A C E G L M N R S W

A

AlignmentConservation - Class in edu.cornell.med.alignments
Takes in an alignment in ClustalW format, parses it into a BiologicalAlignment, and calculates at each position whether the alignment reaches a user-specified conservation cutoff value.
AlignmentConservation() - Constructor for class edu.cornell.med.alignments.AlignmentConservation
Constructor.
AlignmentParser - Interface in edu.cornell.med.alignments
Reads an alignment and converts it into a BiologicalAlignment.
AlignmentWriter - Interface in edu.cornell.med.alignments
Writes a BiologicalAlignment.

C

calculateConservation(double, boolean, char) - Method in class edu.cornell.med.alignments.AlignmentConservation
Calculates the conservation at each position in the alignment.
ClustalwParser - Class in edu.cornell.med.alignments
Takes in an alignment in ClustalW format, parses it into a BiologicalAlignment, and calculates at each position whether the alignment reaches a user-specified conservation cutoff value.
ClustalwParser() - Constructor for class edu.cornell.med.alignments.ClustalwParser
 
ClustalwWriter - Class in edu.cornell.med.alignments
Writes a BiologicalAlignment in ClustalW format.
ClustalwWriter() - Constructor for class edu.cornell.med.alignments.ClustalwWriter
Constructor.

E

edu.cornell.med.alignments - package edu.cornell.med.alignments
Provides utilities for parsing and writing alignment files.

G

getAln() - Method in class edu.cornell.med.alignments.AlignmentConservation
Gets the alignment.
getConservationLine() - Method in interface edu.cornell.med.alignments.AlignmentWriter
Gets the line indicating conservation at each position of the alignment.
getConservationLine() - Method in class edu.cornell.med.alignments.ClustalwWriter
Gets the line indicating conservation at each position of the alignment.

L

length() - Method in class edu.cornell.med.alignments.AlignmentConservation
Gets the length of the alignment.

M

main(String[]) - Static method in class edu.cornell.med.alignments.AlignmentConservation
Main method.

N

numSeqs() - Method in class edu.cornell.med.alignments.AlignmentConservation
Gets the number of sequences in the alignment.

R

readAlignment(Reader) - Method in interface edu.cornell.med.alignments.AlignmentParser
Reads an alignment and converts it into a BiologicalAlignment.
readAlignment(Reader) - Method in class edu.cornell.med.alignments.ClustalwParser
Reads a ClustalW alignment and converts it into a BiologicalAlignment.
readAlignmentFile(String) - Method in interface edu.cornell.med.alignments.AlignmentParser
Reads an alignment from a file and converts it into a BiologicalAlignment.
readAlignmentFile(String) - Method in class edu.cornell.med.alignments.ClustalwParser
Reads a ClustalW alignment from a file and converts it into a BiologicalAlignment.

S

setAln(BiologicalAlignment) - Method in class edu.cornell.med.alignments.AlignmentConservation
Sets the alignment.
setConservationLine(String) - Method in interface edu.cornell.med.alignments.AlignmentWriter
Sets the line indicating conservation at each position of the alignment.
setConservationLine(String) - Method in class edu.cornell.med.alignments.ClustalwWriter
Sets the line indicating conservation at each position of the alignment.

W

writeAlignment(BiologicalAlignment, Writer) - Method in interface edu.cornell.med.alignments.AlignmentWriter
Writes the BiologicalAlignment to a file.
writeAlignment(BiologicalAlignment, Writer) - Method in class edu.cornell.med.alignments.ClustalwWriter
Writes the BiologicalAlignment to a file.
writeAlignmentFile(BiologicalAlignment) - Method in interface edu.cornell.med.alignments.AlignmentWriter
Writes the BiologicalAlignment as a ClustalW formnatted alignment to a String.
writeAlignmentFile(BiologicalAlignment) - Method in class edu.cornell.med.alignments.ClustalwWriter
Writes the BiologicalAlignment as a ClustalW formnatted alignment to a String.

A C E G L M N R S W

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