uk.ac.vamsas.objects.utils
Class Seq
java.lang.Object
uk.ac.vamsas.objects.utils.Seq
- public class Seq
- extends java.lang.Object
- Author:
- jimp
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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 |
Seq
public Seq()
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)