org.emboss.jemboss.editor
Class SequenceReader

java.lang.Object
  org.emboss.jemboss.editor.SequenceReader

public class SequenceReader

extends java.lang.Object

This class reads sequences in FASTA and MSF format. The sequences are read and stored as a Vector.

Field Summary

private boolean	reading true if read ok
private java.io.File	seqFile sequence file
private java.util.Vector	seqs sequence store

Constructor Summary

SequenceReader()

SequenceReader(java.io.File seqFile)

SequenceReader(java.lang.String seqString)

Method Summary

int	getNumberOfSequences() Returns the number of sequences.
Sequence	getSequence(int index) Returns the sequence at a given position in the Sequence Vector store.
java.io.File	getSequenceFile() Get the sequence file
java.util.Vector	getSequenceVector() Returns the Sequence Vector store
boolean	isReading()
java.util.Vector	readClustalFile(java.io.BufferedReader in) Reads in the CLUSTAL sequence file and creates a Vector containing the sequence(s).
java.util.Vector	readFastaFile(java.io.BufferedReader in) Reads in the FASTA sequence file and creates a Vector containing the sequence(s).
java.util.Vector	readJPredFile(java.io.BufferedReader in) Reads in the JPred sequence file and creates a Vector containing the sequence(s).
java.util.Vector	readMSFFile(java.io.BufferedReader in) Reads in the MSF sequence file and creates a Vector containing the sequence(s).
java.util.Vector	readSequenceFile() Read a sequence file and create a vector of sequences
java.util.Vector	readSequenceString(java.lang.String seqString) Read a formatted sequence string (e.g msf) and create a vector of sequences

Methods inherited from class java.lang.Object

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

Field Detail

seqFile

private java.io.File seqFile

sequence file

seqs

private java.util.Vector seqs

sequence store

reading

private boolean reading

true if read ok

Constructor Detail

SequenceReader

public SequenceReader()

SequenceReader

public SequenceReader(java.io.File seqFile)

Parameters:

seqFile - sequence file

SequenceReader

public SequenceReader(java.lang.String seqString)

Parameters:

seqString - sequence

Method Detail

isReading

public boolean isReading()

readSequenceFile

public java.util.Vector readSequenceFile()

Read a sequence file and create a vector of sequences

Returns:

vector of Sequence objects

readSequenceString

public java.util.Vector readSequenceString(java.lang.String seqString)

Read a formatted sequence string (e.g msf) and create a vector of sequences

Returns:

vector of Sequence objects

readFastaFile

public java.util.Vector readFastaFile(java.io.BufferedReader in)

Reads in the FASTA sequence file and creates a Vector containing the sequence(s).

Parameters:

in - buffered reader

readMSFFile

public java.util.Vector readMSFFile(java.io.BufferedReader in)

Reads in the MSF sequence file and creates a Vector containing the sequence(s).

Parameters:

in - buffered reader

readClustalFile

public java.util.Vector readClustalFile(java.io.BufferedReader in)

Reads in the CLUSTAL sequence file and creates a Vector containing the sequence(s).

Parameters:

in - buffered reader

readJPredFile

public java.util.Vector readJPredFile(java.io.BufferedReader in)

Reads in the JPred sequence file and creates a Vector containing the sequence(s).

Parameters:

in - buffered reader

getNumberOfSequences

public int getNumberOfSequences()

Returns the number of sequences.

Returns:

number of sequences

getSequence

public Sequence getSequence(int index)

Returns the sequence at a given position in the Sequence Vector store.

Returns:

sequence object

getSequenceVector

public java.util.Vector getSequenceVector()

Returns the Sequence Vector store

Returns:

collection of Sequence objects

getSequenceFile

public java.io.File getSequenceFile()

Get the sequence file

Returns:

sequence file