X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStructureFile.java;h=ab220f0ade10e31ae6b683fa89ab484a17b2e763;hb=61ba3fbbcf553e5945051ae4f7ab185ddd2e6dca;hp=e2b73d1cf98a62e3cea342d30380c86d95615fdd;hpb=e77a693cf000b4ff8a863411acf8c90c6390a061;p=jalview.git

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index e2b73d1..ab220f0 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -1,18 +1,40 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
 import jalview.analysis.AlignSeq;
+import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 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.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;
 
@@ -20,22 +42,23 @@ import MCview.PDBChain;
 
 public abstract class StructureFile extends AlignFile
 {
-
   private String id;
 
+  private PDBEntry.Type dbRefType;
+
   /**
    * set to true to add derived sequence annotations (temp factor read from
    * file, or computed secondary structure) to the alignment
    */
   protected boolean visibleChainAnnotation = false;
 
-  /*
+  /**
    * Set true to predict secondary structure (using JMol for protein, Annotate3D
    * for RNA)
    */
-  protected boolean predictSecondaryStructure = true;
+  protected boolean predictSecondaryStructure = false;
 
-  /*
+  /**
    * Set true (with predictSecondaryStructure=true) to predict secondary
    * structure using an external service (currently Annotate3D for RNA only)
    */
@@ -43,9 +66,12 @@ 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
@@ -53,10 +79,29 @@ public abstract class StructureFile extends AlignFile
     super(fp);
   }
 
-  public StructureFile(boolean parseImmediately, String inFile, String type)
-          throws IOException
+  public void addSettings(boolean addAlignmentAnnotations,
+          boolean predictSecondaryStructure, boolean externalSecStr)
+  {
+    this.visibleChainAnnotation = addAlignmentAnnotations;
+    this.predictSecondaryStructure = predictSecondaryStructure;
+    this.externalSecondaryStructure = externalSecStr;
+  }
+
+  public void xferSettings()
+  {
+    this.visibleChainAnnotation = StructureImportSettings
+            .isVisibleChainAnnotation();
+    this.predictSecondaryStructure = StructureImportSettings
+            .isProcessSecondaryStructure();
+    this.externalSecondaryStructure = StructureImportSettings
+            .isExternalSecondaryStructure();
+
+  }
+
+  public StructureFile(boolean parseImmediately, String dataObject,
+          DataSourceType sourceType) throws IOException
   {
-    super(parseImmediately, inFile, type);
+    super(parseImmediately, dataObject, sourceType);
   }
 
   public StructureFile(boolean a, FileParse fp) throws IOException
@@ -68,18 +113,16 @@ public abstract class StructureFile extends AlignFile
   {
   }
 
-  @SuppressWarnings("rawtypes")
   protected SequenceI postProcessChain(PDBChain chain)
   {
     SequenceI pdbSequence = chain.sequence;
     pdbSequence.setName(getId() + "|" + pdbSequence.getName());
     PDBEntry entry = new PDBEntry();
     entry.setId(getId());
-    entry.setType(PDBEntry.Type.PDB);
-    entry.setProperty(new Hashtable());
+    entry.setType(getStructureFileType());
     if (chain.id != null)
     {
-      entry.setChainCode(String.valueOf(chain.id));
+      entry.setChainCode(chain.id);
     }
     if (inFile != null)
     {
@@ -93,21 +136,13 @@ 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());
-
-    // PDBChain objects maintain reference to dataset
-
-    // SequenceI chainseq = pdbSequence.deriveSequence();
-    // chainseq.setSourceDBRef(sourceDBRef);
-    // chainseq.addPDBId(entry);
-    // chainseq.addDBRef(sourceDBRef);
-    SequenceI chainseq = chain.sequence;
-    chainseq.addPDBId(entry);
-    chainseq.setSourceDBRef(sourceDBRef);
-    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)
@@ -121,6 +156,26 @@ 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
@@ -140,7 +195,7 @@ 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)
@@ -168,8 +223,7 @@ 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,
@@ -242,8 +296,7 @@ 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
     {
@@ -251,10 +304,15 @@ 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);
+        StructureImportSettings
+                .setProcessSecondaryStructure(predictSecondaryStructure);
+        StructureImportSettings
+                .setExternalSecondaryStructure(externalSecondaryStructure);
         Object jmf = constructor.newInstance(args);
         AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
                 "getSeqsAsArray", new Class[] {}).invoke(jmf));
@@ -276,13 +334,14 @@ 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;
       }
@@ -347,7 +406,8 @@ public abstract class StructureFile extends AlignFile
    * make a friendly ID string.
    * 
    * @param dataName
-   * @return truncated dataName to after last '/'
+   * @return truncated dataName to after last '/' and pruned .extension if
+   *         present
    */
   protected String safeName(String dataName)
   {
@@ -356,6 +416,9 @@ public abstract class StructureFile extends AlignFile
     {
       dataName = dataName.substring(p + 1);
     }
+    if(dataName.indexOf(".") > -1){
+      dataName = dataName.substring(0, dataName.lastIndexOf("."));
+    }
     return dataName;
   }
 
@@ -378,4 +441,49 @@ public abstract class StructureFile extends AlignFile
   {
     this.chains = chains;
   }
+
+  public Type getDbRefType()
+  {
+    return dbRefType;
+  }
+
+  public void setDbRefType(String dbRefType)
+  {
+    this.dbRefType = Type.getType(dbRefType);
+  }
+
+  public void setDbRefType(Type dbRefType)
+  {
+    this.dbRefType = dbRefType;
+  }
+
+  /**
+   * Returns a descriptor for suitable feature display settings with
+   * <ul>
+   * <li>ResNums or insertions features visible</li>
+   * <li>insertions features coloured red</li>
+   * <li>ResNum features coloured by label</li>
+   * <li>Insertions displayed above (on top of) ResNums</li>
+   * </ul>
+   */
+  @Override
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    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;
+  }
 }