\r
id = str.nextToken();\r
id = id.substring(1);\r
+ if(id.indexOf("UniProt/Swiss-Prot")>-1)\r
+ {\r
+ id = id.substring(id.indexOf("UniProt/Swiss-Prot|") + 19);\r
+ if(id.indexOf("|")>-1)\r
+ id = id.substring(id.indexOf("|") + 1);\r
+ }\r
\r
if (id.indexOf("/") > 0 ) {\r
\r
public static String print(SequenceI[] s, int len) {\r
return print(s,len,true);\r
}\r
+\r
public static String print(SequenceI[] s, int len,boolean gaps) {\r
+ return print(s,len,gaps,true);\r
+ }\r
+\r
+ public static String print(SequenceI[] s, int len,boolean gaps, boolean displayId) {\r
StringBuffer out = new StringBuffer();\r
int i = 0;\r
while (i < s.length && s[i] != null) {\r
} else {\r
seq = AlignSeq.extractGaps("-. ",s[i].getSequence());\r
}\r
-\r
- out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" + s[i].getEnd() + "\n");\r
+ // used to always put this here: + "/" + s[i].getStart() + "-" + s[i].getEnd() +\r
+ out.append(">" + ((displayId) ? s[i].getDisplayId() : s[i].getName())+"\n");\r
\r
int nochunks = seq.length() / len + 1;\r
\r