\r
while ( (line = nextLine()) != null)\r
{\r
- if(line.length()==0)\r
+ if (line.length() == 0)\r
{\r
//System.out.println("blank line");\r
continue;\r
}\r
-\r
+ if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)\r
+ {\r
+ continue;\r
+ }\r
Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));\r
\r
sequence = new StringBuffer();\r
}\r
}\r
\r
- if(sequence.length()>0)\r
+ if (sequence.length() > 0)\r
{\r
sequence.setLength(sequence.length() - 1);\r
-\r
newSeq.setSequence(sequence.toString());\r
seqs.addElement(newSeq);\r
+ ModellerDescription md = new ModellerDescription(newSeq.\r
+ getDescription());\r
+ md.updateSequenceI(newSeq);\r
}\r
}\r
}\r
String seq = s[i].getSequence();\r
seq = seq + "*";\r
\r
- out.append(">P1;" + printId(s[i]) + "\n");\r
-\r
- if(s[i].getDescription()!=null)\r
- out.append(s[i].getDescription()+"\n");\r
+ if (is_NA)\r
+ {\r
+ // modeller doesn't really do nucleotides, so we don't do anything fancy\r
+ // Nucleotide sequence tags should have a >DL; prefix\r
+ out.append(">P1;" + s[i].getName() + "\n"); // JBPNote Should change >P to >N\r
+ if (s[i].getDescription() == null)\r
+ {\r
+ out.append(s[i].getName() + " " +\r
+ (s[i].getEnd() - s[i].getStart() + 1));\r
+ out.append(is_NA ? " bases\n" : " residues\n");\r
+ }\r
+ else\r
+ {\r
+ out.append(s[i].getDescription()+"\n");\r
+ }\r
+ }\r
else\r
{\r
- out.append(s[i].getName()+" "+ (s[i].getEnd() - s[i].getStart() + 1));\r
- out.append( is_NA ? " bases\n" : " residues\n");\r
+ out.append(">P1;" + s[i].getName() + "\n");\r
+ ModellerDescription md = new ModellerDescription(s[i]);\r
+ out.append(md.getDescriptionLine() + "\n");\r
}\r
int nochunks = (seq.length() / len) + 1;\r
\r