edu.mssm.crover.tools.tm
Class gpcrMotif

java.lang.Object
  |
  +--edu.mssm.crover.tools.tm.gpcrMotif

public class gpcrMotif

extends java.lang.Object

Field Summary

static BiologicalSequence[]	seqs BiologicalSequence array
static TmDomain_Annotation[]	tmAnn TmDomain_Annotation array

Constructor Summary

gpcrMotif()

Method Summary

static boolean	checkAfterArg(char c)
static boolean	checkArginine(char c)
static boolean	checkBeforeArg(char c)
static boolean	checkC(char c)
static void	checkDRY(java.lang.String subseq, java.io.Writer writer) Checks for the [DE]R[YHS] motif, and a C 25 residues 3' to it.
static boolean	checkLoopC(java.lang.String loop) Returns whether the loop contains a C.
static java.lang.String	getInputFile(java.lang.String[] args) get name of input file with sequences
static boolean	isMotifThere(java.lang.String loop) Returns whether the motif C[CS]XXX[P] is present in the sequence.
static void	main(java.lang.String[] args)
static void	parseSeqs(SequenceReaderFactoryImpl sr, java.lang.String seqfile) Reads the sequences from the file into the BiologicalSequence array.

Methods inherited from class java.lang.Object

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

Field Detail

seqs

public static BiologicalSequence[] seqs

BiologicalSequence array

tmAnn

public static TmDomain_Annotation[] tmAnn

TmDomain_Annotation array

Constructor Detail

gpcrMotif

public gpcrMotif()

Method Detail

getInputFile

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

get name of input file with sequences

parseSeqs

public static void parseSeqs(SequenceReaderFactoryImpl sr,
                             java.lang.String seqfile)

Reads the sequences from the file into the BiologicalSequence array.

checkDRY

public static void checkDRY(java.lang.String subseq,
                            java.io.Writer writer)
                     throws java.io.IOException

Checks for the [DE]R[YHS] motif, and a C 25 residues 3' to it.

java.io.IOException

checkArginine

public static boolean checkArginine(char c)

checkBeforeArg

public static boolean checkBeforeArg(char c)

checkAfterArg

public static boolean checkAfterArg(char c)

checkC

public static boolean checkC(char c)

isMotifThere

public static boolean isMotifThere(java.lang.String loop)

Returns whether the motif C[CS]XXX[P] is present in the sequence.

checkLoopC

public static boolean checkLoopC(java.lang.String loop)

Returns whether the loop contains a C.

main

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