceType);
   }
 
   public StructureFile(boolean a, FileParse fp) throws IOException
@@ -112,7 +119,6 @@ public abstract class StructureFile extends AlignFile
   {
   }
 
-  @SuppressWarnings("rawtypes")
   protected SequenceI postProcessChain(PDBChain chain)
   {
     SequenceI pdbSequence = chain.sequence;
@@ -120,10 +126,9 @@ public abstract class StructureFile extends AlignFile
     PDBEntry entry = new PDBEntry();
     entry.setId(getId());
     entry.setType(getStructureFileType());
-    entry.setProperty(new Hashtable());
     if (chain.id != null)
     {
-      entry.setChainCode(String.valueOf(chain.id));
+      entry.setChainCode(chain.id);
     }
     if (inFile != null)
     {
@@ -196,7 +201,7 @@ public abstract class StructureFile extends AlignFile
                 new Object[] {});
         AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
                 new Class[] { FileParse.class }).invoke(annotate3d,
-                new Object[] { new FileParse(getDataName(), type) }));
+                new Object[] { new FileParse(getDataName(), dataSourceType) }));
         for (SequenceI sq : al.getSequences())
         {
           if (sq.getDatasetSequence() != null)
@@ -305,10 +310,8 @@ public abstract class StructureFile extends AlignFile
       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(),
-                type) };
+        final Constructor constructor = cl.getConstructor(new Class[] {FileParse.class });
+        final Object[] args = new Object[] { new FileParse(getDataName(), dataSourceType) };
 
         StructureImportSettings.setShowSeqFeatures(false);
         StructureImportSettings.setVisibleChainAnnotation(false);
@@ -470,4 +473,35 @@ public abstract class StructureFile extends AlignFile
   {
     return new PDBFeatureSettings();
   }
+
+  /**
+   * Answers true if the structure file has a PDBId
+   * 
+   * @return
+   */
+  public boolean isPPDBIdAvailable()
+  {
+    return pdbIdAvailable;
+  }
+
+  public void setPDBIdAvailable(boolean pdbIdAvailable)
+  {
+    this.pdbIdAvailable = pdbIdAvailable;
+  }
+
+  public static boolean isStructureFile(String fileType)
+  {
+    if (fileType == null)
+    {
+      return false;
+    }
+    for (StructureFileType sfType : StructureFileType.values())
+    {
+      if (sfType.name().equalsIgnoreCase(fileType))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
 }