X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=58f8ed5b7a35f5b7242e24e8e1602bb4d4c3c860;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=019aba946980a7f6604c04233b259f5326f1b450;hpb=e05ad4f9199d673b327277d1266d97f3a51419ae;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 019aba9..58f8ed5 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -31,47 +31,66 @@ import jalview.util.MessageManager;
 
 import java.awt.Color;
 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;
 
 public class PDBfile extends jalview.io.AlignFile
 {
-  public Vector chains;
+  private static String CALC_ID_PREFIX = "JalviewPDB";
+
+  public Vector<PDBChain> chains;
 
   public String id;
 
   /**
-   * set to true to add chain alignment annotation as visible annotation.
+   * 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)
    */
-  boolean VisibleChainAnnotation = false;
+  private boolean predictSecondaryStructure = true;
 
-  boolean processSecondaryStructure=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 visibleChainAnnotation,
-          boolean processSecondaryStructure)
+  public PDBfile(boolean addAlignmentAnnotations,
+          boolean predictSecondaryStructure, boolean externalSecStr)
   {
     super();
-    VisibleChainAnnotation = visibleChainAnnotation;
-    this.processSecondaryStructure = processSecondaryStructure;
+    this.visibleChainAnnotation = addAlignmentAnnotations;
+    this.predictSecondaryStructure = predictSecondaryStructure;
+    this.externalSecondaryStructure = externalSecStr;
   }
 
-  public PDBfile(boolean visibleChainAnnotation,
-          boolean processSecondaryStructure, String file, String protocol) throws IOException
+  public PDBfile(boolean addAlignmentAnnotations,
+          boolean predictSecondaryStructure, boolean externalSecStr,
+          String file, String protocol) throws IOException
   {
     super(false, file, protocol);
-    VisibleChainAnnotation = visibleChainAnnotation;
-    this.processSecondaryStructure = processSecondaryStructure;
+    this.visibleChainAnnotation = addAlignmentAnnotations;
+    this.predictSecondaryStructure = predictSecondaryStructure;
+    this.externalSecondaryStructure = externalSecStr;
     doParse();
   }
 
-  public PDBfile(boolean visibleChainAnnotation,
-          boolean processSecondaryStructure, FileParse source) throws IOException
+  public PDBfile(boolean addAlignmentAnnotations,
+          boolean predictSecondaryStructure, boolean externalSecStr,
+          FileParse source) throws IOException
   {
     super(false, source);
-    VisibleChainAnnotation = visibleChainAnnotation;
-    this.processSecondaryStructure = processSecondaryStructure;
+    this.visibleChainAnnotation = addAlignmentAnnotations;
+    this.predictSecondaryStructure = predictSecondaryStructure;
+    this.externalSecondaryStructure = externalSecStr;
     doParse();
   }
 
@@ -85,15 +104,16 @@ public class PDBfile extends jalview.io.AlignFile
     // TODO set the filename sensibly - try using data source name.
     id = safeName(getDataName());
 
-    chains = new Vector();
-    ArrayList<SequenceI> rna = new ArrayList<SequenceI>(), prot = new ArrayList<SequenceI>();
+    chains = new Vector<PDBChain>();
+    List<SequenceI> rna = new ArrayList<SequenceI>();
+    List<SequenceI> prot = new ArrayList<SequenceI>();
     PDBChain tmpchain;
     String line = null;
     boolean modelFlag = false;
     boolean terFlag = false;
     String lastID = "";
 
-    int index = 0;
+    int indexx = 0;
     String atomnam = null;
     try
     {
@@ -179,33 +199,10 @@ public class PDBfile extends jalview.io.AlignFile
       {
         id = inFile.getName();
       }
-      for (int i = 0; i < chains.size(); i++)
+      for (PDBChain chain : chains)
       {
-        SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence;
-        dataset.setName(id + "|" + dataset.getName());
-        PDBEntry entry = new PDBEntry();
-        entry.setId(id);
-        entry.setProperty(new Hashtable());
-        if (((PDBChain) chains.elementAt(i)).id != null)
-        {
-          entry.getProperty().put("CHAIN",
-                  ((PDBChain) chains.elementAt(i)).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);
-        SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects
-        // maintain reference to
-        // dataset
-        seqs.addElement(chainseq);
-        if (isRNA(chainseq) == true)
+        SequenceI chainseq = postProcessChain(chain);
+        if (isRNA(chainseq))
         {
           rna.add(chainseq);
         }
@@ -213,47 +210,10 @@ public class PDBfile extends jalview.io.AlignFile
         {
           prot.add(chainseq);
         }
-
-        AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
-
-        if (chainannot != null)
-        {
-          for (int ai = 0; ai < chainannot.length; ai++)
-          {
-            chainannot[ai].visible = VisibleChainAnnotation;
-            annotations.addElement(chainannot[ai]);
-          }
-        }
       }
-      if (processSecondaryStructure)
-      {
-      if (rna.size() > 0)
+      if (predictSecondaryStructure)
       {
-        try
-        {
-          processPdbFileWithAnnotate3d(rna);
-        } catch (Exception x)
-        {
-          System.err
-                  .println("Exceptions when dealing with RNA in pdb file");
-          x.printStackTrace();
-
-        }
-      }
-      ;
-      if (prot.size() > 0)
-      {
-        try
-        {
-          processPdbFileWithJmol(prot);
-        } catch (Exception x)
-        {
-          System.err
-                  .println("Exceptions from Jmol when processing data in pdb file");
-          x.printStackTrace();
-
-        }
-      }
+        predictSecondaryStructure(rna, prot);
       }
     } catch (OutOfMemoryError er)
     {
@@ -272,27 +232,117 @@ public class PDBfile extends jalview.io.AlignFile
     markCalcIds();
   }
 
