uk.ac.vamsas.objects.utils
Class Seq

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

public class Seq
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
Seq()
           
 
Method Summary
static boolean is_valid_aa_seq(SequenceType s)
           
static AlignmentSequence newAlignmentSequence(java.lang.String name, java.lang.String alSequence, Sequence refseq, long start, long end)
           
static Sequence newSequence(java.lang.String Name, java.lang.String Sequence, java.lang.String Dictionary, int start, int end)
           
static void write_FastaSeq(java.io.OutputStream os, SequenceType seq)
           
static void write_FastaSeq(java.io.OutputStream os, SequenceType seq, int wid)
           
static void write_PirSeq(java.io.OutputStream os, SequenceType seq, int wid)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Seq

public Seq()
Method Detail

write_PirSeq

public static void write_PirSeq(java.io.OutputStream os,
                                SequenceType seq,
                                int wid)
                         throws java.io.IOException
Throws:
java.io.IOException

write_FastaSeq

public static void write_FastaSeq(java.io.OutputStream os,
                                  SequenceType seq)
                           throws java.io.IOException
Throws:
java.io.IOException

write_FastaSeq

public static void write_FastaSeq(java.io.OutputStream os,
                                  SequenceType seq,
                                  int wid)
                           throws java.io.IOException
Throws:
java.io.IOException

newSequence

public static Sequence newSequence(java.lang.String Name,
                                   java.lang.String Sequence,
                                   java.lang.String Dictionary,
                                   int start,
                                   int end)

newAlignmentSequence

public static AlignmentSequence newAlignmentSequence(java.lang.String name,
                                                     java.lang.String alSequence,
                                                     Sequence refseq,
                                                     long start,
                                                     long end)

is_valid_aa_seq

public static boolean is_valid_aa_seq(SequenceType s)