/*\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 PfamFile(String inStr)\r
- {\r
- super(inStr);\r
- }\r
-\r
public PfamFile(String inFile, String type)\r
throws IOException\r
{\r
.length();\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
seqs.addElement(newSeq);\r
-\r
- if (!isValidProteinSequence(newSeq.getSequence()))\r
- {\r
- throw new IOException(\r
- "Not a valid protein sequence - (PFAM input)");\r
- }\r
}\r
else\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
- out.append(s[j].getSequence() + "\n");\r
+ out.append(s[j].getSequenceAsString() + "\n");\r
j++;\r
}\r
\r