X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStructureFile.java;h=0bc6a73f40c5ebeb40b192b02a430f75fdbd156c;hb=a9a8a71c1682f639552e9954e565042847513195;hp=3a7419c012fbc9d88d11426d0bd1502014d958c3;hpb=94b82b9357592d44785de48290b2c9f2af46b2ca;p=jalview.git

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 3a7419c..0bc6a73 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -8,8 +8,9 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
 
 import java.awt.Color;
 import java.io.IOException;
@@ -25,7 +26,8 @@ public abstract class StructureFile extends AlignFile
 
   private String id;
 
-  private String dbRefType;
+  private PDBEntry.Type dbRefType;
+
   /**
    * set to true to add derived sequence annotations (temp factor read from
    * file, or computed secondary structure) to the alignment
@@ -66,19 +68,19 @@ public abstract class StructureFile extends AlignFile
 
   public void xferSettings()
   {
-    this.visibleChainAnnotation = StructureViewSettings
+    this.visibleChainAnnotation = StructureImportSettings
             .isVisibleChainAnnotation();
-    this.predictSecondaryStructure = StructureViewSettings
-            .isPredictSecondaryStructure();
-    this.externalSecondaryStructure = StructureViewSettings
+    this.predictSecondaryStructure = StructureImportSettings
+            .isProcessSecondaryStructure();
+    this.externalSecondaryStructure = StructureImportSettings
             .isExternalSecondaryStructure();
 
   }
 
-  public StructureFile(boolean parseImmediately, String inFile, String type)
+  public StructureFile(boolean parseImmediately, String dataObject, String type)
           throws IOException
   {
-    super(parseImmediately, inFile, type);
+    super(parseImmediately, dataObject, type);
   }
 
   public StructureFile(boolean a, FileParse fp) throws IOException
@@ -97,7 +99,7 @@ public abstract class StructureFile extends AlignFile
     pdbSequence.setName(getId() + "|" + pdbSequence.getName());
     PDBEntry entry = new PDBEntry();
     entry.setId(getId());
-    entry.setType(this.dbRefType);
+    entry.setType(getStructureFileType());
     entry.setProperty(new Hashtable());
     if (chain.id != null)
     {
@@ -115,16 +117,13 @@ public abstract class StructureFile extends AlignFile
     DBRefEntry sourceDBRef = new DBRefEntry();
     sourceDBRef.setAccessionId(getId());
     sourceDBRef.setSource(DBRefSource.PDB);
-    sourceDBRef.setStartRes(pdbSequence.getStart());
-    sourceDBRef.setEndRes(pdbSequence.getEnd());
-
-    SequenceI chainseq = pdbSequence.deriveSequence();
-    chainseq.setSourceDBRef(sourceDBRef);
-    chainseq.addPDBId(entry);
-    chainseq.addDBRef(sourceDBRef);
-
+    // TODO: specify version for 'PDB' database ref if it is read from a file.
+    // TODO: decide if jalview.io should be creating primary refs!
+    sourceDBRef.setVersion("");
+    pdbSequence.addPDBId(entry);
+    pdbSequence.addDBRef(sourceDBRef);
+    SequenceI chainseq = pdbSequence;
     seqs.addElement(chainseq);
-
     AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
 
     if (chainannot != null && visibleChainAnnotation)
@@ -138,6 +137,26 @@ public abstract class StructureFile extends AlignFile
     return chainseq;
   }
 
+  /**
+   * filetype of structure file - default is PDB
+   */
+  String structureFileType = PDBEntry.Type.PDB.toString();
+
+  protected void setStructureFileType(String structureFileType)
+  {
+    this.structureFileType = structureFileType;
+  }
+
+  /**
+   * filetype of last file processed
+   * 
+   * @return
+   */
+  public String getStructureFileType()
+  {
+    return structureFileType;
+  }
+
   @SuppressWarnings({ "unchecked", "rawtypes" })
   protected void processPdbFileWithAnnotate3d(List<SequenceI> rna)
           throws Exception
@@ -185,8 +204,7 @@ public abstract class StructureFile extends AlignFile
 
   @SuppressWarnings("unchecked")
   protected void replaceAndUpdateChains(List<SequenceI> prot,
-          AlignmentI al,
-          String pep, boolean b)
+          AlignmentI al, String pep, boolean b)
   {
     List<List<? extends Object>> replaced = AlignSeq
             .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
@@ -259,8 +277,7 @@ public abstract class StructureFile extends AlignFile
   }
 
   @SuppressWarnings({ "unchecked", "rawtypes" })
-  private void processWithJmolParser(List<SequenceI> prot)
-          throws Exception
+  private void processWithJmolParser(List<SequenceI> prot) throws Exception
   {
     try
     {
@@ -269,18 +286,15 @@ public abstract class StructureFile extends AlignFile
       if (cl != null)
       {
         final Constructor constructor = cl
-.getConstructor(new Class[] {
-            boolean.class, boolean.class, boolean.class, FileParse.class });
-        final Object[] args = new Object[] { visibleChainAnnotation,
-            predictSecondaryStructure, externalSecondaryStructure,
-            new FileParse(getDataName(),
+                .getConstructor(new Class[] { FileParse.class });
+        final Object[] args = new Object[] { new FileParse(getDataName(),
                 type) };
 
-        StructureViewSettings.setShowSeqFeatures(false);
-        StructureViewSettings.setVisibleChainAnnotation(false);
-        StructureViewSettings
-                .setPredictSecondaryStructure(predictSecondaryStructure);
-        StructureViewSettings
+        StructureImportSettings.setShowSeqFeatures(false);
+        StructureImportSettings.setVisibleChainAnnotation(false);
+        StructureImportSettings
+                .setProcessSecondaryStructure(predictSecondaryStructure);
+        StructureImportSettings
                 .setExternalSecondaryStructure(externalSecondaryStructure);
         Object jmf = constructor.newInstance(args);
         AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
@@ -303,13 +317,14 @@ public abstract class StructureFile extends AlignFile
     } catch (ClassNotFoundException q)
     {
     }
+    StructureImportSettings.setShowSeqFeatures(true);
   }
 
   public PDBChain findChain(String id) throws Exception
   {
     for (PDBChain chain : getChains())
     {
-      if (chain.id.equalsIgnoreCase(id))
+      if (chain.id.equals(id))
       {
         return chain;
       }
@@ -406,13 +421,18 @@ public abstract class StructureFile extends AlignFile
     this.chains = chains;
   }
 
-  public String getDbRefType()
+  public Type getDbRefType()
   {
     return dbRefType;
   }
 
   public void setDbRefType(String dbRefType)
   {
+    this.dbRefType = Type.getType(dbRefType);
+  }
+
+  public void setDbRefType(Type dbRefType)
+  {
     this.dbRefType = dbRefType;
   }