X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=f5a0255094f23ab858ddb3bb5b9df9a7e232aad6;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=6a61f6a980aed41e7cf8fe84bf6a47185ab67656;hpb=2fdd3b15c68d12fcf0c56e2ee70d3ff593f82249;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 6a61f6a..f5a0255 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,81 +1,90 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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/>.
+ * 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 MCview;
 
-import java.io.*;
-import java.util.*;
-
-import java.awt.*;
-
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
 import jalview.io.FileParse;
-import jalview.ws.jws1.Annotate3D;
+import jalview.io.StructureFile;
+import jalview.util.MessageManager;
 
-public class PDBfile extends jalview.io.AlignFile
-{
-  public Vector chains;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
 
-  public String id;
+public class PDBfile extends StructureFile
+{
+  private static String CALC_ID_PREFIX = "JalviewPDB";
 
-  /**
-   * set to true to add chain alignment annotation as visible annotation.
-   */
-  boolean VisibleChainAnnotation = false;
+  public PDBfile(boolean addAlignmentAnnotations,
+          boolean predictSecondaryStructure, boolean externalSecStr)
+  {
+    super();
+    addSettings(addAlignmentAnnotations, predictSecondaryStructure,
+            externalSecStr);
+  }
 
-  public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+          boolean externalSecStr, String dataObject, String protocol)
+          throws IOException
   {
-    super(inFile, inType);
+    super(false, dataObject, protocol);
+    addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+    doParse();
   }
 
-  public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+          boolean externalSecStr, FileParse source) throws IOException
   {
-    super(source);
+    super(false, source);
+    addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+    doParse();
   }
 
+  @Override
   public String print()
   {
     return null;
   }
 
-  public void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+  @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();
-    ArrayList<SequenceI> rna=new ArrayList<SequenceI>(), prot=new ArrayList<SequenceI>();
+    setChains(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
     {
@@ -96,7 +105,7 @@ public class PDBfile extends jalview.io.AlignFile
             }
             if (tid.length() > 0)
             {
-              id = tid;
+              setId(tid);
             }
             continue;
           }
@@ -133,20 +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();
@@ -157,73 +165,32 @@ public class PDBfile extends jalview.io.AlignFile
       makeResidueList();
       makeCaBondList();
 
-      if (id == null)
+      if (getId() == null)
       {
-        id = inFile.getName();
+        setId(inFile.getName());
       }
-      for (int i = 0; i < chains.size(); i++)
+      for (PDBChain chain : getChains())
       {
-        SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence;
-        dataset.setName(id + "|" + dataset.getName());
-        PDBEntry entry = new PDBEntry();
-        entry.setId(id);
-        entry.setProperty(new Hashtable());
-        entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
-        if (inFile != null)
+        SequenceI chainseq = postProcessChain(chain);
+        if (isRNA(chainseq))
         {
-          entry.setFile(inFile.getAbsolutePath());
+          rna.add(chainseq);
         }
         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)
-       {
-         rna.add(chainseq);
-       } else {
-         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]);
-          }
+          prot.add(chainseq);
         }
       }
-      if (rna.size()>0)
-      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)
+      if (predictSecondaryStructure)
       {
-        System.err.println("Exceptions when dealing with RNA in pdb file");
-        x.printStackTrace();
-        
-      };
+        addSecondaryStructure(rna, prot);
+      }
     } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
-      throw new IOException("Out of memory loading PDB File");
+      throw new IOException(
+              MessageManager
+                      .getString("exception.outofmemory_loading_pdb_file"));
     } catch (NumberFormatException ex)
     {
       if (line != null)
@@ -232,153 +199,59 @@ public class PDBfile extends jalview.io.AlignFile
         System.err.println(line);
       }
     }
+    markCalcIds();
   }
-  private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
-  {
-    // process prot sequence with Jmol to get annotated alignment. 
-    // replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
-  }
-  private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
-//    System.out.println("this is a PDB format and RNA sequence");
-    Annotate3D an3d = new Annotate3D();
-    AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
-    replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
-  }
-  private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains, AlignmentI al, String dnaOrProtein)
-  {
-    if (al!=null && al.getHeight()>0)
-    {
-      ArrayList<SequenceI> matches=new ArrayList<SequenceI>();
-      ArrayList<AlignSeq> aligns=new ArrayList<AlignSeq>();
-      
-      for (SequenceI sq:ochains)
-      {
-        SequenceI bestm=null;
-        AlignSeq bestaseq=null;
-        int bestscore=0;
-        for (SequenceI msq:al.getSequences())
-        {
-          AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq, dnaOrProtein);
-          if (bestm==null || aseq.getMaxScore()>bestscore)
-          {
-            bestscore=aseq.getMaxScore();
-            bestaseq= aseq;
-            bestm=msq;
-          }
-        }
-        System.out.println("Best Score for "+(matches.size()+1)+" :"+bestscore);
-        matches.add(bestm);
-        aligns.add(bestaseq);
-        al.deleteSequence(bestm);
-      }
-      for (int p=0,pSize=seqs.size();p<pSize;p++)
-      {
-        SequenceI sq,sp=seqs.get(p);
-        int q;
-        if ((q=ochains.indexOf(sp))>-1)
-        {
-          seqs.set(p, sq=matches.get(q));
-          sq.setName(sp.getName());
-          sq.setDescription(sp.getDescription());
-          sq.transferAnnotation(sp, aligns.get(q).getMappingFromS1(false));
-          int inspos=-1;
-          for (int ap=0;ap<annotations.size();)
-          {
-            if (((AlignmentAnnotation)annotations.get(ap)).sequenceRef==sp) {
-              if (inspos==-1)
-              {
-                inspos=ap;
-              }
-              annotations.remove(ap);
-            } else {
-              ap++;
-            }
-          }
-          annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
-        }
-      }
-    }
-  }
+
   /**
-   * make a friendly ID string.
+   * Process a parsed chain to construct and return a Sequence, and add it to
+   * the list of sequences parsed.
    * 
-   * @param dataName
-   * @return truncated dataName to after last '/'
+   * @param chain
+   * @return
    */
-  private String safeName(String dataName)
+
+  public static boolean isCalcIdHandled(String calcId)
   {
-    int p = 0;
-    while ((p = dataName.indexOf("/")) > -1 && p < dataName.length())
-    {
-      dataName = dataName.substring(p + 1);
-    }
-    return dataName;
+    return calcId != null && (CALC_ID_PREFIX.equals(calcId));
   }
 
