+ if (sequence.length() > 0)\r
+ {\r
+ sequence.setLength(sequence.length() - 1);\r
+ newSeq.setSequence(sequence.toString());\r
+ if (!isValidProteinSequence(newSeq.getSequence()))\r
+ {\r
+ throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
+ +" : "+ newSeq.getName()\r
+ +" : "+invalidCharacter);\r
+ }\r
+\r
+ seqs.addElement(newSeq);\r
+\r
+ md = new ModellerDescription(newSeq.\r
+ getDescription());\r
+ md.updateSequenceI(newSeq);\r
+ }\r
+ }\r
+ }\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].getSequence();\r
+ seq = seq + "*";\r
+\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
+ out.append(s[i].getDescription() + "\n");\r
+ else\r
+ out.append(s[i].getName() + " "\r
+ + (s[i].getEnd() - s[i].getStart() + 1)\r
+ + " residues\n");\r
+ }\r
+ }\r
+ int nochunks = (seq.length() / len) + 1;\r
+\r
+ for (int j = 0; j < nochunks; j++)\r
+ {\r
+ int start = j * len;\r
+ int end = start + len;\r
+\r
+ if (end < seq.length())\r
+ {\r
+ out.append(seq.substring(start, end) + "\n");\r