X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=f246b8cd9c98a9a6bb79e30ea94552e2fd4b6e5d;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=2c7bd9dbd49205afa07ec946bed02cedea67cd94;hpb=ededfcf0edb588601c4354523b0f399c600a7241;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 2c7bd9d..f246b8c 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,20 +1,19 @@
 /*
- * 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
- * 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.
- *
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * 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.
+ * 
+ * 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/>.
  */
 package MCview;
 
@@ -24,49 +23,72 @@ import java.util.*;
 import java.awt.*;
 
 import jalview.datamodel.*;
+import jalview.io.FileParse;
 
-public class PDBfile
-    extends jalview.io.AlignFile
+public class PDBfile extends jalview.io.AlignFile
 {
   public Vector chains;
+
   public String id;
 
   /**
    * set to true to add chain alignment annotation as visible annotation.
    */
-  boolean VisibleChainAnnotation=false;
-  public PDBfile(String inFile, String inType)
-      throws IOException
+  boolean VisibleChainAnnotation = false;
+
+  public PDBfile(String inFile, String inType) throws IOException
   {
     super(inFile, inType);
   }
 
+  public PDBfile(FileParse source) throws IOException
+  {
+    super(source);
+  }
+
   public String print()
   {
     return null;
   }
 
-  public void parse()
-      throws IOException
+  public void parse() throws IOException
   {
-    // TODO set the filename sensibly 
-    id = (inFile==null) ? "PDBFILE" : inFile.getName();
-    try
-    {
-      chains = new Vector();
+    // TODO set the filename sensibly - try using data source name.
+    id = safeName(getDataName());
 
-      PDBChain tmpchain;
-      String line;
-      boolean modelFlag = false;
-      boolean terFlag = false;
+    chains = new Vector();
 
-      int index = 0;
-      while ( (line = nextLine()) != null)
+    PDBChain tmpchain;
+    String line = null;
+    boolean modelFlag = false;
+    boolean terFlag = false;
+    String lastID = "";
+
+    int index = 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)
+            {
+              id = tid;
+            }
+            continue;
+          }
         }
         // Were we to do anything with SEQRES - we start it here
         if (line.indexOf("SEQRES") == 0)
@@ -88,13 +110,13 @@ 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;
           }
@@ -103,6 +125,11 @@ public class PDBfile
           tmpchain = findChain(tmpatom.chain);
           if (tmpchain != null)
           {
+            if (tmpatom.resNumIns.trim().equals(lastID))
+            {
+              // phosphorylated protein - seen both CA and P..
+              continue;
+            }
             tmpchain.atoms.addElement(tmpatom);
           }
           else
@@ -111,6 +138,7 @@ public class PDBfile
             chains.addElement(tmpchain);
             tmpchain.atoms.addElement(tmpatom);
           }
+          lastID = tmpatom.resNumIns.trim();
         }
         index++;
       }
@@ -124,8 +152,7 @@ public class PDBfile
       }
       for (int i = 0; i < chains.size(); i++)
       {
-        SequenceI dataset = ( (PDBChain) chains.elementAt(i)).
-            sequence;
+        SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence;
         dataset.setName(id + "|" + dataset.getName());
         PDBEntry entry = new PDBEntry();
         entry.setId(id);
@@ -133,32 +160,61 @@ public class PDBfile
         {
           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
+        SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects
+        // maintain reference to
+        // dataset
         seqs.addElement(chainseq);
         AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
-        if (chainannot!=null)
+        if (chainannot != null)
         {
-          for (int ai=0; ai<chainannot.length; ai++)
+          for (int ai = 0; ai < chainannot.length; ai++)
           {
-            chainannot[ai].visible=VisibleChainAnnotation;
+            chainannot[ai].visible = VisibleChainAnnotation;
             annotations.addElement(chainannot[ai]);
           }
         }
       }
-    }
-    catch (OutOfMemoryError er)
+    } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
       throw new IOException("Out of memory loading PDB File");
+    } catch (NumberFormatException ex)
+    {
+      if (line != null)
+      {
+        System.err.println("Couldn't read number from line:");
+        System.err.println(line);
+      }
+    }
+  }
+
+  /**
+   * 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++)
     {
-      ( (PDBChain) chains.elementAt(i)).makeResidueList();
+      ((PDBChain) chains.elementAt(i)).makeResidueList();
     }
   }
 
@@ -166,7 +222,7 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ( (PDBChain) chains.elementAt(i)).makeCaBondList();
+      ((PDBChain) chains.elementAt(i)).makeCaBondList();
     }
   }
 
@@ -174,7 +230,7 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      if ( ( (PDBChain) chains.elementAt(i)).id.equals(id))
+      if (((PDBChain) chains.elementAt(i)).id.equals(id))
       {
         return (PDBChain) chains.elementAt(i);
       }
@@ -187,7 +243,7 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ( (PDBChain) chains.elementAt(i)).setChargeColours();
+      ((PDBChain) chains.elementAt(i)).setChargeColours();
     }
   }
 
@@ -195,7 +251,7 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ( (PDBChain) chains.elementAt(i)).setChainColours(cs);
+      ((PDBChain) chains.elementAt(i)).setChainColours(cs);
     }
   }
 
@@ -203,9 +259,8 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ( (PDBChain) chains.elementAt(i)).setChainColours(
-          Color.getHSBColor(1.0f / (float) i, .4f, 1.0f)
-          );
+      ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
+              1.0f / (float) i, .4f, 1.0f));
     }
   }
 }