uk.ac.vamsas.objects.utils
Class SeqAln
java.lang.Object
uk.ac.vamsas.client.Vobject
uk.ac.vamsas.objects.core.Alignment
uk.ac.vamsas.objects.utils.SeqAln
- All Implemented Interfaces:
- java.io.Serializable
- public class SeqAln
- extends Alignment
- Author:
- jimp
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- See Also:
- Serialized Form
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 |
SeqAln
public SeqAln()
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