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)


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