X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=87a1652e39ceac45d00b049b0cb627af3a24e2cd;hb=f24dacb1da56fccf05d684e2f4899facec2aecf7;hp=728d1c6f2ba67d772db86abf71c83f652760d1d2;hpb=133e5d7be0ca295fd4ac4ccfa6c82165c795ea80;p=jalview.git

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 728d1c6..87a1652 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -172,33 +172,22 @@ public class PileUpfile
 
   public static int checkSum(String seq)
   {
-    //String chars =  "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";
+
     int check = 0;
 
     String sequence = seq.toUpperCase();
 
-    String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";
-    index += "--------------------------------------------------------------------------------------------------------------------------------";
-
     for (int i = 0; i < sequence.length(); i++)
     {
-      try
-      {
         if (i < sequence.length())
         {
-          int pos = index.indexOf(sequence.charAt(i));
-
-          if (index.charAt(pos)!='_')
+          int value = sequence.charAt(i);
+          if (value != -1)
           {
-            check += ( ( (i % 57) + 1) * pos);
+            check += (i % 57 + 1) * value;
           }
         }
-      }
-      catch (Exception e)
-      {
-        System.err.println("Exception during MSF Checksum calculation");
-        e.printStackTrace();
-      }
+
     }
 
     return check % 10000;
@@ -212,29 +201,24 @@ public class PileUpfile
     int maxid = 0;
 
     int i = 0;
-    String big = "";
-
-    while ( (i < s.length) && (s[i] != null))
+    int bigChecksum = 0;
+    int[] checksums = new int[s.length];
+    while (i < s.length)
     {
-      big += s[i].getSequence();
+      checksums[i] = checkSum(s[i].getSequence());
+      bigChecksum += checksums[i];
       i++;
     }
 
-    i = 0;
-
-    int bigcheck = checkSum(big);
-
     out.append("   MSF: " + s[0].getSequence().length() +
-               "   Type: P    Check:  " + bigcheck + "   ..\n\n\n");
+               "   Type: P    Check:  " + bigChecksum%10000 + "   ..\n\n\n");
 
+    i=0;
     while ( (i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequence();
-      String name = s[i].getName() + "/" + s[i].getStart() + "-" +
-          s[i].getEnd();
-      int check = checkSum(s[i].getSequence());
-      out.append(" Name: " + name + " oo  Len:  " +
-                 s[i].getSequence().length() + "  Check:  " + check +
+      out.append(" Name: " + s[i].getName() + " oo  Len:  " +
+                 s[i].getSequence().length() + "  Check:  " + checksums[i] +
                  "  Weight:  1.00\n");
 
       if (seq.length() > max)
@@ -242,9 +226,9 @@ public class PileUpfile
         max = seq.length();
       }
 
-      if (name.length() > maxid)
+      if (s[i].getName().length() > maxid)
       {
-        maxid = name.length();
+        maxid = s[i].getName().length();
       }
 
       i++;
@@ -274,8 +258,7 @@ public class PileUpfile
       while ( (j < s.length) && (s[j] != null))
       {
         String name = s[j].getName();
-        out.append(new Format("%-" + maxid + "s").form(name + "/" +
-            s[j].getStart() + "-" + s[j].getEnd()) + " ");
+        out.append(new Format("%-" + maxid + "s").form(name) + " ");
 
         for (int k = 0; k < 5; k++)
         {