/*\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
Vector headers;\r
long start;\r
long end;\r
+ boolean jvSuffix = true;\r
\r
/**\r
* Creates a new AlignFile object.\r
{\r
}\r
\r
- /**\r
- * Creates a new AlignFile object.\r
- *\r
- * @param inStr DOCUMENT ME!\r
- */\r
- public AlignFile(String inStr)\r
- {\r
- initData();\r
- System.out.println("is this ever called??");\r
-\r
- try\r
- {\r
- parse();\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
\r
/**\r
* Constructor which parses the data from a file of some specified type.\r
}\r
\r
// Checks whether sequence is valid aa characters\r
- protected boolean isValidProteinSequence(String sequence)\r
+ protected boolean isValidProteinSequence(char [] sequence)\r
{\r
- for (int i = 0; i < sequence.length(); i++)\r
- if (!jalview.schemes.ResidueProperties.aaHash.containsKey(\r
- String.valueOf(sequence.charAt(i))))\r
+ for (int i = 0; i < sequence.length; i++)\r
+ if (jalview.schemes.ResidueProperties.aaIndex[sequence[i]]==-1)\r
{\r
+ invalidCharacter = sequence[i];\r
return false;\r
}\r
\r
return true;\r
}\r
\r
+ char invalidCharacter;\r
+\r
/**\r
* This method must be implemented to parse the contents of the file.\r
*/\r
* Print out in alignment file format the Sequences in the seqs Vector.\r
*/\r
public abstract String print();\r
+\r
+ public void addJVSuffix(boolean b)\r
+ {\r
+ jvSuffix = b;\r
+ }\r
+\r
+ /**\r
+ * A general parser for ids.\r
+ *\r
+ * @String id Id to be parsed\r
+ */\r
+ Sequence parseId(String id)\r
+ {\r
+ Sequence seq = null;\r
+ id = id.trim();\r
+ int space = id.indexOf(" ");\r
+ if(space>-1)\r
+ {\r
+ seq = new Sequence(id.substring(0, space),"");\r
+ seq.setDescription(id.substring(space+1));\r
+ }\r
+ else\r
+ {\r
+ seq = new Sequence(id, "");\r
+ }\r
+\r
+ return seq;\r
+ }\r
+\r
+ /**\r
+ * Creates the output id.\r
+ * Adds prefix Uniprot format source|id\r
+ * And suffix Jalview /start-end\r
+ *\r
+ * @String id Id to be parsed\r
+ */\r
+ String printId(SequenceI seq)\r
+ {\r
+ return seq.getDisplayId(jvSuffix);\r
+ }\r
+\r
}\r