X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=6055a5b0fc8f48e90ab5c26ad507aac1b9e1e8b4;hb=961eec1363ddc5f0f5a08b9063a7a2a9b1c9d2bd;hp=47f681716ea15683aa67792df3ddf1308a13889a;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 47f6817..6055a5b 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,31 +1,39 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureMapping;
 
+import java.awt.Color;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
 public class PDBChain
 {
   /**
@@ -67,6 +75,21 @@ public class PDBChain
     this.id = id;
   }
 
+  /**
+   * character used to write newlines
+   */
+  protected String newline = System.getProperty("line.separator");
+
+  public void setNewlineString(String nl)
+  {
+    newline = nl;
+  }
+
+  public String getNewlineString()
+  {
+    return newline;
+  }
+
   public String print()
   {
     String tmp = "";
@@ -75,17 +98,30 @@ public class PDBChain
     {
       tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " "
               + ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset
-              + "\n";
+              + newline;
     }
 
     return tmp;
   }
 
+  /**
+   * Annotate the residues with their corresponding positions in s1 using the
+   * alignment in as NOTE: This clears all atom.alignmentMapping values on the
+   * structure.
+   * 
+   * @param as
+   * @param s1
+   */
   public void makeExactMapping(AlignSeq as, SequenceI s1)
   {
     int pdbpos = as.getSeq2Start() - 2;
     int alignpos = s1.getStart() + as.getSeq1Start() - 3;
-
+    // first clear out any old alignmentMapping values:
+    for (Atom atom : (Vector<Atom>) atoms)
+    {
+      atom.alignmentMapping = -1;
+    }
+    // and now trace the alignment onto the atom set.
     for (int i = 0; i < as.astr1.length(); i++)
     {
       if (as.astr1.charAt(i) != '-')
@@ -156,7 +192,9 @@ public class PDBChain
                 + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
                         : ":" + tx.getStatus()));
         if (tx.begin != 0 && tx.end != 0)
+        {
           sq.addSequenceFeature(tx);
+        }
       }
     }
     return features;
@@ -221,6 +259,7 @@ public class PDBChain
   {
     int count = 0;
     Object symbol;
+    boolean deoxyn = false;
     boolean nucleotide = false;
     StringBuffer seq = new StringBuffer();
     Vector resFeatures = new Vector();
@@ -243,7 +282,7 @@ public class PDBChain
       // remains the same as the first atom's resNumber (res)
       while ((resNumber == res) && (i < atoms.size()))
       {
-        resAtoms.addElement((Atom) atoms.elementAt(i));
+        resAtoms.addElement(atoms.elementAt(i));
         i++;
 
         if (i < atoms.size())
@@ -275,7 +314,13 @@ public class PDBChain
       if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
       {
         String nucname = tmpat.resName.trim();
-        if (ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
+        // use the aaIndex rather than call 'toLower' - which would take a bit
+        // more time.
+        deoxyn = nucname.length() == 2
+                && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D'];
+        if (tmpat.name.equalsIgnoreCase("CA")
+                || ResidueProperties.nucleotideIndex[nucname
+                        .charAt((deoxyn ? 1 : 0))] == -1)
         {
           seq.append("X");
           // System.err.println("PDBReader:Null aa3Hash for " +
@@ -285,7 +330,7 @@ public class PDBChain
         {
           // nucleotide flag
           nucleotide = true;
-          seq.append(nucname.charAt(0));
+          seq.append(nucname.charAt((deoxyn ? 1 : 0)));
         }
       }
       else
@@ -326,7 +371,9 @@ public class PDBChain
     {
       annots[i] = (Annotation) resAnnotation.elementAt(i);
       if (annots[i].value > max)
+      {
         max = annots[i].value;
+      }
       resAnnotation.setElementAt(null, i);
     }
     AlignmentAnnotation tfactorann = new AlignmentAnnotation(
@@ -458,7 +505,7 @@ public class PDBChain
       {
         int prn = mapping.getPDBResNum(k + 1);
 
-        an[k] = new Annotation((float) prn);
+        an[k] = new Annotation(prn);
         if (min == -1)
         {
           min = k;
@@ -478,7 +525,8 @@ public class PDBChain
       }
       sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
               "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
-              an, (float) min, (float) max, AlignmentAnnotation.LINE_GRAPH));
+              an, min, max, AlignmentAnnotation.LINE_GRAPH));
+
     }
   }
 }