X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=f5a0255094f23ab858ddb3bb5b9df9a7e232aad6;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=4039cdd32e88b94f15b5c0e3e6d41d2fbe6b1e6f;hpb=a394f0df3650d5b1e0b76e0319b650fe8ac98e41;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 4039cdd..f5a0255 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -20,90 +20,62 @@
  */
 package MCview;
 
-import java.awt.Color;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+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;
 import java.util.Vector;
 
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
-import jalview.util.MessageManager;
-
-public class PDBfile extends jalview.io.AlignFile
+public class PDBfile extends StructureFile
 {
   private static String CALC_ID_PREFIX = "JalviewPDB";
 
-  public Vector<PDBChain> chains;
-
-  public String id;
-
-  /**
-   * set to true to add derived sequence annotations (temp factor read from
-   * file, or computed secondary structure) to the alignment
-   */
-  private boolean visibleChainAnnotation = false;
-
-  /*
-   * Set true to predict secondary structure (using JMol for protein, Annotate3D
-   * for RNA)
-   */
-  private boolean predictSecondaryStructure = true;
-
-  /*
-   * Set true (with predictSecondaryStructure=true) to predict secondary
-   * structure using an external service (currently Annotate3D for RNA only)
-   */
-  private boolean externalSecondaryStructure = false;
-
-  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecondaryStructure,
-          boolean externalSecStr)
+  public PDBfile(boolean addAlignmentAnnotations,
+          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)
+  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+          boolean externalSecStr, String dataObject, String protocol)
           throws IOException
   {
-    super(false, file, protocol);
-    this.visibleChainAnnotation = addAlignmentAnnotations;
-    this.predictSecondaryStructure = predictSecondaryStructure;
-    this.externalSecondaryStructure = externalSecStr;
+    super(false, dataObject, protocol);
+    addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
     doParse();
   }
 
-  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecondaryStructure,
+  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()
   {
     return null;
   }
 
+  @Override
   public void parse() throws IOException
   {
+    setDbRefType(DBRefSource.PDB);
     // TODO set the filename sensibly - try using data source name.
-    id = safeName(getDataName());
+    setId(safeName(getDataName()));
 
-    chains = new Vector<PDBChain>();
+    setChains(new Vector<PDBChain>());
     List<SequenceI> rna = new ArrayList<SequenceI>();
     List<SequenceI> prot = new ArrayList<SequenceI>();
     PDBChain tmpchain;
@@ -133,7 +105,7 @@ public class PDBfile extends jalview.io.AlignFile
             }
             if (tid.length() > 0)
             {
-              id = tid;
+              setId(tid);
             }
             continue;
           }
@@ -170,20 +142,19 @@ public class PDBfile extends jalview.io.AlignFile
           }
 
           Atom tmpatom = new Atom(line);
-          tmpchain = findChain(tmpatom.chain);
-          if (tmpchain != null)
+          try
           {
+            tmpchain = findChain(tmpatom.chain);
             if (tmpatom.resNumIns.trim().equals(lastID))
             {
               // phosphorylated protein - seen both CA and P..
               continue;
             }
             tmpchain.atoms.addElement(tmpatom);
-          }
-          else
+          } catch (Exception e)
           {
-            tmpchain = new PDBChain(id, tmpatom.chain);
-            chains.addElement(tmpchain);
+            tmpchain = new PDBChain(getId(), tmpatom.chain);
+            getChains().add(tmpchain);
             tmpchain.atoms.addElement(tmpatom);
           }
           lastID = tmpatom.resNumIns.trim();
@@ -194,11 +165,11 @@ public class PDBfile extends jalview.io.AlignFile
       makeResidueList();
       makeCaBondList();
 
-      if (id == null)
+      if (getId() == null)
       {
-        id = inFile.getName();
+        setId(inFile.getName());
       }
-      for (PDBChain chain : chains)
+      for (PDBChain chain : getChains())
       {
         SequenceI chainseq = postProcessChain(chain);
         if (isRNA(chainseq))
@@ -212,7 +183,7 @@ public class PDBfile extends jalview.io.AlignFile
       }
       if (predictSecondaryStructure)
       {
-        predictSecondaryStructure(rna, prot);
+        addSecondaryStructure(rna, prot);
       }
     } catch (OutOfMemoryError er)
     {
@@ -232,96 +203,12 @@ public class PDBfile extends jalview.io.AlignFile
   }
 
   /**
-   * 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.
    * 
    * @param chain
    * @return
    */
-  protected SequenceI postProcessChain(PDBChain chain)
-  {
-    SequenceI dataset = chain.sequence;
-    dataset.setName(id + "|" + dataset.getName());
-    PDBEntry entry = new PDBEntry();
-    entry.setId(id);
-    entry.setType(PDBEntry.Type.PDB);
-    entry.setProperty(new Hashtable());
-    if (chain.id != null)
-    {
-      // entry.getProperty().put("CHAIN", chains.elementAt(i).id);
-      entry.setChainCode(String.valueOf(chain.id));
-    }
-    if (inFile != null)
-    {
-      entry.setFile(inFile.getAbsolutePath());
-    }
-    else
-    {
-      // TODO: decide if we should dump the datasource to disk
-      entry.setFile(getDataName());
-    }
-    dataset.addPDBId(entry);
-    // PDBChain objects maintain reference to dataset
-    SequenceI chainseq = dataset.deriveSequence();
-    seqs.addElement(chainseq);
-
-    AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
-
-    if (chainannot != null && visibleChainAnnotation)
-    {
-      for (int ai = 0; ai < chainannot.length; ai++)
-      {
-        chainannot[ai].visible = visibleChainAnnotation;
-        annotations.addElement(chainannot[ai]);
-      }
-    }
-    return chainseq;
-  }
 
