X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=cb3698995c4c2d708463237e56e7300118db6852;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=3f9bc9def3b3f22e6ddeb5cc43d7fc62667abc26;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 3f9bc9d..cb36989 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,33 +1,44 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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 jalview.datamodel.*;
+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;
+
+import java.awt.Color;
+import java.io.IOException;
+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;
+  public Vector<PDBChain> chains;
 
   public String id;
 
@@ -36,14 +47,39 @@ public class PDBfile extends jalview.io.AlignFile
    */
   boolean VisibleChainAnnotation = false;
 
-  public PDBfile(String inFile, String inType) throws IOException
+  boolean processSecondaryStructure = true;
+
+  boolean externalSecondaryStructure = false;
+
+  public PDBfile(boolean visibleChainAnnotation,
+          boolean processSecondaryStructure, boolean externalSecStr)
   {
-    super(inFile, inType);
+    super();
+    VisibleChainAnnotation = visibleChainAnnotation;
+    this.processSecondaryStructure = processSecondaryStructure;
+    this.externalSecondaryStructure = externalSecStr;
   }
 
-  public PDBfile(FileParse source) throws IOException
+  public PDBfile(boolean visibleChainAnnotation,
+          boolean processSecondaryStructure, boolean externalSecStr,
+          String file, String protocol) throws IOException
   {
-    super(source);
+    super(false, file, protocol);
+    VisibleChainAnnotation = visibleChainAnnotation;
+    this.processSecondaryStructure = processSecondaryStructure;
+    this.externalSecondaryStructure = externalSecStr;
+    doParse();
+  }
+
+  public PDBfile(boolean visibleChainAnnotation,
+          boolean processSecondaryStructure, boolean externalSecStr,
+          FileParse source) throws IOException
+  {
+    super(false, source);
+    VisibleChainAnnotation = visibleChainAnnotation;
+    this.processSecondaryStructure = processSecondaryStructure;
+    this.externalSecondaryStructure = externalSecStr;
+    doParse();
   }
 
   public String print()
@@ -56,18 +92,18 @@ public class PDBfile extends jalview.io.AlignFile
     // TODO set the filename sensibly - try using data source name.
     id = safeName(getDataName());
 
-      chains = new Vector();
-
-      PDBChain tmpchain;
-      String line=null;
-      boolean modelFlag = false;
-      boolean terFlag = false;
-      String lastID = "";
+    chains = new Vector();
+    ArrayList<SequenceI> rna = new ArrayList<SequenceI>(), prot = new ArrayList<SequenceI>();
+    PDBChain tmpchain;
+    String line = null;
+    boolean modelFlag = false;
+    boolean terFlag = false;
+    String lastID = "";
 
-      int index = 0;
-      String atomnam = null;
-      try
-      {
+    int index = 0;
+    String atomnam = null;
+    try
+    {
       while ((line = nextLine()) != null)
       {
         if (line.indexOf("HEADER") == 0)
@@ -152,10 +188,15 @@ public class PDBfile extends jalview.io.AlignFile
       }
       for (int i = 0; i < chains.size(); i++)
       {
-        SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence;
+        SequenceI dataset = chains.elementAt(i).sequence;
         dataset.setName(id + "|" + dataset.getName());
         PDBEntry entry = new PDBEntry();
         entry.setId(id);
+        entry.setProperty(new Hashtable());
+        if (chains.elementAt(i).id != null)
+        {
+          entry.getProperty().put("CHAIN", chains.elementAt(i).id);
+        }
         if (inFile != null)
         {
           entry.setFile(inFile.getAbsolutePath());
@@ -170,8 +211,18 @@ public class PDBfile extends jalview.io.AlignFile
         // 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)
+
+        if (chainannot != null && VisibleChainAnnotation)
         {
           for (int ai = 0; ai < chainannot.length; ai++)
           {
@@ -180,18 +231,206 @@ public class PDBfile extends jalview.io.AlignFile
           }
         }
       }
+      if (processSecondaryStructure)
+      {
+        if (externalSecondaryStructure && 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)
+          {
+            System.err
+                    .println("Exceptions from Jmol when processing data in pdb file");
+            x.printStackTrace();
+
+          }
+        }
+      }
     } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
-      throw new IOException("Out of memory loading PDB File");
-    }
-    catch (NumberFormatException ex)
+      throw new IOException(
+              MessageManager
+                      .getString("exception.outofmemory_loading_pdb_file"));
+    } catch (NumberFormatException ex)
     {
-      if (line!=null) {
+      if (line != null)
+      {
         System.err.println("Couldn't read number from line:");
         System.err.println(line);
       }
     }
+    markCalcIds();
+  }
+
+  private static String calcIdPrefix = "JalviewPDB";
+
+  public static boolean isCalcIdHandled(String calcId)
+  {
+    return calcId != null && (calcIdPrefix.equals(calcId));
+  }
+
+  public static boolean isCalcIdForFile(AlignmentAnnotation alan,
+          String pdbFile)
+  {
+    return alan.getCalcId() != null
+            && calcIdPrefix.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);
+    String between = calcId.substring(s, end - 1);
+    return calcIdPrefix + alreadyLoadedPDB.get(between) + ":"
+            + calcId.substring(end);
+  }
+
+  private void markCalcIds()
+  {
+    for (SequenceI sq : seqs)
+    {
+      if (sq.getAnnotation() != null)
+      {
+        for (AlignmentAnnotation aa : sq.getAnnotation())
+        {
+          String oldId = aa.getCalcId();
+          if (oldId == null)
+          {
+            oldId = "";
+          }
+          aa.setCalcId(calcIdPrefix);
+          aa.setProperty("PDBID", id);
+          aa.setProperty("oldCalcId", oldId);
+        }
+      }
+    }
+  }
+
+  private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
+          throws Exception
+  {
+    try
+    {
+      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);
+        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(ArrayList<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(ArrayList<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
+    }
+    ;
   }
 
   /**
@@ -214,7 +453,7 @@ 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);
     }
   }
 
@@ -222,7 +461,7 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ((PDBChain) chains.elementAt(i)).makeCaBondList();
+      chains.elementAt(i).makeCaBondList();
     }
   }
 
@@ -230,9 +469,9 @@ 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);
       }
     }
 
@@ -243,7 +482,7 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ((PDBChain) chains.elementAt(i)).setChargeColours();
+      chains.elementAt(i).setChargeColours();
     }
   }
 
@@ -251,7 +490,7 @@ 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);
     }
   }
 
@@ -259,8 +498,23 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
-              1.0f / (float) i, .4f, 1.0f));
+      chains.elementAt(i).setChainColours(
+              Color.getHSBColor(1.0f / 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;
+
   }
 }