edu.mssm.crover.tools.blast
Class BlastGeneProduct

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

public class BlastGeneProduct

extends java.lang.Object

Blast gene products, as predicted with genescan from a dna sequence. The sequences can be dna sequence (-dna must be supplied on the command line), in which case gene products are predicted (with genScan) before blasting the protein sequences.

Field Summary

static int

OUTPUT_PAIRWISE

Constructor Summary

BlastGeneProduct()

Method Summary

static void	copy(java.io.File inf, java.io.File dest)
static int	getIntOption(java.lang.String[] args, java.lang.String keyword, int default_value)
static java.lang.String	getOption(java.lang.String[] args, java.lang.String option_keywork, java.lang.String default_value)
static boolean	isKeywordGiven(java.lang.String[] args, java.lang.String option_keyword)
static void	main(java.lang.String[] args)

Methods inherited from class java.lang.Object

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

Field Detail

OUTPUT_PAIRWISE

public static final int OUTPUT_PAIRWISE

See Also:

Constant Field Values

Constructor Detail

BlastGeneProduct

public BlastGeneProduct()

Method Detail

main

public static void main(java.lang.String[] args)
                 throws CommandNotInstalled,
                        DatabaseNotFound

CommandNotInstalled

DatabaseNotFound

getOption

public static java.lang.String getOption(java.lang.String[] args,
                                         java.lang.String option_keywork,
                                         java.lang.String default_value)

isKeywordGiven

public static boolean isKeywordGiven(java.lang.String[] args,
                                     java.lang.String option_keyword)

getIntOption

public static int getIntOption(java.lang.String[] args,
                               java.lang.String keyword,
                               int default_value)

copy

public static void copy(java.io.File inf,
                        java.io.File dest)