+ }\r
+\r
+ public String print()\r
+ {\r
+ return print(getSeqsAsArray());\r
+ }\r
+\r
+ public String print(SequenceI[] s)\r
+ {\r
+ boolean is_NA = jalview.util.Comparison.isNucleotide(s);\r
+ int len = 72;\r
+ StringBuffer out = new StringBuffer();\r
+ int i = 0;\r
+ ModellerDescription md;\r
+\r
+ while ( (i < s.length) && (s[i] != null))\r
+ {\r
+ String seq = s[i].getSequenceAsString();\r
+ seq = seq + "*";\r
+\r
+ if (is_NA)\r
+ {\r
+ // modeller doesn't really do nucleotides, so we don't do anything fancy\r
+ // Official tags area as follows, for now we'll use P1 and DL\r
+ // Protein (complete) P1\r
+ // Protein (fragment) F1\r
+ // DNA (linear) Dl\r
+ // DNA (circular) DC\r
+ // RNA (linear) RL\r
+ // RNA (circular) RC\r
+ // tRNA N3\r
+ // other functional RNA N1\r
+\r
+ out.append(">N1;" + s[i].getName() + "\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
+\r
+ if (useModellerOutput)\r
+ {\r
+ out.append(">P1;" + s[i].getName() + "\n");\r
+ md = new ModellerDescription(s[i]);\r
+ out.append(md.getDescriptionLine() + "\n");\r
+ }\r
+ else\r
+ {\r
+ out.append(">P1;" + printId(s[i]) + "\n");\r
+ if (s[i].getDescription() != null)\r
+ {\r
+ out.append(s[i].getDescription() + "\n");\r
+ }\r
+ else\r
+ {\r
+ out.append(s[i].getName() + " "\r
+ + (s[i].getEnd() - s[i].getStart() + 1)\r
+ + " residues\n");\r
+ }\r
+ }\r
+ }\r
+ int nochunks = (seq.length() / len) + 1;\r