info.bioinfweb.jphyloio.formats.nexus

Class NexusReaderStreamDataProvider

java.lang.Object

info.bioinfweb.jphyloio.ReaderStreamDataProvider<R>

info.bioinfweb.jphyloio.formats.text.TextReaderStreamDataProvider<NexusEventReader>

info.bioinfweb.jphyloio.formats.nexus.NexusReaderStreamDataProvider

All Implemented Interfaces:

NexusConstants

public class NexusReaderStreamDataProvider
extends TextReaderStreamDataProvider<NexusEventReader>
implements NexusConstants

Stores data that shall be shared among different implementations of NexusCommandEventReader reading from the same document.

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	INFO_CHARACTER_NAME_TO_INDEX_MAP
static java.lang.String	INFO_KEY_BLOCK_ID_MAP
static java.lang.String	INFO_KEY_BLOCK_LINKS
static java.lang.String	INFO_KEY_BLOCK_START_EVENT_FIRED
static java.lang.String	INFO_KEY_BLOCK_TITLE Used to store the title of the current block if specified by a TITLE command.
static java.lang.String	INFO_KEY_CURRENT_BLOCK_ID Used to store the ID of the according JPhyloIO event to the current Nexus block (if one exists).
static java.lang.String	INFO_KEY_ELEMENT_LIST
static java.lang.String	INFO_KEY_MATRIX_WIDTHS_MAP Used to Determine the lengths of character set intervals that shall reach until the end of a matrix.
static java.lang.String	INFO_KEY_NEXUS_NAME_TO_ID_MAP
static java.lang.String	INFO_KEY_TREES_TRANSLATION

Fields inherited from interface info.bioinfweb.jphyloio.formats.nexus.NexusConstants

ALTERNATIVE_END_COMMAND, BEGIN_COMMAND, BLOCK_NAME_CHARACTERS, BLOCK_NAME_DATA, BLOCK_NAME_NETWORKS, BLOCK_NAME_SETS, BLOCK_NAME_TAXA, BLOCK_NAME_TREES, BLOCK_NAME_UNALIGNED, CHARACTER_NAME_STATES_SEPARATOR, COMMAND_END, COMMAND_NAME_CHAR_LABELS, COMMAND_NAME_CHAR_SET, COMMAND_NAME_CHAR_STATE_LABELS, COMMAND_NAME_DIMENSIONS, COMMAND_NAME_FORMAT, COMMAND_NAME_LINK, COMMAND_NAME_MATRIX, COMMAND_NAME_NETWORK, COMMAND_NAME_TAX_LABELS, COMMAND_NAME_TAXON_SET, COMMAND_NAME_TITLE, COMMAND_NAME_TRANSLATE, COMMAND_NAME_TREE, COMMAND_NAME_TREE_SET, COMMENT_END, COMMENT_START, DIMENSIONS_SUBCOMMAND_NCHAR, DIMENSIONS_SUBCOMMAND_NEW_TAXA, DIMENSIONS_SUBCOMMAND_NTAX, ELEMENT_SEPARATOR, END_COMMAND, FIRST_LINE, FORMAT_NAME_STANDARD, FORMAT_NAME_VECTOR, FORMAT_SUBCOMMAND_DATA_TYPE, FORMAT_SUBCOMMAND_GAP_CHAR, FORMAT_SUBCOMMAND_INTERLEAVE, FORMAT_SUBCOMMAND_MATCH_CHAR, FORMAT_SUBCOMMAND_MISSING_CHAR, FORMAT_SUBCOMMAND_NO_LABELS, FORMAT_SUBCOMMAND_NO_TOKENS, FORMAT_SUBCOMMAND_SYMBOLS, FORMAT_SUBCOMMAND_TOKENS, FORMAT_SUBCOMMAND_TRANSPOSE, FORMAT_VALUE_CONTINUOUS_DATA_TYPE, FORMAT_VALUE_DNA_DATA_TYPE, FORMAT_VALUE_MIXED_DATA_TYPE, FORMAT_VALUE_NUCLEOTIDE_DATA_TYPE, FORMAT_VALUE_PROTEIN_DATA_TYPE, FORMAT_VALUE_RNA_DATA_TYPE, FORMAT_VALUE_STANDARD_DATA_TYPE, KEY_VALUE_SEPARATOR, MATRIX_POLYMORPHIC_TOKEN_END, MATRIX_POLYMORPHIC_TOKEN_START, MATRIX_UNCERTAINS_TOKEN_END, MATRIX_UNCERTAINS_TOKEN_START, NEXUS_FORMAT_NAME, NEXUS_NAMESPACE_PREFIX, NEXUS_PREDICATE_NAMESPACE, SET_END_INDEX_SYMBOL, SET_KEY_WORD_ALL, SET_KEY_WORD_REMAINING, SET_REGULAR_INTERVAL_SYMBOL, SET_TO_SYMBOL, SET_VECTOR_CONTAINED, SET_VECTOR_NOT_CONTAINED, UNTIL_WHITESPACE_COMMENT_COMMAND_EQUAL_PATTERN, UNTIL_WHITESPACE_COMMENT_COMMAND_PATTERN, VALUE_DELIMITER, WORD_DELIMITER

