edu.mssm.crover.util
Class ScanForTms

java.lang.Object
  |
  +--edu.mssm.crover.util.ScanForTms

public class ScanForTms

extends java.lang.Object

Scans a set of sequences, taken from a file, for potential TM segments. The sequences can be dna sequence (-dna must be supplied on the command line), in which case gene products are predicted (with genScan) before the protein sequences are searched for TM segments. in project: The -homologs option can be used to provide a set of sequences against which predicted proteins will be screened for homology.

Constructor Summary

ScanForTms()

Method Summary

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

Constructor Detail

ScanForTms

public ScanForTms()

Method Detail

main

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

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)