/*\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
{\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
/**\r
* DOCUMENT ME!\r
*/\r
- public void parse()\r
+ public void parse() throws IOException\r
{\r
int i = 0;\r
boolean seqFlag = false;\r
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
}\r
\r
- if (head.indexOf("/") > 0)\r
+ // Replace ~ with a sensible gap character\r
+ seq = seq.replace('~', '-');\r
+ if (!isValidProteinSequence(seq))\r
{\r
- StringTokenizer st = new StringTokenizer(head, "/");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- head = st.nextToken();\r
-\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp, "-");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- start = Integer.valueOf(st.nextToken()).intValue();\r
- end = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- }\r
+ throw new IOException(AppletFormatAdapter.\r
+ INVALID_CHARACTERS\r
+ + " : " + head\r
+ + " : " + invalidCharacter);\r
}\r
\r
\r
- // Replace ~ with a sensible gap character\r
- seq = seq.replace('~', '-');\r
+ Sequence newSeq = parseId(head);\r
\r
- Sequence newSeq = new Sequence(head, seq, start, end);\r
+ newSeq.setSequence(seq);\r
\r
seqs.addElement(newSeq);\r
}\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public static int checkSum(String seq)\r
+ public int checkSum(String seq)\r
{\r
int check = 0;\r
String sequence = seq.toUpperCase();\r
return check % 10000;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static String print(SequenceI[] s)\r
- {\r
- return print(s, false);\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public static String print(SequenceI[] seqs, boolean is_NA)\r
+ public String print(SequenceI[] seqs)\r
{\r
\r
+ boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);\r
+\r
SequenceI [] s = new SequenceI[seqs.length];\r
\r
StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +\r
{\r
if (sb.charAt(ii) == '.')\r
{\r
- sb.replace(ii, ii + 1, "~");\r
+ sb.setCharAt(ii, '~');\r
}\r
else\r
break;\r
{\r
if (sb.charAt(ii) == '.')\r
{\r
- sb.replace(ii, ii + 1, "~");\r
+ sb.setCharAt(ii,'~');\r
}\r
else\r
break;\r
while ((i < s.length) && (s[i] != null))\r
{\r
\r
- nameBlock[i] = new String(" Name: " + s[i].getName()\r
- + "/" + s[i].getStart() + "-" + s[i].getEnd()\r
- +" ");\r
+ nameBlock[i] = new String(" Name: " + printId(s[i])+" ");\r
\r
idBlock[i] = new String("Len: " +\r
maxLenpad.form(s[i].getSequence().length()) + " Check: " +\r
\r
while ((j < s.length) && (s[j] != null))\r
{\r
- String name = s[j].getName();\r
- // out.append(new Format("%-" + maxid + "s").form(name)+ " ");\r
+ String name = printId( s[j] );\r
\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
\r
for (int k = 0; k < 5; k++)\r