From a4e00252bb8629013635f2d577f9af28c92d76d8 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 11 Apr 2005 16:54:38 +0000
Subject: [PATCH] added the alignment quality calculation from the old
 jalview, and tried to debug conservation calculation based
 on existing alscript code.

---
 src/jalview/analysis/Conservation.java |   53 ++++++++++++++++++++++++++++----
 1 file changed, 47 insertions(+), 6 deletions(-)

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 9786362..2b4ef63 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -98,7 +98,8 @@ public class Conservation {
       residueHash = new Hashtable();
 
       for (int j=0; j < sequences.size(); j++) {
-
+        // JBPNote - have to make sure elements of the sequences vector
+        //  are tested like this everywhere...
         if (sequences.elementAt(j) instanceof Sequence) {
           Sequence s = (Sequence)sequences.elementAt(j);
 
@@ -155,6 +156,7 @@ public class Conservation {
           }
         }
       }
+      
       total.addElement(resultHash);
     }
   }
@@ -175,14 +177,53 @@ public class Conservation {
     }
     return count;
   }
+  /*** 
+   * countConsNGaps
+   * returns gap count in int[0], and conserved residue count in int[1]
+   */
+  public int[] countConsNGaps(int j)
+  {
+    int count = 0;
+    int cons=0;
+    int nres = 0;
+    int[] r = new int[2];
+    char f='$';
+    for (int i = 0; i < sequences.size();i++)
+    {
+      if( j >= ((Sequence)sequences.elementAt(i)).getSequence().length())
+      {  count++; 
+      continue;}
+
+      char c = ((Sequence)sequences.elementAt(i)).getSequence().charAt(j);
+      if (jalview.util.Comparison.isGap((c)))
+        count++;
+      else {
+        nres++;
+        if (nres==1) {
+          f = c;
+          cons++;
+        } else
+          if (f == c) {
+            cons++;
+          }
+      }
+    }
+    r[0] = (nres==cons) ? 1 : 0;
+    r[1] = count;
+
+    
+    return r;
+  }
 
   public  void  verdict(boolean consflag, float percentageGaps) {
     String consString = "";
 
     for (int i=start; i <= end; i++) {
-      int totGaps = countGaps(i);
+      int[] gapcons = countConsNGaps(i);
+      boolean cons = (gapcons[0]==1) ? true : false;
+      int totGaps = gapcons[1];
       float pgaps = (float)totGaps*100/(float)sequences.size();
-
+      //      System.out.println("percentage gaps = "+pgaps+"\n");
       if (percentageGaps > pgaps)
       {
         Hashtable resultHash = (Hashtable)total.elementAt(i-start);
@@ -211,9 +252,9 @@ public class Conservation {
         }
 
         if (count < 10)
-          consString = consString + String.valueOf(count);
+          consString = consString + String.valueOf(count);// Conserved props!=Identity
         else
-          consString = consString + "*";
+          consString = consString + ((gapcons[0]==1) ? "*" : "+");
 
       }
       else
@@ -331,7 +372,7 @@ public void findQuality(int start, int end) {
           try {
             sr = (double)BLOSUM62[i][seqNum]+4;
           } catch (Exception e) {
-            System.out.println("Exception in sr " + e);
+            System.out.println("Exception in sr: " + e);
           }
           //Calculate X with another loop over residues
 
-- 
1.7.10.2