Remove redundancy in Eclipse

[jalview.git] / src / jalview / io / PileUpfile.java

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