Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3' into releases/Release_2_...

[jalview.git] / src / MCview / PDBfile.java

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 0934fdb..ebc52aa 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -20,17 +20,15 @@
  */
 package MCview;
 
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.util.MessageManager;
 
 import java.io.IOException;
-import java.lang.reflect.Constructor;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
@@ -44,35 +42,29 @@ public class PDBfile extends StructureFile
           boolean predictSecondaryStructure, boolean externalSecStr)
   {
     super();
-    this.visibleChainAnnotation = addAlignmentAnnotations;
-    this.predictSecondaryStructure = predictSecondaryStructure;
-    this.externalSecondaryStructure = externalSecStr;
+    addSettings(addAlignmentAnnotations, predictSecondaryStructure,
+            externalSecStr);
   }
 
-  public PDBfile(boolean addAlignmentAnnotations,
-          boolean predictSecondaryStructure, boolean externalSecStr,
-          String file, String protocol) throws IOException
+  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+          boolean externalSecStr, String dataObject,
+          DataSourceType sourceType) throws IOException
   {
-    super(false, file, protocol);
-    this.visibleChainAnnotation = addAlignmentAnnotations;
-    this.predictSecondaryStructure = predictSecondaryStructure;
-    this.externalSecondaryStructure = externalSecStr;
+    super(false, dataObject, sourceType);
+    addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
     doParse();
   }
 
-  public PDBfile(boolean addAlignmentAnnotations,
-          boolean predictSecondaryStructure, boolean externalSecStr,
-          FileParse source) throws IOException
+  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+          boolean externalSecStr, FileParse source) throws IOException
   {
     super(false, source);
-    this.visibleChainAnnotation = addAlignmentAnnotations;
-    this.predictSecondaryStructure = predictSecondaryStructure;
-    this.externalSecondaryStructure = externalSecStr;
+    addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
     doParse();
   }
 
   @Override
-  public String print()
+  public String print(SequenceI[] seqs, boolean jvSuffix)
   {
     return null;
   }
@@ -80,6 +72,7 @@ public class PDBfile extends StructureFile
   @Override
   public void parse() throws IOException
   {
+    setDbRefType(DBRefSource.PDB);
     // TODO set the filename sensibly - try using data source name.
     setId(safeName(getDataName()));
 
@@ -152,7 +145,7 @@ public class PDBfile extends StructureFile
           Atom tmpatom = new Atom(line);
           try
           {
-          tmpchain = findChain(tmpatom.chain);
+            tmpchain = findChain(tmpatom.chain);
             if (tmpatom.resNumIns.trim().equals(lastID))
             {
               // phosphorylated protein - seen both CA and P..
@@ -191,14 +184,13 @@ public class PDBfile extends StructureFile
       }
       if (predictSecondaryStructure)
       {
-        predictSecondaryStructure(rna, prot);
+        addSecondaryStructure(rna, prot);
       }
     } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
-      throw new IOException(
-              MessageManager
-                      .getString("exception.outofmemory_loading_pdb_file"));
+      throw new IOException(MessageManager
+              .getString("exception.outofmemory_loading_pdb_file"));
     } catch (NumberFormatException ex)
     {
       if (line != null)
@@ -211,50 +203,6 @@ public class PDBfile extends StructureFile
   }
 
   /**
-   * Predict secondary structure for RNA and/or protein sequences and add as
-   * annotations
-   * 
-   * @param rnaSequences
-   * @param proteinSequences
-   */
-  protected void predictSecondaryStructure(List<SequenceI> rnaSequences,
-          List<SequenceI> proteinSequences)
-  {
-    /*
-     * Currently using Annotate3D for RNA, but only if the 'use external
-     * prediction' flag is set
-     */
-    if (externalSecondaryStructure && rnaSequences.size() > 0)
-    {
-      try
-      {
-        processPdbFileWithAnnotate3d(rnaSequences);
-      } catch (Exception x)
-      {
-        System.err.println("Exceptions when dealing with RNA in pdb file");
-        x.printStackTrace();
-
-      }
-    }
-
-    /*
-     * Currently using JMol PDB parser for peptide
-     */
-    if (proteinSequences.size() > 0)
-    {
-      try
-      {
-        processPdbFileWithJmol(proteinSequences);
-      } catch (Exception x)
-      {
-        System.err
-                .println("Exceptions from Jmol when processing data in pdb file");
-        x.printStackTrace();
-      }
-    }
-  }
-
-  /**
    * Process a parsed chain to construct and return a Sequence, and add it to
    * the list of sequences parsed.
    * 
@@ -278,8 +226,8 @@ public class PDBfile extends StructureFile
   public static String relocateCalcId(String calcId,
           Hashtable<String, String> alreadyLoadedPDB) throws Exception
   {
-    int s = CALC_ID_PREFIX.length(), end = calcId
-            .indexOf(CALC_ID_PREFIX, s);
+    int s = CALC_ID_PREFIX.length(),
+            end = calcId.indexOf(CALC_ID_PREFIX, s);
     String between = calcId.substring(s, end - 1);
     return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
             + calcId.substring(end);
@@ -306,39 +254,4 @@ public class PDBfile extends StructureFile
     }
   }
 
-  private void processPdbFileWithJmol(List<SequenceI> prot)
-          throws Exception
-  {
-    try
-    {
-
-      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) };
-        Object jmf = constructor.newInstance(args);
-        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())
-        {
-          if (sq.getDatasetSequence() != null)
-          {
-            sq.getDatasetSequence().getAllPDBEntries().clear();
-          }
-          else
-          {
-            sq.getAllPDBEntries().clear();
-          }
-        }
-        replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
-      }
-    } catch (ClassNotFoundException q)
-    {
-    }
-  }
 }