-  private static String calcIdPrefix = "JalviewPDB:";
+  /**
+   * 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)
   {
-    return calcId != null
-            && (calcId.startsWith(calcIdPrefix) && calcId.indexOf(
-                    calcIdPrefix,
-            calcIdPrefix.length() + 1) > -1);
+    return calcId != null && (CALC_ID_PREFIX.equals(calcId));
   }
-  public static boolean isCalcIdForFile(String calcId, String pdbFile)
+
+  public static boolean isCalcIdForFile(AlignmentAnnotation alan,
+          String pdbFile)
   {
-    return (calcId != null && calcId.startsWith(calcIdPrefix + pdbFile
-            + ":" + calcIdPrefix));
+    return alan.getCalcId() != null
+            && CALC_ID_PREFIX.equals(alan.getCalcId())
+            && pdbFile.equals(alan.getProperty("PDBID"));
   }
 
   public static String relocateCalcId(String calcId,
           Hashtable<String, String> alreadyLoadedPDB) throws Exception
   {
-    int s = calcIdPrefix.length(), end = calcId.indexOf(calcIdPrefix, s);
+    int s = CALC_ID_PREFIX.length(), end = calcId
+            .indexOf(CALC_ID_PREFIX, s);
     String between = calcId.substring(s, end - 1);
-    return calcIdPrefix + alreadyLoadedPDB.get(between) + ":"
+    return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
             + calcId.substring(end);
   }
 
@@ -300,18 +350,24 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (SequenceI sq : seqs)
     {
-      for (AlignmentAnnotation aa : sq.getAnnotation())
+      if (sq.getAnnotation() != null)
       {
-        String oldId = aa.getCalcId();
-        if (oldId == null)
+        for (AlignmentAnnotation aa : sq.getAnnotation())
         {
-          oldId = "";
+          String oldId = aa.getCalcId();
+          if (oldId == null)
+          {
+            oldId = "";
+          }
+          aa.setCalcId(CALC_ID_PREFIX);
+          aa.setProperty("PDBID", id);
+          aa.setProperty("oldCalcId", oldId);
         }
-        aa.setCalcId("JalviewPDB:" + id + ":JalviewPDB:" + oldId);
       }
     }
   }
-  private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
+
+  private void processPdbFileWithJmol(List<SequenceI> prot)
           throws Exception
   {
     try
@@ -319,22 +375,63 @@ public class PDBfile extends jalview.io.AlignFile
       Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
       if (cl != null)
       {
-        Object jmf = cl.getConstructor(new Class[]
-        { FileParse.class }).newInstance(new Object[]
-        { new FileParse(getDataName(), type) });
-        Alignment al = new Alignment((SequenceI[]) cl.getMethod(
-                "getSeqsAsArray", new Class[]
-                {}).invoke(jmf));
-        cl.getMethod("addAnnotations", new Class[]
-        { Alignment.class }).invoke(jmf, al);
-        AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false);
+        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)
     {
     }
   }
 
-  private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna)
+  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");
@@ -348,14 +445,29 @@ public class PDBfile extends jalview.io.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[]
-        {});
+        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) }));
-        AlignSeq.replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false);
+                new Class[] { FileParse.class }).invoke(annotate3d,
+                new Object[] { new FileParse(getDataName(), type) }));
+        for (SequenceI sq : al.getSequences())
+        {
+          if (sq.getDatasetSequence() != null)
+          {
+            if (sq.getDatasetSequence().getAllPDBEntries() != null)
+            {
+              sq.getDatasetSequence().getAllPDBEntries().clear();
+            }
+          }
+          else
+          {
+            if (sq.getAllPDBEntries() != null)
+            {
+              sq.getAllPDBEntries().clear();
+            }
+          }
+        }
+        replaceAndUpdateChains(rna, al, AlignSeq.DNA, false);
       }
     } catch (ClassNotFoundException x)
     {
@@ -384,7 +496,7 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ((PDBChain) chains.elementAt(i)).makeResidueList();
+      chains.elementAt(i).makeResidueList(visibleChainAnnotation);
     }
   }
 
@@ -392,7 +504,7 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ((PDBChain) chains.elementAt(i)).makeCaBondList();
+      chains.elementAt(i).makeCaBondList();
     }
   }
 
@@ -400,9 +512,9 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      if (((PDBChain) chains.elementAt(i)).id.equals(id))
+      if (chains.elementAt(i).id.equals(id))
       {
-        return (PDBChain) chains.elementAt(i);
+        return chains.elementAt(i);
       }
     }
 
@@ -413,7 +525,7 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ((PDBChain) chains.elementAt(i)).setChargeColours();
+      chains.elementAt(i).setChargeColours();
     }
   }
 
@@ -421,7 +533,7 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ((PDBChain) chains.elementAt(i)).setChainColours(cs);
+      chains.elementAt(i).setChainColours(cs);
     }
   }
 
@@ -429,17 +541,17 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
-              1.0f / i, .4f, 1.0f));
+      // divide by zero --> infinity --> 255 ;-)
+      chains.elementAt(i).setChainColours(
+              Color.getHSBColor(1.0f / i, .4f, 1.0f));
     }
   }
 
-  public boolean isRNA(SequenceI seqs)
+  public static boolean isRNA(SequenceI seq)
   {
-    for (int i = 0; i < seqs.getLength(); i++)
+    for (char c : seq.getSequence())
     {
-      if ((seqs.getCharAt(i) != 'A') && (seqs.getCharAt(i) != 'C')
-              && (seqs.getCharAt(i) != 'G') && (seqs.getCharAt(i) != 'U'))
+      if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U'))
       {
         return false;
       }