edu.mssm.crover.util
Class CompareSeqSets

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

public class CompareSeqSets

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

CompareSeqSets()

Method Summary

static RandomAccessAlignment	align(clustalnet.AlignmentServer server, BiologicalSequence seq1, BiologicalSequence seq2)
static float	getFloatOption(java.lang.String[] args, java.lang.String keyword, float default_value)
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)
static float	sequenceIdentity(RandomAccessAlignment ra) Returns the sequence identity between the sequences in ra.

Methods inherited from class java.lang.Object

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

Constructor Detail

CompareSeqSets

public CompareSeqSets()

Method Detail

main

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

sequenceIdentity

public static float sequenceIdentity(RandomAccessAlignment ra)

Returns the sequence identity between the sequences in ra. Assumes ra contains only two sequences.

align

public static RandomAccessAlignment align(clustalnet.AlignmentServer server,
                                          BiologicalSequence seq1,
                                          BiologicalSequence seq2)

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)

getFloatOption

public static float getFloatOption(java.lang.String[] args,
                                   java.lang.String keyword,
                                   float default_value)