info.bioinfweb.jphyloio.objecttranslation.implementations

Class ListTranslator

java.lang.Object

info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractObjectTranslator<O>

info.bioinfweb.jphyloio.objecttranslation.implementations.SimpleValueTranslator<java.util.List<java.lang.Object>>

info.bioinfweb.jphyloio.objecttranslation.implementations.ListTranslator

All Implemented Interfaces:

NewickConstants, ObjectTranslator<java.util.List<java.lang.Object>>

public class ListTranslator
extends SimpleValueTranslator<java.util.List<java.lang.Object>>
implements NewickConstants

Reads and writes string representations of simple values as used in Newick or Nexus. Elements can either be strings or numeric values.

Example:

{18.2, 'AB C', 22}

For a possible format independent use, the data type ReadWriteConstants.DATA_TYPE_SIMPLE_VALUE_LIST allows to use this translator also in NeXML, although it primarily meant for Newick and Nexus.

Author:

Ben Stöver

See Also:

ReadWriteConstants.DATA_TYPE_SIMPLE_VALUE_LIST, ObjectTranslatorFactory.addJPhyloIOTranslators(boolean)

Field Summary

Fields inherited from class info.bioinfweb.jphyloio.objecttranslation.implementations.SimpleValueTranslator

MAX_STRING_REPRESENTATION_LENGTH

Fields inherited from interface info.bioinfweb.jphyloio.formats.newick.NewickConstants

ALLOCATION_SEPARATOR_SYMBOL, ALLOCATION_SYMBOL, ALTERNATIVE_NAME_DELIMITER, COMMENT_END, COMMENT_START, DATA_TYPE_NEWICK_ARRAY, E_NEWICK_EDGE_TYPE_HYBRIDIZATION, E_NEWICK_EDGE_TYPE_LATERAL_GENE_TRANSFER, E_NEWICK_EDGE_TYPE_RECOMBINATION, E_NEWICK_NAMESPACE_PREFIX, E_NEWICK_NETWORK_DATA_SEPARATOR, ELEMENT_SEPERATOR, FIELD_END_SYMBOL, FIELD_START_SYMBOL, FIELD_VALUE_SEPARATOR_SYMBOL, FREE_NAME_BLANK, HOT_COMMENT_START_SYMBOL, INDEX_END_SYMBOL, INDEX_START_SYMBOL, LENGTH_SEPERATOR, NAME_DELIMITER, NEWICK_DATA_TYPE_NAMESPACE, NEWICK_FORMAT_NAME, NEWICK_NAMESPACE_PREFIX, NHX_KEY_CONFIDENCE, NHX_KEY_EVENT, NHX_KEY_GENE_NAME, NHX_KEY_PREFIX, NHX_KEY_SCIENTIFIC_NAME, NHX_KEY_SEQUENCE_ACCESSION, NHX_KEY_TAXONOMY_ID, NHX_START, NHX_VALUE_SEPARATOR_SYMBOL, PREDICATE_E_NEWICK_EDGE_TYPE, ROOTED_HOT_COMMENT, SUBTREE_END, SUBTREE_START, TERMINAL_SYMBOL, UNROOTED_HOT_COMMENT

Constructor Summary

Constructors

Constructor and Description
ListTranslator()

Method Summary

Modifier and Type	Method and Description
java.lang.Class<java.util.List<java.lang.Object>>	getObjectClass() Returns the Java class of object instances created by this translator.
java.lang.String	javaToRepresentation(java.lang.Object object, WriterStreamDataProvider<?> streamDataProvider) Creates the string representation of a simple value list from any object that implements Iterable.
static java.lang.String	listToString(java.lang.Iterable<?> list)
static java.util.List<java.lang.Object>	parseList(java.lang.String representation) Reads a string representation of a simple value list into an implementation of List.
java.util.List<java.lang.Object>	representationToJava(java.lang.String representation, ReaderStreamDataProvider<?> streamDataProvider) Reads a string representation of a simple value list into an implementation of List.

Methods inherited from class info.bioinfweb.jphyloio.objecttranslation.implementations.SimpleValueTranslator

hasStringRepresentation, readXMLRepresentation, writeXMLRepresentation

Methods inherited from class info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractObjectTranslator

equals, hashCode

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ListTranslator

public ListTranslator()

Method Detail

getObjectClass

public java.lang.Class<java.util.List<java.lang.Object>> getObjectClass()

Description copied from interface: ObjectTranslator

Returns the Java class of object instances created by this translator.

Note that ObjectTranslator.javaToRepresentation(Object, WriterStreamDataProvider) and ObjectTranslator.writeXMLRepresentation(XMLStreamWriter, Object, WriterStreamDataProvider) may also accept instances of other classes. This is independent from the return value here.

Specified by:

getObjectClass in interface ObjectTranslator<java.util.List<java.lang.Object>>

Returns:

the class of the handled objects

parseList

public static java.util.List<java.lang.Object> parseList(java.lang.String representation)
                                                  throws InvalidObjectSourceDataException

Reads a string representation of a simple value list into an implementation of List. The single elements are either instances of String or any implementation of Number. Double will be used by default, for values having a higher precision, BigDecimal will be used instead.

Parameters:

representation - the string representation of the list

Returns:

a list instance

Throws:

InvalidObjectSourceDataException

representationToJava

public java.util.List<java.lang.Object> representationToJava(java.lang.String representation,
                                                             ReaderStreamDataProvider<?> streamDataProvider)
                                                      throws InvalidObjectSourceDataException,
                                                             java.lang.UnsupportedOperationException

Reads a string representation of a simple value list into an implementation of List. The single elements are either instances of String or any implementation of Number. Double will be used by default, for values having a higher precision, BigDecimal will be used instead.

Specified by:

representationToJava in interface ObjectTranslator<java.util.List<java.lang.Object>>

Parameters:

representation - the string representation of the object to be created

streamDataProvider - the stream data provider of the calling reader (Maybe null. Some translators will use it to gain additional status information required for translating, e.g. prefix to namespace mapping for creating QNames.)

Returns:

the new object

Throws:

InvalidObjectSourceDataException - if the specified string representation cannot be parsed to a supported object

java.lang.UnsupportedOperationException - if objects handled by this instance can only be represented as XML

See Also:

ObjectTranslator.representationToJava(java.lang.String, info.bioinfweb.jphyloio.ReaderStreamDataProvider)

listToString

public static java.lang.String listToString(java.lang.Iterable<?> list)
                                     throws java.lang.ClassCastException

Throws:

java.lang.ClassCastException

javaToRepresentation

public java.lang.String javaToRepresentation(java.lang.Object object,
                                             WriterStreamDataProvider<?> streamDataProvider)
                                      throws java.lang.ClassCastException

Creates the string representation of a simple value list from any object that implements Iterable.

Specified by:

javaToRepresentation in interface ObjectTranslator<java.util.List<java.lang.Object>>

Overrides:

javaToRepresentation in class SimpleValueTranslator<java.util.List<java.lang.Object>>

Parameters:

object - the Iterable to be converted

streamDataProvider - TODO

Returns:

the string representation of the list

Throws:

java.lang.ClassCastException - if object does not implement Iterable

See Also:

ObjectTranslator.javaToRepresentation(java.lang.Object, WriterStreamDataProvider)