X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStructureFile.java;h=6b623a1e2d43e31c55256097388ed7117b6f7728;hb=5a352aa2f3330ae269d9b70c4a7374c2518bfb2e;hp=d39ab387b90a466a297d9dce3120f46b957d467a;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index d39ab38..6b623a1 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -38,18 +38,12 @@ import java.lang.reflect.Constructor;
 import java.util.List;
 import java.util.Vector;
 
-import MCview.PDBChain;
+import mc_view.PDBChain;
 
 public abstract class StructureFile extends AlignFile
 {
-
   private String id;
 
-  public enum StructureFileType
-  {
-    PDB, MMCIF, MMTF
-  };
-
   private PDBEntry.Type dbRefType;
 
   /**
@@ -74,7 +68,7 @@ public abstract class StructureFile extends AlignFile
 
   private boolean pdbIdAvailable;
 
-  public StructureFile(String inFile, DataSourceType sourceType)
+  public StructureFile(Object inFile, DataSourceType sourceType)
           throws IOException
   {
     super(inFile, sourceType);
@@ -104,7 +98,7 @@ public abstract class StructureFile extends AlignFile
 
   }
 
-  public StructureFile(boolean parseImmediately, String dataObject,
+  public StructureFile(boolean parseImmediately, Object dataObject,
           DataSourceType sourceType) throws IOException
   {
     super(parseImmediately, dataObject, sourceType);
@@ -125,6 +119,7 @@ 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)
     {
@@ -197,11 +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(), dataSourceType) }));
+        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)
@@ -228,8 +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,
@@ -294,8 +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();
       }
     }
@@ -310,8 +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[] {FileParse.class });
-        final Object[] args = new Object[] { new FileParse(getDataName(), dataSourceType) };
+        final Constructor constructor = cl
+                .getConstructor(new Class[]
+                { FileParse.class });
+        final Object[] args = new Object[] {
+            new FileParse(getDataName(), dataSourceType) };
 
         StructureImportSettings.setShowSeqFeatures(false);
         StructureImportSettings.setVisibleChainAnnotation(false);
@@ -320,8 +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())
@@ -343,7 +343,14 @@ 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())
     {
@@ -352,7 +359,7 @@ public abstract class StructureFile extends AlignFile
         return chain;
       }
     }
-    throw new Exception("PDB chain not Found!");
+    return null;
   }
 
   public void makeResidueList()
@@ -398,8 +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;
@@ -412,7 +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)
   {
@@ -421,6 +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;
   }
 
@@ -488,20 +502,4 @@ public abstract class StructureFile extends AlignFile
   {
     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;
-  }
 }