X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=c9301e862bcd98e6a820925528c34145a83b44aa;hb=a0d3647da9f02df7c5a13f59e5db552e7567974f;hp=2eaf8a3d8ffe210147491569cd8b2d724fad5fec;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 2eaf8a3..c9301e8 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * 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;
 
@@ -47,6 +50,8 @@ public class PDBChain
 
   public Sequence sequence;
 
+  public boolean isNa = false;
+
   public boolean isVisible = true;
 
   public int pdbstart = 0;
@@ -65,6 +70,21 @@ 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 = "";
@@ -73,17 +93,30 @@ 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) != '-')
@@ -150,10 +183,9 @@ public class PDBChain
                 - offset)).atoms.elementAt(0)).alignmentMapping);
         tx.setEnd(1 + ((Atom) ((Residue) residues.elementAt(tx.getEnd()
                 - offset)).atoms.elementAt(0)).alignmentMapping);
-        tx
-                .setStatus(status
-                        + ((tx.getStatus() == null || tx.getStatus()
-                                .length() == 0) ? "" : ":" + tx.getStatus()));
+        tx.setStatus(status
+                + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
+                        : ":" + tx.getStatus()));
         if (tx.begin != 0 && tx.end != 0)
           sq.addSequenceFeature(tx);
       }
@@ -163,17 +195,29 @@ public class PDBChain
 
   public void makeCaBondList()
   {
+    boolean na = false;
+    int numNa = 0;
     for (int i = 0; i < (residues.size() - 1); i++)
     {
       Residue tmpres = (Residue) residues.elementAt(i);
       Residue tmpres2 = (Residue) residues.elementAt(i + 1);
       Atom at1 = tmpres.findAtom("CA");
       Atom at2 = tmpres2.findAtom("CA");
-
+      na = false;
+      if ((at1 == null) && (at2 == null))
+      {
+        na = true;
+        at1 = tmpres.findAtom("P");
+        at2 = tmpres2.findAtom("P");
+      }
       if ((at1 != null) && (at2 != null))
       {
         if (at1.chain.equals(at2.chain))
         {
+          if (na)
+          {
+            numNa++;
+          }
           makeBond(at1, at2);
         }
       }
@@ -182,6 +226,10 @@ public class PDBChain
         System.out.println("not found " + i);
       }
     }
+    if (numNa > 0 && ((numNa / residues.size()) > 0.99))
+    {
+      isNa = true;
+    }
   }
 
   public void makeBond(Atom at1, Atom at2)
@@ -204,6 +252,7 @@ public class PDBChain
   {
     int count = 0;
     Object symbol;
+    boolean deoxyn = false;
     boolean nucleotide = false;
     StringBuffer seq = new StringBuffer();
     Vector resFeatures = new Vector();
@@ -257,7 +306,14 @@ public class PDBChain
       // Keep totting up the sequence
       if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
       {
-        if (ResidueProperties.nucleotideIndex[tmpat.resName.charAt(0)] == -1)
+        String nucname = tmpat.resName.trim();
+        // 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 " +
@@ -267,7 +323,7 @@ public class PDBChain
         {
           // nucleotide flag
           nucleotide = true;
-          seq.append(tmpat.resName.charAt(0));
+          seq.append(nucname.charAt((deoxyn ? 1 : 0)));
         }
       }
       else
@@ -286,7 +342,7 @@ public class PDBChain
     {
       id = " ";
     }
-
+    isNa = nucleotide;
     sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
     // resNumber-offset
     // ~=
@@ -458,11 +514,9 @@ 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));
+      sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
+              "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
+              an, (float) min, (float) max, AlignmentAnnotation.LINE_GRAPH));
     }
   }
 }