Sequence is char []

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

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 179204e..61b3528 100755 (executable)
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -44,15 +44,6 @@ public class MSFfile extends AlignFile
     {\r
     }\r
 \r
-    /**\r
-     * Creates a new MSFfile object.\r
-     *\r
-     * @param inStr DOCUMENT ME!\r
-     */\r
-    public MSFfile(String inStr)\r
-    {\r
-        super(inStr);\r
-    }\r
 \r
     /**\r
      * Creates a new MSFfile object.\r
@@ -70,7 +61,7 @@ public class MSFfile extends AlignFile
     /**\r
      * DOCUMENT ME!\r
      */\r
-    public void parse()\r
+    public void parse() throws IOException\r
     {\r
         int i = 0;\r
         boolean seqFlag = false;\r
@@ -147,9 +138,6 @@ public class MSFfile extends AlignFile
                 String head = headers.elementAt(i).toString();\r
                 String seq = seqhash.get(head).toString();\r
 \r
-                int start = -1;\r
-                int end =  -1;\r
-\r
                 if (maxLength < head.length())\r
                 {\r
                     maxLength = head.length();\r
@@ -157,8 +145,17 @@ public class MSFfile extends AlignFile
 \r
                 // Replace ~ with a sensible gap character\r
                 seq = seq.replace('~', '-');\r
+                if (!isValidProteinSequence(seq.toCharArray()))\r
+                {\r
+                    throw new IOException(AppletFormatAdapter.\r
+                                          INVALID_CHARACTERS\r
+                                          + " : " + head\r
+                                          + " : " + invalidCharacter);\r
+                }\r
+\r
 \r
                 Sequence newSeq = parseId(head);\r
+\r
                 newSeq.setSequence(seq);\r
 \r
                 seqs.addElement(newSeq);\r
@@ -230,9 +227,11 @@ public class MSFfile extends AlignFile
         while ((i < seqs.length) && (seqs[i] != null))\r
         {\r
           // Replace all internal gaps with . and external spaces with ~\r
-          s[i] =new Sequence(seqs[i].getName(),seqs[i].getSequence().replace('-', '.'));\r
+          s[i] =new Sequence(seqs[i].getName(),seqs[i].getSequenceAsString().replace('-', '.'));\r
+\r
+          StringBuffer sb = new StringBuffer();\r
+          sb.append(s[i].getSequence());\r
 \r
-          StringBuffer sb = new StringBuffer(s[i].getSequence());\r
           for (int ii = 0; ii < sb.length(); ii++)\r
           {\r
             if (sb.charAt(ii) == '.')\r
@@ -255,9 +254,9 @@ public class MSFfile extends AlignFile
 \r
             s[i].setSequence(sb.toString());\r
 \r
-            if (s[i].getSequence().length() > max)\r
+            if (s[i].getSequence().length > max)\r
             {\r
-                max = s[i].getSequence().length();\r
+                max = s[i].getSequence().length;\r
             }\r
 \r
             i++;\r
@@ -273,13 +272,13 @@ public class MSFfile extends AlignFile
         int [] checksums = new int[s.length];\r
         while ( i < s.length )\r
         {\r
-          checksums[i] = checkSum(s[i].getSequence());\r
+          checksums[i] = checkSum(s[i].getSequenceAsString());\r
           bigChecksum += checksums[i];\r
           i++;\r
         }\r
 \r
         long maxNB = 0;\r
-        out.append("   MSF: " + s[0].getSequence().length() + "   Type: " +\r
+        out.append("   MSF: " + s[0].getSequence().length + "   Type: " +\r
             (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum%10000) + "   ..\n\n\n");\r
 \r
         String[] nameBlock = new String[s.length];\r
@@ -292,7 +291,7 @@ public class MSFfile extends AlignFile
             nameBlock[i] = new String("  Name: " + printId(s[i])+" ");\r
 \r
             idBlock[i] = new String("Len: " +\r
-                    maxLenpad.form(s[i].getSequence().length()) + "  Check: " +\r
+                    maxLenpad.form(s[i].getSequence().length) + "  Check: " +\r
                     maxChkpad.form(checksums[i]) + "  Weight: 1.00\n");\r
 \r
             if (s[i].getName().length() > maxid)\r
@@ -353,10 +352,10 @@ public class MSFfile extends AlignFile
                     int start = (i * 50) + (k * 10);\r
                     int end = start + 10;\r
 \r
-                    if ((end < s[j].getSequence().length()) &&\r
-                            (start < s[j].getSequence().length()))\r
+                    if ((end < s[j].getSequence().length) &&\r
+                            (start < s[j].getSequence().length))\r
                     {\r
-                        out.append(s[j].getSequence().substring(start, end));\r
+                        out.append(s[j].getSequence(start, end));\r
 \r
                         if (k < 4)\r
                         {\r
@@ -369,9 +368,9 @@ public class MSFfile extends AlignFile
                     }\r
                     else\r
                     {\r
-                        if (start < s[j].getSequence().length())\r
+                        if (start < s[j].getSequence().length)\r
                         {\r
-                            out.append(s[j].getSequence().substring(start));\r
+                            out.append(s[j].getSequenceAsString().substring(start));\r
                             out.append("\n");\r
                         }\r
                         else\r