- if (hmm.getMaxInstanceLength() != null)
- {
- line = String.format("%-5s %1s", "MAXL", hmm.getMaxInstanceLength());
- writer.println((line));
- }
- line = String.format("%-5s %1s", "ALPH", hmm.getAlphabetType());
- writer.println((line));
-
- boolean status;
- String statusStr;
-
- status = hmm.referenceAnnotationIsActive();
- statusStr = HiddenMarkovModel.findStringFromBoolean(status);
- line = String.format("%-5s %1s", "RF",
- statusStr);
- writer.println((line));
-
- status = hmm.maskValueIsActive();
- statusStr = HiddenMarkovModel.findStringFromBoolean(status);
- line = String.format("%-5s %1s", "MM",
- statusStr);
- writer.println((line));
-
- status = hmm.consensusResidueIsActive();
- statusStr = HiddenMarkovModel.findStringFromBoolean(status);
- line = String.format("%-5s %1s", "CONS",
- statusStr);
- writer.println((line));
-
- status = hmm.consensusStructureIsActive();
- statusStr = HiddenMarkovModel.findStringFromBoolean(status);
- line = String.format("%-5s %1s", "CS",
- statusStr);
- writer.println((line));
-
- status = hmm.mapIsActive();
- statusStr = HiddenMarkovModel.findStringFromBoolean(status);
- line = String.format("%-5s %1s", "MAP",
- statusStr);
- writer.println((line));
-
-
- if (hmm.getDate() != null)
- {
- line = String.format("%-5s %1s", "DATE", hmm.getDate());
- writer.println((line));
- }
- if (hmm.getNumberOfSequences() != null)
- {
- line = String.format("%-5s %1s", "NSEQ", hmm.getNumberOfSequences());
- writer.println((line));
- }
- if (hmm.getEffectiveNumberOfSequences() != null)
- {
- line = String.format("%-5s %1s", "EFFN",
- hmm.getEffectiveNumberOfSequences());
- writer.println((line));
- }
- if (hmm.getCheckSum() != null)
- {
- line = String.format("%-5s %1s", "CKSUM", hmm.getCheckSum());
- writer.println((line));
- }
- if (hmm.getGatheringThreshold() != null)
- {
- line = String.format("%-5s %1s", "GA", hmm.getGatheringThreshold());
- writer.println((line));
- }
-
- if (hmm.getTrustedCutoff() != null)
- {
- line = String.format("%-5s %1s", "TC", hmm.getTrustedCutoff());
- writer.println((line));
- }
- if (hmm.getNoiseCutoff() != null)
- {
- line = String.format("%-5s %1s", "NC", hmm.getNoiseCutoff());
- writer.println((line));
- }
- if (hmm.getMSV() != null)
- {
- line = String.format("%-19s %18s", "STATS LOCAL MSV", hmm.getMSV());
- writer.println((line));
-
- line = String.format("%-19s %18s", "STATS LOCAL VITERBI",
- hmm.getViterbi());
- writer.println((line));
-
- line = String.format("%-19s %18s", "STATS LOCAL FORWARD",
- hmm.getForward());
- writer.println((line));