   public static boolean isCalcIdHandled(String calcId)
   {
@@ -339,7 +226,8 @@ public class PDBfile extends jalview.io.AlignFile
   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);
@@ -359,207 +247,11 @@ public class PDBfile extends jalview.io.AlignFile
             oldId = "";
           }
           aa.setCalcId(CALC_ID_PREFIX);
-          aa.setProperty("PDBID", id);
+          aa.setProperty("PDBID", getId());
           aa.setProperty("oldCalcId", oldId);
         }
       }
     }
   }
 
-  private void processPdbFileWithJmol(List<SequenceI> prot)
-          throws Exception
-  {
-    try
-    {
-      Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
-      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[]
-        { Alignment.class }).invoke(jmf, al);
-        for (SequenceI sq : al.getSequences())
-        {
-          if (sq.getDatasetSequence() != null)
-          {
-            sq.getDatasetSequence().getPDBId().clear();
-          }
-          else
-          {
-            sq.getPDBId().clear();
-          }
-        }
-        replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
-      }
-    } catch (ClassNotFoundException q)
-    {
-    }
-  }
-
-  private void replaceAndUpdateChains(List<SequenceI> prot,
-          AlignmentI al, String pep, boolean b)
-  {
-    List<List<? extends Object>> replaced = AlignSeq
-            .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
-                    false);
-    for (PDBChain ch : chains)
-    {
-      int p = 0;
-      for (SequenceI sq : (List<SequenceI>) replaced.get(0))
-      {
-        p++;
-        if (sq == ch.sequence || sq.getDatasetSequence() == ch.sequence)
-        {
-          p = -p;
-          break;
-        }
-      }
-      if (p < 0)
-      {
-        p = -p - 1;
-        // set shadow entry for chains
-        ch.shadow = (SequenceI) replaced.get(1).get(p);
-        ch.shadowMap = ((AlignSeq) replaced.get(2).get(p))
-                .getMappingFromS1(false);
-      }
-    }
-  }
-
-  private void processPdbFileWithAnnotate3d(List<SequenceI> rna)
-          throws Exception
-  {
-    // System.out.println("this is a PDB format and RNA sequence");
-    // note: we use reflection here so that the applet can compile and run
-    // without the HTTPClient bits and pieces needed for accessing Annotate3D
-    // web service
-    try
-    {
-      Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
-      if (cl != null)
-      {
-        // 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) }));
-        for (SequenceI sq : al.getSequences())
-        {
-          if (sq.getDatasetSequence() != null)
-          {
-            if (sq.getDatasetSequence().getPDBId() != null)
-            {
-              sq.getDatasetSequence().getPDBId().clear();
-            }
-          }
-          else
-          {
-            if (sq.getPDBId() != null)
-            {
-              sq.getPDBId().clear();
-            }
-          }
-        }
-        replaceAndUpdateChains(rna, al, AlignSeq.DNA, false);
-      }
-    } catch (ClassNotFoundException x)
-    {
-      // ignore classnotfounds - occurs in applet
-    }
-    ;
-  }
-
-  /**
-   * make a friendly ID string.
-   * 
-   * @param dataName
-   * @return truncated dataName to after last '/'
-   */
-  private String safeName(String dataName)
-  {
-    int p = 0;
-    while ((p = dataName.indexOf("/")) > -1 && p < dataName.length())
-    {
-      dataName = dataName.substring(p + 1);
-    }
-    return dataName;
-  }
-
-  public void makeResidueList()
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      chains.elementAt(i).makeResidueList(visibleChainAnnotation);
-    }
-  }
-
-  public void makeCaBondList()
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      chains.elementAt(i).makeCaBondList();
-    }
-  }
-
-  public PDBChain findChain(String id)
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      if (chains.elementAt(i).id.equals(id))
-      {
-        return chains.elementAt(i);
-      }
-    }
-
-    return null;
-  }
-
-  public void setChargeColours()
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      chains.elementAt(i).setChargeColours();
-    }
-  }
-
-  public void setColours(jalview.schemes.ColourSchemeI cs)
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      chains.elementAt(i).setChainColours(cs);
-    }
-  }
-
-  public void setChainColours()
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      // divide by zero --> infinity --> 255 ;-)
-      chains.elementAt(i).setChainColours(
-              Color.getHSBColor(1.0f / i, .4f, 1.0f));
-    }
-  }
-
-  public static boolean isRNA(SequenceI seq)
-  {
-    for (char c : seq.getSequence())
-    {
-      if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U'))
-      {
-        return false;
-      }
-    }
-
-    return true;
-
-  }
 }