edu.mssm.crover.tools.blast
Class seqinfo

java.lang.Object
  |
  +--edu.mssm.crover.tools.blast.seqinfo

public class seqinfo

extends java.lang.Object

Constructor Summary

seqinfo()

Method Summary

static int	fromFastaLen(java.lang.String ac) Returns the length of the query sequence.
static java.lang.String	getAC(java.lang.String line) gets the accession number from a FASTA header line that starts with >gi|.
static int	getBValue(java.lang.String[] args) Returns the number of alignments to be returned from BLAST.
static java.lang.String	getDatabase(java.lang.String[] args)
static double	getEValue(java.lang.String[] args) Returns the expectation value.
static java.lang.String	getFastaFile(java.lang.String[] args) Returns the name of the fasta sequence file.
static java.lang.String	getMbFilename(java.lang.String[] args) Returns the name of the megablast output file.
static java.lang.String	getOutFilename(java.lang.String[] args) Returns the name of the output file.
static double	getProportionQuery(java.lang.String[] args) Returns the percent length.
static int	getQLen(java.lang.String[] args) Returns the length of the query sequence.
static double	getSeqError(java.lang.String[] args) Returns the allowed sequencing error.
static java.lang.String	getSeqFilename(java.lang.String[] args) Returns the name of the query sequence input file.
static int	getSeqType(java.lang.String[] args) Returns the type of sequence that will be used as query.
static int	getVValue(java.lang.String[] args) Returns the number of descriptions to be returned from BLAST.
static java.lang.String	getXMLFilename(java.lang.String[] args) Returns the name of the XML input file.
static java.lang.String	getXMLOutFilename(java.lang.String[] args) Returns the name of the output file into which to copy the XML file that results from BLAST.
static void	main(java.lang.String[] args)
static void	printHelpFile()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

seqinfo

public seqinfo()

Method Detail

getDatabase

public static java.lang.String getDatabase(java.lang.String[] args)

getEValue

public static double getEValue(java.lang.String[] args)

Returns the expectation value. Read from the command line, after "-e" flag.

getBValue

public static int getBValue(java.lang.String[] args)

Returns the number of alignments to be returned from BLAST. Read from the command line, after "-b" flag.

getVValue

public static int getVValue(java.lang.String[] args)

Returns the number of descriptions to be returned from BLAST. Read from the command line, after "-v" flag.

getSeqError

public static double getSeqError(java.lang.String[] args)

Returns the allowed sequencing error. Read from the command line, after "-error" flag.

getProportionQuery

public static double getProportionQuery(java.lang.String[] args)

Returns the percent length. Read from the command line, after "-len" flag.

getQLen

public static int getQLen(java.lang.String[] args)

Returns the length of the query sequence. Read from the command line, after "-len" flag.

getSeqType

public static int getSeqType(java.lang.String[] args)

Returns the type of sequence that will be used as query. Possible values are: dna = 0; protein = 1. Default is protein. Read from the command line, either as "-dna" or "-protein". If neither flag is given, the sequence type is assumed to be protein.

getSeqFilename

public static java.lang.String getSeqFilename(java.lang.String[] args)

Returns the name of the query sequence input file. Read from the command line, after "-seqs" flag.

getMbFilename

public static java.lang.String getMbFilename(java.lang.String[] args)

Returns the name of the megablast output file. Read from the command line, after "-mb" flag.

getFastaFile

public static java.lang.String getFastaFile(java.lang.String[] args)

Returns the name of the fasta sequence file. Read from the command line, after "-fasta" flag.

getXMLFilename

public static java.lang.String getXMLFilename(java.lang.String[] args)

Returns the name of the XML input file. Read from the command line, after "-xml" flag.

getOutFilename

public static java.lang.String getOutFilename(java.lang.String[] args)

Returns the name of the output file. Read from the command line, after "-out". If no output file name given, output file will be named "seqs.info".

getXMLOutFilename

public static java.lang.String getXMLOutFilename(java.lang.String[] args)

Returns the name of the output file into which to copy the XML file that results from BLAST. Read from the command line, after "-xmlkeep". If no output file name given, output file will be named "blast.xml".

getAC

public static java.lang.String getAC(java.lang.String line)

gets the accession number from a FASTA header line that starts with >gi|.

fromFastaLen

public static int fromFastaLen(java.lang.String ac)

Returns the length of the query sequence. Taken from the Hashtable created when -fasta option invoked.

printHelpFile

public static void printHelpFile()

main

public static void main(java.lang.String[] args)