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

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index a556137..2eaf8a3 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,20 +1,19 @@
 /*
- * 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 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 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.
  * 
- * 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 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;
 
@@ -116,7 +115,7 @@ public class PDBChain
    * 
    * @param seq
    * @param status
-   *                The Status of the transferred annotation
+   *          The Status of the transferred annotation
    * @return the features added to sq (or its dataset)
    */
   public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
@@ -134,8 +133,8 @@ public class PDBChain
     /**
      * Remove any existing features for this chain if they exist ?
      * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
-     * totfeat=seqsfeatures.length; // Remove any features for this exact chain ?
-     * for (int i=0; i<seqsfeatures.length; i++) { }
+     * totfeat=seqsfeatures.length; // Remove any features for this exact chain
+     * ? for (int i=0; i<seqsfeatures.length; i++) { }
      */
     if (status == null)
     {
@@ -205,7 +204,7 @@ public class PDBChain
   {
     int count = 0;
     Object symbol;
-    boolean nucleotide=false;
+    boolean nucleotide = false;
     StringBuffer seq = new StringBuffer();
     Vector resFeatures = new Vector();
     Vector resAnnotation = new Vector();
@@ -256,16 +255,18 @@ public class PDBChain
       resFeatures.addElement(sf);
       resAnnotation.addElement(new Annotation(tmpat.tfactor));
       // Keep totting up the sequence
-      if ((symbol=ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
+      if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
       {
-        if (ResidueProperties.nucleotideIndex[tmpat.resName.charAt(0)]==-1)
+        if (ResidueProperties.nucleotideIndex[tmpat.resName.charAt(0)] == -1)
         {
           seq.append("X");
-        // System.err.println("PDBReader:Null aa3Hash for " +
-        // tmpat.resName);
-        } else {
+          // System.err.println("PDBReader:Null aa3Hash for " +
+          // tmpat.resName);
+        }
+        else
+        {
           // nucleotide flag
-          nucleotide=true;
+          nucleotide = true;
           seq.append(tmpat.resName.charAt(0));
         }
       }
@@ -273,7 +274,8 @@ public class PDBChain
       {
         if (nucleotide)
         {
-          System.err.println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
+          System.err
+                  .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
         }
         seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
       }
@@ -286,13 +288,12 @@ public class PDBChain
     }
 
     sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
-                                                                        // resNumber-offset
-                                                                        // ~=
-                                                                        // seq.size()
+    // resNumber-offset
+    // ~=
+    // seq.size()
     // Add normalised feature scores to RESNUM indicating start/end of sequence
-    //      sf.setScore(offset+count);
-                                                                           
-                                                                       
+    // sf.setScore(offset+count);
+
     // System.out.println("PDB Sequence is :\nSequence = " + seq);
     // System.out.println("No of residues = " + residues.size());
     for (i = 0, iSize = resFeatures.size(); i < iSize; i++)