JAL-1503 update version in GPL header

[jalview.git] / src / MCview / PDBfile.java

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index c671ec2..aab4081 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,20 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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;
 
@@ -54,28 +54,39 @@ public class PDBfile extends jalview.io.AlignFile
 
   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());
+
+    chains = new Vector();
 
-      PDBChain tmpchain;
-      String line;
-      boolean modelFlag = false;
-      boolean terFlag = false;
+    PDBChain tmpchain;
+    String line = null;
+    boolean modelFlag = false;
+    boolean terFlag = false;
+    String lastID = "";
 
-      int index = 0;
+    int index = 0;
+    String atomnam = null;
+    try
+    {
       while ((line = nextLine()) != null)
       {
         if (line.indexOf("HEADER") == 0)
         {
-          if (line.length()>62)
+          if (line.length() > 62)
           {
-            if (line.length()>67) {
-              id = line.substring(62, 67).trim();
-            } else {
-              id=line.substring(62).trim();
+            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;
           }
@@ -105,7 +116,8 @@ public class PDBfile extends jalview.io.AlignFile
           terFlag = false;
 
           // Jalview is only interested in CA bonds????
-          if (!line.substring(12, 15).trim().equals("CA"))
+          atomnam = line.substring(12, 15).trim();
+          if (!atomnam.equals("CA") && !atomnam.equals("P"))
           {
             continue;
           }
@@ -114,6 +126,11 @@ public class PDBfile extends jalview.io.AlignFile
           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
@@ -122,6 +139,7 @@ public class PDBfile extends jalview.io.AlignFile
             chains.addElement(tmpchain);
             tmpchain.atoms.addElement(tmpatom);
           }
+          lastID = tmpatom.resNumIns.trim();
         }
         index++;
       }
@@ -143,10 +161,15 @@ public class PDBfile extends jalview.io.AlignFile
         {
           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
+        // maintain reference to
+        // dataset
         seqs.addElement(chainseq);
         AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
         if (chainannot != null)
@@ -162,7 +185,30 @@ public class PDBfile extends jalview.io.AlignFile
     {
       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()