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Packages that use Alignment | |
uk.ac.vamsas.objects | |
uk.ac.vamsas.objects.core | |
uk.ac.vamsas.objects.utils | |
uk.ac.vamsas.test.simpleclient |
Uses of Alignment in uk.ac.vamsas.objects |
Methods in uk.ac.vamsas.objects with parameters of type Alignment | |
void |
EmptyDocumentUpdater.update(Alignment vobj)
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void |
IDocumentUpdater.update(Alignment vobj)
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Uses of Alignment in uk.ac.vamsas.objects.core |
Methods in uk.ac.vamsas.objects.core that return Alignment | |
static Alignment |
Alignment.unmarshal(java.io.Reader reader)
Method unmarshal. |
Alignment |
DataSet.getAlignment(int index)
Method getAlignment. |
Alignment[] |
DataSet.getAlignment()
Method getAlignment.Returns the contents of the collection in an Array. |
Alignment |
DataSet.removeAlignmentAt(int index)
Method removeAlignmentAt. |
Methods in uk.ac.vamsas.objects.core with parameters of type Alignment | |
void |
DataSet.addAlignment(Alignment vAlignment)
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void |
DataSet.addAlignment(int index,
Alignment vAlignment)
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boolean |
DataSet.removeAlignment(Alignment vAlignment)
Method removeAlignment. |
void |
DataSet.setAlignment(int index,
Alignment vAlignment)
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void |
DataSet.setAlignment(Alignment[] vAlignmentArray)
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Uses of Alignment in uk.ac.vamsas.objects.utils |
Subclasses of Alignment in uk.ac.vamsas.objects.utils | |
class |
SeqAln
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Methods in uk.ac.vamsas.objects.utils that return Alignment | |
static Alignment |
SeqAln.make_Alignment(Entry origin,
Sequence[] seqs)
manufacture an alignment/dataset from an array of sequences |
static Alignment |
SeqAln.read_FastaAlignment(java.io.InputStream os,
Entry entry)
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static Alignment |
SeqAln.read_ClustalAlignment(java.io.InputStream os,
Entry entry)
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Methods in uk.ac.vamsas.objects.utils with parameters of type Alignment | |
static void |
SeqAln.WriteClustalWAlignment(java.io.OutputStream os,
Alignment seqAl)
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Uses of Alignment in uk.ac.vamsas.test.simpleclient |
Methods in uk.ac.vamsas.test.simpleclient with parameters of type Alignment | |
static boolean |
ArchiveReports.alignmentReport(Alignment[] al,
boolean cascade,
java.io.PrintStream outstr)
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