apply version 2.7 copyright

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

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index bd1f640..0004308 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,6 +1,6 @@
 /*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -46,7 +46,9 @@ public class PDBChain
   public int offset;
 
   public Sequence sequence;
-  public boolean isNa=false;
+
+  public boolean isNa = false;
+
   public boolean isVisible = true;
 
   public int pdbstart = 0;
@@ -65,6 +67,21 @@ 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 +90,28 @@ 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 +178,9 @@ 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);
       }
@@ -163,22 +190,22 @@ public class PDBChain
 
   public void makeCaBondList()
   {
-    boolean na=false;
-    int numNa=0;
+    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;
+      na = false;
       if ((at1 == null) && (at2 == null))
       {
-        na=true;
+        na = true;
         at1 = tmpres.findAtom("P");
-        at1 = tmpres2.findAtom("P");
+        at2 = tmpres2.findAtom("P");
       }
-      if ((at1 == null) && (at2 == null))
+      if ((at1 != null) && (at2 != null))
       {
         if (at1.chain.equals(at2.chain))
         {
@@ -194,9 +221,9 @@ public class PDBChain
         System.out.println("not found " + i);
       }
     }
-    if (numNa>0 && ((numNa/residues.size())>0.99))
+    if (numNa > 0 && ((numNa / residues.size()) > 0.99))
     {
-      isNa=true;
+      isNa = true;
     }
   }
 
@@ -220,6 +247,7 @@ public class PDBChain
   {
     int count = 0;
     Object symbol;
+    boolean deoxyn=false;
     boolean nucleotide = false;
     StringBuffer seq = new StringBuffer();
     Vector resFeatures = new Vector();
@@ -273,8 +301,11 @@ public class PDBChain
       // Keep totting up the sequence
       if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
       {
-        String nucname=tmpat.resName.trim();
-        if (ResidueProperties.nucleotideIndex[nucname.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 " +
@@ -284,7 +315,7 @@ public class PDBChain
         {
           // nucleotide flag
           nucleotide = true;
-          seq.append(nucname.charAt(0));
+          seq.append(nucname.charAt((deoxyn ? 1 : 0)));
         }
       }
       else
@@ -303,7 +334,7 @@ public class PDBChain
     {
       id = " ";
     }
-    isNa=nucleotide;
+    isNa = nucleotide;
     sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
     // resNumber-offset
     // ~=
@@ -475,11 +506,9 @@ 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));
     }
   }
 }