Uses of Class
compbio.data.sequence.UnknownFileFormatException

Packages that use UnknownFileFormatException

Package	Description
compbio.data.sequence	A data model for multiple sequence alignment web services and utility methods that work on the objects of this model.

Uses of UnknownFileFormatException in compbio.data.sequence

Methods in compbio.data.sequence that throw UnknownFileFormatException

Modifier and Type	Method and Description
private static float[]	SequenceUtil.convertToNumber(java.lang.String[] annotValues)
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
private static float[]	SequenceUtil.parseIUPredScores(java.util.Scanner scan)
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
private static java.util.Map<java.lang.String,Score>	SequenceUtil.readIUPred(java.io.InputStream input, IUPredResult type) ## Long Disorder # P53_HUMAN 1 M 0.9943 2 E 0.9917 3 E 0.9879 (every line)
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