added the alignment quality calculation from the old jalview, and

tried to debug conservation calculation based on existing alscript
code.

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