uk.ac.vamsas.objects.utils
Class SeqSet
java.lang.Object
uk.ac.vamsas.objects.utils.SeqSet
- public class SeqSet
- extends java.lang.Object
- Author:
- jimp
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SeqSet
public SeqSet()
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)