X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStructureFile.java;h=94a832b2e7a6c1f29cae64c19b1ce529dbc47cf0;hb=cf02a7088e2835fa4764d034e662f4319073c8a9;hp=995e6d3301f29dcd058581adf7101b71af253676;hpb=3bf65c1e2b0df047a97fdd2f9e1874462fde8b02;p=jalview.git

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 995e6d3..94a832b 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -15,15 +35,13 @@ 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;
 
-import MCview.PDBChain;
+import mc_view.PDBChain;
 
 public abstract class StructureFile extends AlignFile
 {
-
   private String id;
 
   private PDBEntry.Type dbRefType;
@@ -48,9 +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(Object inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public StructureFile(FileParse fp) throws IOException
@@ -77,10 +98,10 @@ public abstract class StructureFile extends AlignFile
 
   }
 
-  public StructureFile(boolean parseImmediately, String dataObject, String type)
-          throws IOException
+  public StructureFile(boolean parseImmediately, Object dataObject,
+          DataSourceType sourceType) throws IOException
   {
-    super(parseImmediately, dataObject, type);
+    super(parseImmediately, dataObject, sourceType);
   }
 
   public StructureFile(boolean a, FileParse fp) throws IOException
@@ -92,18 +113,17 @@ 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(this.dbRefType);
-    entry.setProperty(new Hashtable());
+    entry.setFakedPDBId(!isPPDBIdAvailable());
+    entry.setType(getStructureFileType());
     if (chain.id != null)
     {
-      entry.setChainCode(String.valueOf(chain.id));
+      entry.setChainCode(chain.id);
     }
     if (inFile != null)
     {
@@ -137,6 +157,26 @@ 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
@@ -152,11 +192,13 @@ public abstract class StructureFile extends AlignFile
       {
         // TODO: use the PDB ID of the structure if one is available, to save
         // bandwidth and avoid uploading the whole structure to the service
-        Object annotate3d = cl.getConstructor(new Class[] {}).newInstance(
-                new Object[] {});
-        AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
-                new Class[] { FileParse.class }).invoke(annotate3d,
-                new Object[] { new FileParse(getDataName(), type) }));
+        Object annotate3d = cl.getConstructor(new Class[] {})
+                .newInstance(new Object[] {});
+        AlignmentI al = ((AlignmentI) cl
+                .getMethod("getRNAMLFor", new Class[]
+                { FileParse.class })
+                .invoke(annotate3d, new Object[]
+                { new FileParse(getDataName(), dataSourceType) }));
         for (SequenceI sq : al.getSequences())
         {
           if (sq.getDatasetSequence() != null)
@@ -183,8 +225,8 @@ public abstract class StructureFile extends AlignFile
   }
 
   @SuppressWarnings("unchecked")
-  protected void replaceAndUpdateChains(List<SequenceI> prot,
-          AlignmentI al, String pep, boolean b)
+  protected void replaceAndUpdateChains(List<SequenceI> prot, AlignmentI al,
+          String pep, boolean b)
   {
     List<List<? extends Object>> replaced = AlignSeq
             .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
@@ -249,8 +291,8 @@ public abstract class StructureFile extends AlignFile
         processWithJmolParser(proteinSequences);
       } catch (Exception x)
       {
-        System.err
-                .println("Exceptions from Jmol when processing data in pdb file");
+        System.err.println(
+                "Exceptions from Jmol when processing data in pdb file");
         x.printStackTrace();
       }
     }
@@ -265,11 +307,11 @@ public abstract class StructureFile extends AlignFile
       Class cl = Class.forName("jalview.ext.jmol.JmolParser");
       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(), 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);
@@ -278,8 +320,8 @@ public abstract class StructureFile extends AlignFile
         StructureImportSettings
                 .setExternalSecondaryStructure(externalSecondaryStructure);
         Object jmf = constructor.newInstance(args);
-        AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
-                "getSeqsAsArray", new Class[] {}).invoke(jmf));
+        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())
@@ -300,8 +342,15 @@ 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())
     {
@@ -310,7 +359,7 @@ public abstract class StructureFile extends AlignFile
         return chain;
       }
     }
-    throw new Exception("PDB chain not Found!");
+    return null;
   }
 
   public void makeResidueList()
@@ -356,8 +405,10 @@ public abstract class StructureFile extends AlignFile
 
   public static boolean isRNA(SequenceI seq)
   {
-    for (char c : seq.getSequence())
+    int length = seq.getLength();
+    for (int i = 0; i < length; i++)
     {
+      char c = seq.getCharAt(i);
       if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U'))
       {
         return false;
@@ -370,7 +421,8 @@ 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)
   {
@@ -379,6 +431,10 @@ public abstract class StructureFile extends AlignFile
     {
       dataName = dataName.substring(p + 1);
     }
+    if (dataName.indexOf(".") > -1)
+    {
+      dataName = dataName.substring(0, dataName.lastIndexOf("."));
+    }
     return dataName;
   }
 
@@ -431,4 +487,19 @@ 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;
+  }
 }