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)


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.