X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=ebc52aaf0aa0643410590de2c330fd5611782160;hb=e94c33abc7983e947f64803ab294282a236bf671;hp=2c7bd9dbd49205afa07ec946bed02cedea67cd94;hpb=ededfcf0edb588601c4354523b0f399c600a7241;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 2c7bd9d..ebc52aa 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,72 +1,115 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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 jalview.datamodel.AlignmentAnnotation;
+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.awt.*;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
 
-import jalview.datamodel.*;
-
-public class PDBfile
-    extends jalview.io.AlignFile
+public class PDBfile extends StructureFile
 {
-  public Vector chains;
-  public String id;
+  private static String CALC_ID_PREFIX = "JalviewPDB";
 
-  /**
-   * set to true to add chain alignment annotation as visible annotation.
-   */
-  boolean VisibleChainAnnotation=false;
-  public PDBfile(String inFile, String inType)
-      throws IOException
+  public PDBfile(boolean addAlignmentAnnotations,
+          boolean predictSecondaryStructure, boolean externalSecStr)
   {
-    super(inFile, inType);
+    super();
+    addSettings(addAlignmentAnnotations, predictSecondaryStructure,
+            externalSecStr);
   }
 
-  public String print()
+  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+          boolean externalSecStr, String dataObject,
+          DataSourceType sourceType) throws IOException
+  {
+    super(false, dataObject, sourceType);
+    addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+    doParse();
+  }
+
+  public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+          boolean externalSecStr, FileParse source) throws IOException
+  {
+    super(false, source);
+    addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+    doParse();
+  }
+
+  @Override
+  public String print(SequenceI[] seqs, boolean jvSuffix)
   {
     return null;
   }
 
-  public void parse()
-      throws IOException
+  @Override
+  public void parse() throws IOException
   {
-    // TODO set the filename sensibly 
-    id = (inFile==null) ? "PDBFILE" : inFile.getName();
-    try
-    {
-      chains = new Vector();
+    setDbRefType(DBRefSource.PDB);
+    // TODO set the filename sensibly - try using data source name.
+    setId(safeName(getDataName()));
 
-      PDBChain tmpchain;
-      String line;
-      boolean modelFlag = false;
-      boolean terFlag = false;
+    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;
-      while ( (line = nextLine()) != null)
+    int indexx = 0;
+    String atomnam = null;
+    try
+    {
+      while ((line = nextLine()) != null)
       {
         if (line.indexOf("HEADER") == 0)
         {
-          id = line.substring(62, 67).trim();
-          continue;
+          if (line.length() > 62)
+          {
+            String tid;
+            if (line.length() > 67)
+            {
+              tid = line.substring(62, 67).trim();
+            }
+            else
+            {
+              tid = line.substring(62).trim();
+            }
+            if (tid.length() > 0)
+            {
+              setId(tid);
+            }
+            continue;
+          }
         }
         // Were we to do anything with SEQRES - we start it here
         if (line.indexOf("SEQRES") == 0)
@@ -88,29 +131,34 @@ public class PDBfile
           break;
         }
         if (line.indexOf("ATOM") == 0
-            || (line.indexOf("HETATM") == 0 && !terFlag)
-            )
+                || (line.indexOf("HETATM") == 0 && !terFlag))
         {
           terFlag = false;
 
-          //Jalview is only interested in CA bonds????
-          if (!line.substring(12, 15).trim().equals("CA"))
+          // Jalview is only interested in CA bonds????
+          atomnam = line.substring(12, 15).trim();
+          if (!atomnam.equals("CA") && !atomnam.equals("P"))
           {
             continue;
           }
 
           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();
         }
         index++;
       }
@@ -118,94 +166,92 @@ public class PDBfile
       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);
-        if (inFile != null)
+        SequenceI chainseq = postProcessChain(chain);
+        if (isRNA(chainseq))
         {
-          entry.setFile(inFile.getAbsolutePath());
+          rna.add(chainseq);
         }
-        dataset.addPDBId(entry);
-        SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects maintain reference to dataset
-        seqs.addElement(chainseq);
-        AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
-        if (chainannot!=null)
+        else
         {
-          for (int ai=0; ai<chainannot.length; ai++)
-          {
-            chainannot[ai].visible=VisibleChainAnnotation;
-            annotations.addElement(chainannot[ai]);
-          }
+          prot.add(chainseq);
         }
       }
-    }
-    catch (OutOfMemoryError er)
+      if (predictSecondaryStructure)
+      {
+        addSecondaryStructure(rna, prot);
+      }
+    } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
-      throw new IOException("Out of memory loading PDB File");
-    }
-  }
-
-  public void makeResidueList()
-  {
-    for (int i = 0; i < chains.size(); i++)
+      throw new IOException(MessageManager
+              .getString("exception.outofmemory_loading_pdb_file"));
+    } catch (NumberFormatException ex)
     {
-      ( (PDBChain) chains.elementAt(i)).makeResidueList();
+      if (line != null)
+      {
+        System.err.println("Couldn't read number from line:");
+        System.err.println(line);
+      }
     }
+    markCalcIds();
   }
 
-  public void makeCaBondList()
-  {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      ( (PDBChain) chains.elementAt(i)).makeCaBondList();
-    }
-  }
+  /**
+   * Process a parsed chain to construct and return a Sequence, and add it to
+   * the list of sequences parsed.
+   * 
+   * @param chain
+   * @return
+   */
 
-  public PDBChain findChain(String id)
+  public static boolean isCalcIdHandled(String calcId)
   {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      if ( ( (PDBChain) chains.elementAt(i)).id.equals(id))
-      {
-        return (PDBChain) chains.elementAt(i);
-      }
-    }
-
-    return null;
+    return calcId != null && (CALC_ID_PREFIX.equals(calcId));
   }
 
-  public void setChargeColours()
+  public static boolean isCalcIdForFile(AlignmentAnnotation alan,
+          String pdbFile)
   {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      ( (PDBChain) chains.elementAt(i)).setChargeColours();
-    }
+    return alan.getCalcId() != null
+            && CALC_ID_PREFIX.equals(alan.getCalcId())
+            && pdbFile.equals(alan.getProperty("PDBID"));
   }
 
-  public void setColours(jalview.schemes.ColourSchemeI cs)
+  public static String relocateCalcId(String calcId,
+          Hashtable<String, String> alreadyLoadedPDB) throws Exception
   {
-    for (int i = 0; i < chains.size(); i++)
-    {
-      ( (PDBChain) chains.elementAt(i)).setChainColours(cs);
-    }
+    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 void setChainColours()
+  private void markCalcIds()
   {
-    for (int i = 0; i < chains.size(); i++)
+    for (SequenceI sq : seqs)
     {
-      ( (PDBChain) chains.elementAt(i)).setChainColours(
-          Color.getHSBColor(1.0f / (float) i, .4f, 1.0f)
-          );
+      if (sq.getAnnotation() != null)
+      {
+        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);
+        }
+      }
     }
   }
+
 }