int noSeqs = 0;\r
int maxLength = 0;\r
Vector seqs;\r
- Vector headers;\r
+ Vector annotations;\r
long start;\r
long end;\r
boolean jvSuffix = true;\r
return s;\r
}\r
\r
+ public void addAnnotations(Alignment al)\r
+ {\r
+ for(int i=0; i<annotations.size(); i++)\r
+ {\r
+ al.addAnnotation(\r
+ (AlignmentAnnotation)annotations.elementAt(i)\r
+ );\r
+ }\r
+\r
+ }\r
+\r
/**\r
* Initialise objects to store sequence data in.\r
*/\r
protected void initData()\r
{\r
seqs = new Vector();\r
- headers = new Vector();\r
+ annotations = new Vector();\r
}\r
\r
/**\r
}\r
}\r
\r
- // Checks whether sequence is valid aa characters\r
- protected boolean isValidProteinSequence(String sequence)\r
- {\r
- for (int i = 0; i < sequence.length(); i++)\r
- if (jalview.schemes.ResidueProperties.aaIndex[sequence.charAt(i)]==-1)\r
- {\r
- invalidCharacter = sequence.charAt(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