- cmds.addHMMConsensusSequences(af);
- FileLoader loader = new FileLoader();
- loader.LoadFileOntoAlignmentWaitTillLoaded(af.getViewport(),
- hmmTemp.getAbsolutePath(), DataSourceType.FILE,
- FileFormat.HMMER3);
+ if (af != null)
+ {
+ cmds.addHMMConsensusSequences(af);
+
+ FileLoader loader = new FileLoader();
+ loader.LoadFileOntoAlignmentWaitTillLoaded(viewport,
+ hmmTemp.getAbsolutePath(), DataSourceType.FILE,
+ FileFormat.HMMER3);
+ }
+ else
+ {
+ HMMFile file = new HMMFile(new FileParse(hmmTemp.getAbsolutePath(),
+ DataSourceType.FILE));
+ alignment.addSequence(file.getSeqsAsArray()[0]);
+ }