/*\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) 2007 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
- public ClustalFile(String inStr)\r
- {\r
- super(inStr);\r
- }\r
-\r
public ClustalFile(String inFile, String type)\r
throws IOException\r
{\r
}\r
\r
public void parse()\r
+ throws IOException\r
{\r
int i = 0;\r
boolean flag = false;\r
}\r
}\r
else\r
+ {\r
flag = true;\r
+ }\r
}\r
}\r
}\r
}\r
\r
Sequence newSeq = parseId(headers.elementAt(i).toString());\r
- newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString() );\r
+ newSeq.setSequence(seqhash.get(headers.elementAt(i).toString()).\r
+ toString());\r
\r
seqs.addElement(newSeq);\r
}\r
{\r
String tmp = printId(s[i]);\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
if (tmp.length() > maxid)\r
\r
while ( (j < s.length) && (s[j] != null))\r
{\r
- out.append(new Format("%-" + maxid + "s").form( printId(s[j]) + " "));\r
+ out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));\r
\r
int start = i * len;\r
int end = start + len;\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].getSequenceAsString(start, end));\r
}\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
}\r
}\r
\r