uk.ac.vamsas.objects.utils
Class SeqAln

java.lang.Object
  extended byuk.ac.vamsas.client.Vobject
      extended byuk.ac.vamsas.objects.core.Alignment
          extended byuk.ac.vamsas.objects.utils.SeqAln
All Implemented Interfaces:
java.io.Serializable

public class SeqAln
extends Alignment

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

Field Summary
 
Fields inherited from class uk.ac.vamsas.client.Vobject
__added_since_last_read, __last_hash, __stored_in_document, __updated_since_last_read, __visited, __vorba, registerable, V_parent, vorbaId
 
Constructor Summary
SeqAln()
           
 
Method Summary
static Alignment make_Alignment(Entry origin, Sequence[] seqs)
          manufacture an alignment/dataset from an array of sequences
static Alignment read_ClustalAlignment(java.io.InputStream os, Entry entry)
           
static Alignment read_FastaAlignment(java.io.InputStream os, Entry entry)
           
static Sequence[] ReadClustalFile(java.io.InputStream os)
           
static void WriteClustalWAlignment(java.io.OutputStream os, Alignment seqAl)
           
 
Methods inherited from class uk.ac.vamsas.objects.core.Alignment
addAlignmentAnnotation, addAlignmentAnnotation, addAlignmentSequence, addAlignmentSequence, addProperty, addProperty, addTree, addTree, deleteAligned, enumerateAlignmentAnnotation, enumerateAlignmentSequence, enumerateProperty, enumerateTree, equals, getAligned, getAlignmentAnnotation, getAlignmentAnnotation, getAlignmentAnnotationAsReference, getAlignmentAnnotationCount, getAlignmentSequence, getAlignmentSequence, getAlignmentSequenceAsReference, getAlignmentSequenceCount, getGapChar, getId, getModifiable, getProperty, getProperty, getPropertyAsReference, getPropertyCount, getProvenance, getTree, getTree, getTreeAsReference, getTreeCount, hasAligned, hashCode, isAligned, isValid, marshal, marshal, removeAlignmentAnnotation, removeAlignmentAnnotationAt, removeAlignmentSequence, removeAlignmentSequenceAt, removeAllAlignmentAnnotation, removeAllAlignmentSequence, removeAllProperty, removeAllTree, removeProperty, removePropertyAt, removeTree, removeTreeAt, setAligned, setAlignmentAnnotation, setAlignmentAnnotation, setAlignmentAnnotation, setAlignmentAnnotationAsReference, setAlignmentSequence, setAlignmentSequence, setAlignmentSequence, setAlignmentSequenceAsReference, setGapChar, setId, setModifiable, setProperty, setProperty, setProperty, setPropertyAsReference, setProvenance, setTree, setTree, setTree, setTreeAsReference, unmarshal, validate
 
Methods inherited from class uk.ac.vamsas.client.Vobject
__callHash, __ensure_instance_ids, __ensure_instance_ids, __getInstanceIdField, __getLHash, __setFinalHash, __setInitHash, doHash, finalize, get__last_hash, getV_parent, getVorbaId, is__stored_in_document, isNewInDocument, isRegisterable, isRegistered, isUpdated, merge, set__added_since_last_read, set__stored_in_document, set__updated_since_last_read, setInstanceIdField, setRegisterable, setV_parent, setVorbaId
 
Methods inherited from class java.lang.Object
clone, getClass, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SeqAln

public SeqAln()
Method Detail

ReadClustalFile

public static Sequence[] ReadClustalFile(java.io.InputStream os)
                                  throws java.lang.Exception
Throws:
java.lang.Exception

WriteClustalWAlignment

public static void WriteClustalWAlignment(java.io.OutputStream os,
                                          Alignment seqAl)
                                   throws java.io.IOException
Throws:
java.io.IOException

make_Alignment

public static Alignment make_Alignment(Entry origin,
                                       Sequence[] seqs)
                                throws java.lang.Exception
manufacture an alignment/dataset from an array of sequences

Parameters:
origin -
seqs -
Returns:
Throws:
java.lang.Exception

read_FastaAlignment

public static Alignment read_FastaAlignment(java.io.InputStream os,
                                            Entry entry)
                                     throws java.lang.Exception
Throws:
java.lang.Exception

read_ClustalAlignment

public static Alignment read_ClustalAlignment(java.io.InputStream os,
                                              Entry entry)
                                       throws java.lang.Exception
Throws:
java.lang.Exception