-  public void makeResidueList()
+  public static boolean isCalcIdForFile(AlignmentAnnotation alan,
+          String pdbFile)
   {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      ((PDBChain) chains.elementAt(i)).makeResidueList();
-    }
+    return alan.getCalcId() != null
+            && CALC_ID_PREFIX.equals(alan.getCalcId())
+            && pdbFile.equals(alan.getProperty("PDBID"));
   }
 
-  public void makeCaBondList()
+  public static String relocateCalcId(String calcId,
+          Hashtable<String, String> alreadyLoadedPDB) throws Exception
   {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      ((PDBChain) chains.elementAt(i)).makeCaBondList();
-    }
+    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);
   }
 
-  public PDBChain findChain(String id)
+  private void markCalcIds()
   {
-    for (int i = 0; i < chains.size(); i++)
+    for (SequenceI sq : seqs)
     {
-      if (((PDBChain) chains.elementAt(i)).id.equals(id))
+      if (sq.getAnnotation() != null)
       {
-        return (PDBChain) chains.elementAt(i);
+        for (AlignmentAnnotation aa : sq.getAnnotation())
+        {
+          String oldId = aa.getCalcId();
+          if (oldId == null)
+          {
+            oldId = "";
+          }
+          aa.setCalcId(CALC_ID_PREFIX);
+          aa.setProperty("PDBID", getId());
+          aa.setProperty("oldCalcId", oldId);
+        }
       }
     }
-
-    return null;
-  }
-
-  public void setChargeColours()
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      ((PDBChain) chains.elementAt(i)).setChargeColours();
-    }
   }
 
-  public void setColours(jalview.schemes.ColourSchemeI cs)
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      ((PDBChain) chains.elementAt(i)).setChainColours(cs);
-    }
-  }
-
-  public void setChainColours()
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
-              1.0f / (float) i, .4f, 1.0f));
-    }
-  }
-  public boolean isRNA(SequenceI seqs)
-  {
-	  for (int i=0;i<seqs.getLength();i++){
-		  if((seqs.getCharAt(i)!='A') &&(seqs.getCharAt(i)!='C')&&(seqs.getCharAt(i)!='G')&&(seqs.getCharAt(i)!='U'))
-		  {
-			  return false;
-		  }
-	  }
-	 
-		  return true;
-	  
-	  
-  }
 }