public class CDMSequenceMatrixAdapter extends info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter implements info.bioinfweb.jphyloio.ReadWriteConstants, SingleReadAlignmentRDFXMLConstants
MatrixDataAdapter
that delegates to a Sequence
object.
Note that this adapter stores information on the Sequence
in creation. Modifying the sequence or linked
objects will require to create a new instance of this class. Otherwise unexpected behavior may be the consequence.
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
CONSENSUS_SEQUENCE_ID |
static java.lang.String |
MATRIX_ID |
static java.lang.String |
SINGLE_READ_SEQUENCE_ID_PREFIX |
ATTRIBUTE_STRING_KEY, ATTRIBUTES_NAMESPACE_FOLDER, DATA_TYPE_NAMESPACE_FOLDER, DATA_TYPE_SIMPLE_VALUE_LIST, DEFAULT_CHAR_SET_ID_PREFIX, DEFAULT_CHARACTER_DEFINITION_ID_PREFIX, DEFAULT_EDGE_ID_PREFIX, DEFAULT_GENERAL_ID_PREFIX, DEFAULT_MATRIX_ID_PREFIX, DEFAULT_MAX_COMMENT_LENGTH, DEFAULT_MAX_TOKENS_TO_READ, DEFAULT_META_ID_PREFIX, DEFAULT_NETWORK_ID_PREFIX, DEFAULT_NODE_EDGE_SET_ID_PREFIX, DEFAULT_NODE_ID_PREFIX, DEFAULT_OTU_ID_PREFIX, DEFAULT_OTU_LIST_ID_PREFIX, DEFAULT_OTU_SET_ID_PREFIX, DEFAULT_SEQUENCE_ID_PREFIX, DEFAULT_SEQUENCE_SET_ID_PREFIX, DEFAULT_TOKEN_DEFINITION_ID_PREFIX, DEFAULT_TOKEN_SET_ID_PREFIX, DEFAULT_TREE_ID_PREFIX, DEFAULT_TREE_NETWORK_GROUP_ID_PREFIX, DEFAULT_TREE_NETWORK_SET_ID_PREFIX, JPHYLOIO_ATTRIBUTES_NAMESPACE, JPHYLOIO_ATTRIBUTES_PREFIX, JPHYLOIO_DATA_TYPE_NAMESPACE, JPHYLOIO_DATA_TYPE_PREFIX, JPHYLOIO_FORMATS_NAMESPACE_PREFIX, JPHYLOIO_GENERAL_NAMESPACE, JPHYLOIO_NAMESPACE_PREFIX, JPHYLOIO_PREDICATE_NAMESPACE, JPHYLOIO_PREDICATE_PREFIX, PREDICATE_CHARACTER_COUNT, PREDICATE_EDGE_LENGTH, PREDICATE_EDGE_SOURCE_NODE, PREDICATE_EDGE_TARGET_NODE, PREDICATE_HAS_CUSTOM_XML, PREDICATE_HAS_LITERAL_METADATA, PREDICATE_HAS_RESOURCE_METADATA, PREDICATE_IS_CROSSLINK, PREDICATE_NAMESPACE_FOLDER, PREDICATE_PART_SEPERATOR, PREDICATE_SEQUENCE_COUNT, RESERVED_ID_PREFIX
ATTR_POSITION, ATTR_SHIFT, DATA_TYPE_NAMESPACE_PREFIX, DATA_TYPE_NAMESPACE_URI, DATA_TYPE_PHERORAGM_ALIGNMENT, NAMESPACE_URI_PREFIX, PHEROGRAM_ALIGNMENT_NAMESPACE_PREFIX, PHEROGRAM_ALIGNMENT_NAMESPACE_URI, PREDICATE_HAS_LEFT_CUT_POSITION, PREDICATE_HAS_PHEROGRAM, PREDICATE_HAS_PHEROGRAM_ALIGNMENT, PREDICATE_HAS_RIGHT_CUT_POSITION, PREDICATE_IS_CONSENSUS_SEQUENCE, PREDICATE_IS_REVERSE_COMPLEMENTED, PREDICATE_IS_SINGLE_READ, PREDICATE_NAMESPACE_PREFIX, PREDICATE_NAMESPACE_URI, TAG_SHIFT, TAG_SHIFTS
Constructor and Description |
---|
CDMSequenceMatrixAdapter(eu.etaxonomy.cdm.model.molecular.Sequence sequence,
java.lang.String consensusSequenceLabel,
boolean exportConsensus,
boolean exportSingleReads)
Creates a new instance of this class.
|
Modifier and Type | Method and Description |
---|---|
boolean |
containsLongTokens(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters) |
eu.etaxonomy.cdm.model.molecular.Sequence |
getCDMSequence() |
long |
getColumnCount(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters) |
long |
getSequenceCount(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters) |
java.util.Iterator<java.lang.String> |
getSequenceIDIterator(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters) |
long |
getSequenceLength(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters,
java.lang.String sequenceID) |
info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent |
getSequenceStartEvent(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters,
java.lang.String sequenceID) |
info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent |
getStartEvent(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters) |
info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter<info.bioinfweb.jphyloio.events.TokenSetDefinitionEvent> |
getTokenSets(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters) |
void |
writeSequencePartContentData(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters,
info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver receiver,
java.lang.String sequenceID,
long startColumn,
long endColumn) |
getCharacterDefinitions, getCharacterSets, getSequenceSets
writeMetadata
public static final java.lang.String MATRIX_ID
public static final java.lang.String SINGLE_READ_SEQUENCE_ID_PREFIX
public static final java.lang.String CONSENSUS_SEQUENCE_ID
public CDMSequenceMatrixAdapter(eu.etaxonomy.cdm.model.molecular.Sequence sequence, java.lang.String consensusSequenceLabel, boolean exportConsensus, boolean exportSingleReads)
sequence
- the CDM sequence object containing the data to be exportedconsensusSequenceLabel
- the label to be used for the consensus sequence (Maybe null
.)exportConsensus
- Specify true
here, if the consensus sequence shall be included in the export or false
otherwise.exportSingleReads
- Specify true
here, if the single reads shall be included in the export or false
otherwise.java.lang.IllegalArgumentException
- if both exportConsensus
and exportSingleReads
are false
public eu.etaxonomy.cdm.model.molecular.Sequence getCDMSequence()
public info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent getStartEvent(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
getStartEvent
in interface info.bioinfweb.jphyloio.dataadapters.ElementDataAdapter<info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent>
public boolean containsLongTokens(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
containsLongTokens
in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
public long getColumnCount(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
getColumnCount
in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
public long getSequenceCount(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
getSequenceCount
in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
public java.util.Iterator<java.lang.String> getSequenceIDIterator(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
getSequenceIDIterator
in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
public long getSequenceLength(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters, java.lang.String sequenceID) throws java.lang.IllegalArgumentException
getSequenceLength
in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
java.lang.IllegalArgumentException
public info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent getSequenceStartEvent(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters, java.lang.String sequenceID)
getSequenceStartEvent
in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
public void writeSequencePartContentData(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters, info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver receiver, java.lang.String sequenceID, long startColumn, long endColumn) throws java.io.IOException, java.lang.IllegalArgumentException
writeSequencePartContentData
in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
java.io.IOException
java.lang.IllegalArgumentException
public info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter<info.bioinfweb.jphyloio.events.TokenSetDefinitionEvent> getTokenSets(info.bioinfweb.jphyloio.ReadWriteParameterMap parameters)
getTokenSets
in interface info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter
getTokenSets
in class info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter
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