info.bioinfweb.jphyloio

Class ReadWriteParameterMap

java.lang.Object

java.util.AbstractMap<K,V>

java.util.TreeMap<java.lang.String,java.lang.Object>

info.bioinfweb.commons.collections.ParameterMap

info.bioinfweb.jphyloio.ReadWriteParameterMap

All Implemented Interfaces:

ReadWriteParameterNames, java.io.Serializable, java.lang.Cloneable, java.util.Map<java.lang.String,java.lang.Object>, java.util.NavigableMap<java.lang.String,java.lang.Object>, java.util.SortedMap<java.lang.String,java.lang.Object>

public class ReadWriteParameterMap
extends ParameterMap
implements ReadWriteParameterNames

Parameter map that allows to specify (optional) parameters to implementations of JPhyloIOEventReader or JPhyloIOEventWriter.

Author:

Ben Stöver

See Also:

ReadWriteParameterNames, JPhyloIOFormatInfo.getSupportedParameters(boolean), Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class java.util.AbstractMap

java.util.AbstractMap.SimpleEntry<K,V>, java.util.AbstractMap.SimpleImmutableEntry<K,V>

Field Summary

Fields inherited from interface info.bioinfweb.jphyloio.ReadWriteParameterNames

KEY_ALLOW_DEFAULT_NAMESPACE, KEY_ALLOW_INTERLEAVED_PARSING, KEY_ALWAYS_WRITE_NEXUS_NODE_LABELS, KEY_APPLICATION_NAME, KEY_APPLICATION_URL, KEY_APPLICATION_VERSION, KEY_CREATE_UNKNOWN_COMMAND_EVENTS, KEY_CUSTOM_XML_NAMESPACE_HANDLING, KEY_EXPECT_E_NEWICK, KEY_GENERATE_NEXUS_TRANSLATION_TABLE, KEY_IGNORE_COMMENTS, KEY_LABEL_EDITING_REPORTER, KEY_LINE_LENGTH, KEY_LINE_SEPARATOR, KEY_LOGGER, KEY_MATCH_TOKEN, KEY_MAXIMUM_COMMENT_LENGTH, KEY_MAXIMUM_NAME_LENGTH, KEY_MAXIMUM_TOKENS_TO_READ, KEY_NEXML_TOKEN_DEFINITION_LABEL, KEY_NEXML_TOKEN_DEFINITION_LABEL_METADATA, KEY_NEXML_TOKEN_TRANSLATION_STRATEGY, KEY_NEXUS_BLOCK_HANDLER_MAP, KEY_NEXUS_COMMAND_READER_FACTORY, KEY_OBJECT_TRANSLATOR_FACTORY, KEY_PHYLOXML_CONSIDER_PHYLOGENY_AS_TREE, KEY_PHYLOXML_EVENT_ID_TRANSLATION_MAP, KEY_PHYLOXML_METADATA_TREATMENT, KEY_PREFIX, KEY_RELAXED_PHYLIP, KEY_REPLACE_MATCH_TOKENS, KEY_SEQUENCE_EXTENSION_TOKEN, KEY_TRANSLATE_INTERNAL_NODE_NAMES, KEY_USE_OTU_LABEL, KEY_WRITER_INSTANCE

Constructor Summary

Constructors

Constructor and Description
ReadWriteParameterMap()

Method Summary

Modifier and Type	Method and Description
LabelEditingReporter	getLabelEditingReporter() Returns the label editing reporter of this map stored under ReadWriteParameterNames.KEY_LABEL_EDITING_REPORTER.
TokenDefinitionLabelHandling	getLabelHandling()
ApplicationLogger	getLogger()
java.lang.String	getMatchToken()
int	getMaxCommentLength()
int	getMaxTokensToRead()
ObjectTranslatorFactory	getObjectTranslatorFactory() Returns the object translator factory stored under ReadWriteParameterNames.KEY_OBJECT_TRANSLATOR_FACTORY.
java.util.Map<java.lang.String,java.lang.String>	getPhyloXMLEventIDTranslationMap()
PhyloXMLMetadataTreatment	getPhyloXMLMetadataTreatment()
TokenTranslationStrategy	getTranslateTokens()
JPhyloIOEventWriter	getWriterInstance() Returns the writer instance registered under ReadWriteParameterNames.KEY_WRITER_INSTANCE.

Methods inherited from class info.bioinfweb.commons.collections.ParameterMap

getApplicationLogger, getApplicationLogger, getBoolean, getDouble, getFile, getFile, getFloat, getInteger, getLong, getObject, getObject, getString, getString

Methods inherited from class java.util.TreeMap

ceilingEntry, ceilingKey, clear, clone, comparator, containsKey, containsValue, descendingKeySet, descendingMap, entrySet, firstEntry, firstKey, floorEntry, floorKey, forEach, get, headMap, headMap, higherEntry, higherKey, keySet, lastEntry, lastKey, lowerEntry, lowerKey, navigableKeySet, pollFirstEntry, pollLastEntry, put, putAll, remove, replace, replace, replaceAll, size, subMap, subMap, tailMap, tailMap, values

Methods inherited from class java.util.AbstractMap

equals, hashCode, isEmpty, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Map

compute, computeIfAbsent, computeIfPresent, equals, getOrDefault, hashCode, isEmpty, merge, putIfAbsent, remove

Constructor Detail

ReadWriteParameterMap

public ReadWriteParameterMap()

Method Detail

getWriterInstance

public JPhyloIOEventWriter getWriterInstance()

Returns the writer instance registered under ReadWriteParameterNames.KEY_WRITER_INSTANCE.

Returns:

the current writer instance or null if none is present in the map (e.g. because it is used in a reader).

getLogger

public ApplicationLogger getLogger()

getMaxTokensToRead

public int getMaxTokensToRead()

getMaxCommentLength

public int getMaxCommentLength()

getMatchToken

public java.lang.String getMatchToken()

getLabelEditingReporter

public LabelEditingReporter getLabelEditingReporter()

Returns the label editing reporter of this map stored under ReadWriteParameterNames.KEY_LABEL_EDITING_REPORTER. If no object for this key is present in this instance, a new one is created, added to this instance and returned. The same is done, if an object which is not an instance of LabelEditingReporter is found for this key.

Returns:

the map instance

getTranslateTokens

public TokenTranslationStrategy getTranslateTokens()

getLabelHandling

public TokenDefinitionLabelHandling getLabelHandling()

getPhyloXMLMetadataTreatment

public PhyloXMLMetadataTreatment getPhyloXMLMetadataTreatment()

getPhyloXMLEventIDTranslationMap

public java.util.Map<java.lang.String,java.lang.String> getPhyloXMLEventIDTranslationMap()

getObjectTranslatorFactory

public ObjectTranslatorFactory getObjectTranslatorFactory()

Returns the object translator factory stored under ReadWriteParameterNames.KEY_OBJECT_TRANSLATOR_FACTORY. If no object for this key is present in this instance, a new one is created, added to this instance and returned. The same is done, if an object which is not an instance of LabelEditingReporter is found for this key. The created default instance will contain all default translators provided with JPhyloIO.

Returns:

the factory instance