Uses of Class
compbio.data.sequence.UnknownFileFormatException

Packages that use UnknownFileFormatException

compbio.data.sequence	A data model for multiple sequence alignment web services and utility methods that work on the objects of this model.
compbio.runner	Utilities commonly used by all runners.

Uses of UnknownFileFormatException in compbio.data.sequence

Methods in compbio.data.sequence that throw UnknownFileFormatException

static java.util.List<FastaSequence>	SequenceUtil.openInputStream(java.lang.String inFilePath) Reads and parses Fasta or Clustal formatted file into a list of FastaSequence objects
static Alignment	ClustalAlignmentUtil.readClustalFile(java.io.File file)
static Alignment	ClustalAlignmentUtil.readClustalFile(java.io.InputStream instream) Read Clustal formatted alignment.
static java.util.HashMap<java.lang.String,java.util.Set<Score>>	SequenceUtil.readDisembl(java.io.InputStream input) > Foobar_dundeefriends # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 # REM465 355-368 # HOTLOOPS 190-204 # RESIDUE COILS REM465 HOTLOOPS M 0.86010 0.88512 0.37094 T 0.79983 0.85864 0.44331 >Next Sequence name
static java.util.HashMap<java.lang.String,java.util.Set<Score>>	SequenceUtil.readGlobPlot(java.io.InputStream input) > Foobar_dundeefriends # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 # REM465 355-368 # HOTLOOPS 190-204 # RESIDUE COILS REM465 HOTLOOPS M 0.86010 0.88512 0.37094 T 0.79983 0.85864 0.44331 >Next Sequence name
static java.util.Map<java.lang.String,Score>	SequenceUtil.readIUPred(java.io.File result) Read IUPred output
static java.util.Map<java.lang.String,Score>	SequenceUtil.readJRonn(java.io.File result)
static java.util.Map<java.lang.String,Score>	SequenceUtil.readJRonn(java.io.InputStream inStream) Reader for JRonn horizontal file format

Uses of UnknownFileFormatException in compbio.runner

Methods in compbio.runner that throw UnknownFileFormatException

static Alignment	Util.readClustalFile(java.lang.String workDirectory, java.lang.String clustFile)
static java.util.Map<java.lang.String,Score>	Util.readJronnFile(java.lang.String workDirectory, java.lang.String clustFile)