Constructor Summary

Constructors

Constructor and Description
NexusReaderStreamDataProvider(NexusEventReader nexusReader)

Method Summary

Modifier and Type	Method and Description
void	clearBlockInformation()
void	consumeWhiteSpaceAndComments() Calls #consumeWhiteSpaceAndComments(char, char) with according parameters and ensures visibility for NexusReaderStreamDataProvider.
java.util.Map<java.lang.String,java.lang.String>	getBlockLinks() Returns the map that contains links to other blocks that are explicitly linked to this block.
BlockTitleToIDMap	getBlockTitleToIDMap() Returns a map object that can translate Nexus block titles to the IDs of the according JPhyloIO start events.
java.lang.String	getCurrentLinkedBlockID(java.lang.String blockTypeName) Returns the JPhyloIO ID of the start event describing the Nexus block of the specified type that is linked to the current block.
java.util.List<java.lang.String>	getElementList(EventContentType type, java.lang.String listID)
NexusEventReader	getEventReader()
java.util.Map<?,?>	getMap(java.lang.String key) Gets a map object from the shared information map.
java.lang.String	getMatrixLink() Returns the ID if a CHARACTERS, DATA or UNALIGNED block that is linked to the current block.
java.util.Map<java.lang.String,java.lang.Long>	getMatrixWidthsMap() Returns a map object that stores the widths of all sequence matrices encountered until now.
java.util.Map<java.lang.String,java.lang.String>	getNexusNameToIDMap(EventContentType type, java.lang.String listID) Returns a map object that translates between a Nexus name and the JPhyloIO ID of the according event.
ParameterMap	getSharedInformationMap() This map can be used to store objects to be shared between different instances of NexusCommandEventReader.
NexusTranslationTable	getTreesTranslationTable() Returns the current Nexus translation table object.
void	readComment()
KeyValueInformation	readKeyValueMetaInformation()
java.lang.String	readNexusWord()
long	readPositiveInteger(long startOrEndIndex) Tries to read a positive integer from the current position of the underlying stream-

Methods inherited from class info.bioinfweb.jphyloio.formats.text.TextReaderStreamDataProvider

getDataReader

Methods inherited from class info.bioinfweb.jphyloio.ReaderStreamDataProvider

eventsUpcoming, getCurrentEventCollection, getIDManager, getParameters, getSequenceTokensEventManager, hasSpecialEventCollection, resetCurrentEventCollection, setCurrentEventCollection

Methods inherited from class java.lang.Object

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

Field Detail

INFO_KEY_BLOCK_START_EVENT_FIRED

public static final java.lang.String INFO_KEY_BLOCK_START_EVENT_FIRED

See Also:

Constant Field Values

INFO_KEY_CURRENT_BLOCK_ID

public static final java.lang.String INFO_KEY_CURRENT_BLOCK_ID

Used to store the ID of the according JPhyloIO event to the current Nexus block (if one exists).

See Also:

Constant Field Values

INFO_KEY_BLOCK_TITLE

public static final java.lang.String INFO_KEY_BLOCK_TITLE

Used to store the title of the current block if specified by a TITLE command.

