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apollo.seq.io
Class FastaFile  

java.lang.Object
  apollo.io.FileParse
      apollo.seq.io.FastaFile

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public class FastaFile

extends apollo.io.FileParse

Parses a fasta file into a Vector of Sequence objects, which can be retrieved with getSeqs

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Field Summary
(package private)  long	end
(package private)  java.util.Vector	headers
(package private)  int	maxLength
(package private)  java.util.Hashtable	myHash
(package private)  int	noSeqs
java.util.Vector	seqs
(package private)  long	start
(package private)  java.util.Vector	words

 

Fields inherited from class apollo.io.FileParse

dataArray, fileSize, inFile, lineArray, noLines

 

Constructor Summary

FastaFile(java.io.DataInputStream in, boolean inHtml)

FastaFile(java.lang.String inStr)

FastaFile(java.lang.String inFile, java.lang.String type)

 

Method Summary
static java.lang.String	format(java.lang.String header, java.lang.String residues, int linesize)
java.util.Vector	getSeqs()
static void	main(java.lang.String[] args)
void	parse()
static java.lang.String	print_cDNA(apollo.datamodel.SeqFeatureI feature)
static java.lang.String	print(apollo.datamodel.SequenceI s)
static java.lang.String	print(apollo.datamodel.SequenceI[] s)
static java.lang.String	print(apollo.datamodel.SequenceI[] s, int len)
static java.lang.String	print(apollo.datamodel.SequenceI[] s, int linesize, boolean gaps)
static java.lang.String	printGenomic(apollo.datamodel.SeqFeatureI feature)
static java.lang.String	printTranslation(apollo.datamodel.SeqFeatureI feature)

 

Methods inherited from class apollo.io.FileParse

readLines, readLines, splitLine

 

Methods inherited from class java.lang.Object

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

 

Field Detail

noSeqs

int noSeqs

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maxLength

int maxLength

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myHash

java.util.Hashtable myHash

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seqs

public java.util.Vector seqs

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headers

java.util.Vector headers

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words

java.util.Vector words

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start

long start

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end

long end

Constructor Detail

FastaFile

public FastaFile(java.io.DataInputStream in,
                 boolean inHtml)

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FastaFile

public FastaFile(java.lang.String inStr)

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FastaFile

public FastaFile(java.lang.String inFile,
                 java.lang.String type)
          throws java.io.IOException

Method Detail

getSeqs

public java.util.Vector getSeqs()

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parse

public void parse()

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print

public static java.lang.String print(apollo.datamodel.SequenceI s)

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print

public static java.lang.String print(apollo.datamodel.SequenceI[] s)

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print

public static java.lang.String print(apollo.datamodel.SequenceI[] s,
                                     int len)

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print

public static java.lang.String print(apollo.datamodel.SequenceI[] s,
                                     int linesize,
                                     boolean gaps)

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printGenomic

public static java.lang.String printGenomic(apollo.datamodel.SeqFeatureI feature)

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print_cDNA

public static java.lang.String print_cDNA(apollo.datamodel.SeqFeatureI feature)

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printTranslation

public static java.lang.String printTranslation(apollo.datamodel.SeqFeatureI feature)

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format

public static java.lang.String format(java.lang.String header,
                                      java.lang.String residues,
                                      int linesize)

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main

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

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> apollo >> seq >> [ io overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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