uk.ac.vamsas.objects.utils
Class SeqSet

java.lang.Object
  extended byuk.ac.vamsas.objects.utils.SeqSet

public class SeqSet
extends java.lang.Object

Author:
jimp TODO To change the template for this generated type comment go to Window - Preferences - Java - Code Style - Code Templates

Constructor Summary
SeqSet()
           
 
Method Summary
static boolean deuniquify(java.util.Hashtable map, SequenceType[] sequences)
           
static Sequence[] read_SeqFasta(java.io.InputStream os)
          TODO: introduce a dictionary parameter for qualified sequence symbols Reads a sequence set from a stream - will only read prescribed amino acid symbols.
static java.util.Hashtable uniquify(SequenceType[] sequences)
           
static void write_Fasta(java.io.OutputStream os, SequenceType[] seqs)
           
static void write_Fasta(java.io.OutputStream os, SequenceType[] seqs, boolean width80)
           
static void write_Fasta(java.io.OutputStream os, SequenceType[] seqs, int width)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SeqSet

public SeqSet()
Method Detail

write_Fasta

public static void write_Fasta(java.io.OutputStream os,
                               SequenceType[] seqs)
                        throws java.io.IOException
Throws:
java.io.IOException

write_Fasta

public static void write_Fasta(java.io.OutputStream os,
                               SequenceType[] seqs,
                               boolean width80)
                        throws java.io.IOException
Throws:
java.io.IOException

write_Fasta

public static void write_Fasta(java.io.OutputStream os,
                               SequenceType[] seqs,
                               int width)
                        throws java.io.IOException
Throws:
java.io.IOException

read_SeqFasta

public static Sequence[] read_SeqFasta(java.io.InputStream os)
                                throws java.io.IOException
TODO: introduce a dictionary parameter for qualified sequence symbols Reads a sequence set from a stream - will only read prescribed amino acid symbols.

Parameters:
os -
Returns:
Throws:
java.io.IOException

uniquify

public static java.util.Hashtable uniquify(SequenceType[] sequences)

deuniquify

public static boolean deuniquify(java.util.Hashtable map,
                                 SequenceType[] sequences)