X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=d35cbe851af4a23ed6033ae791fb8f87c9968164;hb=d4ede6b61d4abab78200f334d8df07879dfe6741;hp=18755572deb5f08171d8867b8ae915354e8e74c7;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 1875557..d35cbe8 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,9 +1,13 @@
 package jalview.datamodel;
 
-
+import jalview.analysis.*;
 import java.awt.*;
+import java.util.StringTokenizer;
+import MCview.*;
+
 
-public class Sequence implements SequenceI {
+public class Sequence implements SequenceI
+{
   protected String   name;
   protected String   sequence;
   protected int      start;
@@ -11,7 +15,55 @@ public class Sequence implements SequenceI {
   protected String   description;
   protected int      charHeight;
   protected String   displayId;
-  protected Color    color = Color.black;
+  protected Color    color = Color.white;
+  PDBfile pdb;
+   public int maxchain = -1;
+
+   public int pdbstart;
+   public int pdbend;
+   public int seqstart;
+   public int seqend;
+   public void setPDBfile(PDBfile pdb)
+   {
+     this.pdb = pdb;
+     int max = -10;
+     maxchain = -1;
+
+     for (int i=0; i < pdb.chains.size(); i++) {
+
+       System.out.println("PDB sequence = " + ((PDBChain)pdb.chains.elementAt(i)).sequence);
+       // Now lets compare the sequences to get
+       // the start and end points.
+
+
+     StringTokenizer str = new StringTokenizer(sequence, ".");
+     String newString = "";
+
+     while (str.hasMoreTokens()) {
+         newString += str.nextToken();
+     }
+       // Align the sequence to the pdb
+       AlignSeq as = new AlignSeq(this,((PDBChain)pdb.chains.elementAt(i)).sequence,"pep");
+       as.calcScoreMatrix();
+       as.traceAlignment();
+       as.printAlignment();
+
+       System.out.println("Score = " + as.maxscore);
+       if (as.maxscore > max) {
+         System.out.println("New max score");
+         max = as.maxscore;
+         maxchain = i;
+
+         pdbstart = as.seq2start;
+         pdbend = as.seq2end;
+         seqstart = as.seq1start  - 1 ;
+         seqend = as.seq1end  -1;
+       }
+
+       System.out.println("PDB start/end " + pdbstart + " " + pdbend);
+       System.out.println("SEQ start/end " + seqstart + " " + seqend);
+     }
+   }
 
   public Sequence(String name, String sequence, int start, int end)
   {
@@ -92,19 +144,18 @@ public class Sequence implements SequenceI {
 
     while (i< sequence.length() && j <= end && j <= pos) {
 
-      String s = sequence.substring(i,i+1);
+      char c = sequence.charAt(i);
 
-      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
+      if (!jalview.util.Comparison.isGap((c)))
         j++;
-      }
+
       i++;
     }
-    if (j == end && j < pos) {
+    if (j == end && j < pos)
       return end+1;
-    } else {
-
+    else
       return i;
-    }
+
   }
 
   public int findPosition(int i) {
@@ -112,12 +163,13 @@ public class Sequence implements SequenceI {
     int j   = 0;
     int pos = start;
 
-    while (j < i) {
-      String s = sequence.substring(j,j+1);
+    while (j < i)
+    {
+      char c = sequence.charAt(j);
 
-      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {
+      if (!jalview.util.Comparison.isGap((c)))
         pos++;
-      }
+
       j++;
     }
     return pos;