apollo.seq.io
Class FastaFile

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

public class FastaFile
extends FileParse

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

Field Summary

protected static org.apache.log4j.Logger	logger
protected static java.util.Vector	seqs

Fields inherited from class apollo.io.FileParse

dataArray, fileSize, inFile, lineArray, noLines

Constructor Summary

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

FastaFile(java.io.Reader reader, boolean inHtml)
Construct a FastaFile object from a Reader.

FastaFile(java.lang.String inStr)

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

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

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(SeqFeatureI feature)
static java.lang.String	print(SequenceI s)
static java.lang.String	print(SequenceI[] s)
static java.lang.String	print(SequenceI[] s, int len)
static java.lang.String	print(SequenceI[] s, int linesize, boolean gaps)
static java.lang.String	printGenomic(SeqFeatureI feature)
static java.lang.String	printTranslation(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

logger

protected static final org.apache.log4j.Logger logger

seqs

protected static java.util.Vector seqs

Constructor Detail

FastaFile

public FastaFile(java.io.Reader reader,
                 boolean inHtml)

Construct a FastaFile object from a Reader. It does not care what the source is

Parameters:

reader - - Reader source

inHtml - - is the data encoded in html

FastaFile

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

FastaFile

public FastaFile(java.lang.String inStr)

FastaFile

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

Throws:

java.io.IOException

FastaFile

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

Throws:

java.io.IOException

Method Detail

getSeqs

public java.util.Vector getSeqs()

parse

public void parse()

print

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

print

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

print

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

print

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

printGenomic

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

print_cDNA

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

printTranslation

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

format

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

main

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