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
           
private  java.io.File seqFile
           
private  java.util.Vector seqs
           
 
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()
           
 java.util.Vector getSequenceVector()
          Returns the Sequence Vector store
 boolean isReading()
           
 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 readMSFFile(java.io.BufferedReader in)
          Reads in the MSF sequence file and creates a Vector containing the sequence(s).
 java.util.Vector readSequenceFile()
           
 java.util.Vector readSequenceString(java.lang.String seqString)
           
 
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

seqs

private java.util.Vector seqs

reading

private boolean reading
Constructor Detail

SequenceReader

public SequenceReader()

SequenceReader

public SequenceReader(java.io.File seqFile)

SequenceReader

public SequenceReader(java.lang.String seqString)
Method Detail

isReading

public boolean isReading()

readSequenceFile

public java.util.Vector readSequenceFile()

readSequenceString

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

readFastaFile

public java.util.Vector readFastaFile(java.io.BufferedReader in)
Reads in the FASTA sequence file and creates a Vector containing the sequence(s).


readMSFFile

public java.util.Vector readMSFFile(java.io.BufferedReader in)
Reads in the MSF sequence file and creates a Vector containing the sequence(s).


getNumberOfSequences

public int getNumberOfSequences()
Returns the number of sequences.


getSequence

public Sequence getSequence(int index)
Returns the sequence at a given position in the Sequence Vector store.


getSequenceVector

public java.util.Vector getSequenceVector()
Returns the Sequence Vector store


getSequenceFile

public java.io.File getSequenceFile()