See Also:

Constant Field Values

INFO_KEY_BLOCK_LINKS

public static final java.lang.String INFO_KEY_BLOCK_LINKS

See Also:

Constant Field Values

INFO_KEY_BLOCK_ID_MAP

public static final java.lang.String INFO_KEY_BLOCK_ID_MAP

See Also:

Constant Field Values

INFO_KEY_ELEMENT_LIST

public static final java.lang.String INFO_KEY_ELEMENT_LIST

See Also:

Constant Field Values

INFO_KEY_NEXUS_NAME_TO_ID_MAP

public static final java.lang.String INFO_KEY_NEXUS_NAME_TO_ID_MAP

See Also:

Constant Field Values

INFO_CHARACTER_NAME_TO_INDEX_MAP

public static final java.lang.String INFO_CHARACTER_NAME_TO_INDEX_MAP

See Also:

Constant Field Values

INFO_KEY_TREES_TRANSLATION

public static final java.lang.String INFO_KEY_TREES_TRANSLATION

See Also:

Constant Field Values

INFO_KEY_MATRIX_WIDTHS_MAP

public static final java.lang.String INFO_KEY_MATRIX_WIDTHS_MAP

Used to Determine the lengths of character set intervals that shall reach until the end of a matrix.

See Also:

Constant Field Values

Constructor Detail

NexusReaderStreamDataProvider

public NexusReaderStreamDataProvider(NexusEventReader nexusReader)

Method Detail

getEventReader

public NexusEventReader getEventReader()

Overrides:

getEventReader in class ReaderStreamDataProvider<NexusEventReader>

consumeWhiteSpaceAndComments

public void consumeWhiteSpaceAndComments()
                                  throws java.io.IOException

Calls #consumeWhiteSpaceAndComments(char, char) with according parameters and ensures visibility for NexusReaderStreamDataProvider.

Throws:

java.io.IOException - if an I/O error occurs during the read operation

readNexusWord

public java.lang.String readNexusWord()
                               throws java.io.IOException

Throws:

java.io.IOException

readPositiveInteger

public long readPositiveInteger(long startOrEndIndex)
                         throws java.io.IOException

Tries to read a positive integer from the current position of the underlying stream-

Parameters:

startOrEndIndex - the value to be returned, if '.' is encountered (It is used as a placeholder for the highest possible index in some commands.)

Returns:

the read positive integer or startOrEndIndex or -2 if neither a positive integer nor '.' was found

Throws:

java.io.IOException

readComment

public void readComment()
                 throws java.io.IOException

Throws:

java.io.IOException

readKeyValueMetaInformation

public KeyValueInformation readKeyValueMetaInformation()
                                                throws java.io.IOException

Throws:

java.io.IOException

getSharedInformationMap

public ParameterMap getSharedInformationMap()

This map can be used to store objects to be shared between different instances of NexusCommandEventReader.

Returns:

a map providing access to shared data objects

getBlockLinks

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

Returns the map that contains links to other blocks that are explicitly linked to this block.

The returned map is used internally in JPhyloIO to manage links of the current block that are defined with a LINK command. It should never be used to determine a currently linked block, but getCurrentLinkedBlockID(String) should be used instead.

Returns:

the map containing the blocks explicitly linked to the current block

getMatrixLink

public java.lang.String getMatrixLink()

Returns the ID if a CHARACTERS, DATA or UNALIGNED block that is linked to the current block. If none of these blocks is explicitly linked, returning a default linked block will be tried in this order. If no default linked block is found, null will be returned.

Returns:

a linked block containing sequences or null

clearBlockInformation

public void clearBlockInformation()

getMap

public java.util.Map<?,?> getMap(java.lang.String key)

Gets a map object from the shared information map. If no such object if found, a new HashMap instance is stored under the specified key and returned.

Parameters:

key - the key in the shared information map

Returns:

the map object contained in the shared information map

getBlockTitleToIDMap

public BlockTitleToIDMap getBlockTitleToIDMap()

Returns a map object that can translate Nexus block titles to the IDs of the according JPhyloIO start events. The returned object can also determine default block links.

Returns:

the translation map

getCurrentLinkedBlockID

public java.lang.String getCurrentLinkedBlockID(java.lang.String blockTypeName)

Returns the JPhyloIO ID of the start event describing the Nexus block of the specified type that is linked to the current block. It will first look for an explicitly linked block in getBlockLinks(). If no link is found, the default link from BlockTitleToIDMap.getDefaultBlockID(String) will be returned.

Parameters:

blockTypeName - the name of the Nexus block type that could be linked

Returns:

the start event ID or null if no according block could be found

getElementList

public java.util.List<java.lang.String> getElementList(EventContentType type,
                                                       java.lang.String listID)

getNexusNameToIDMap

public java.util.Map<java.lang.String,java.lang.String> getNexusNameToIDMap(EventContentType type,
                                                                            java.lang.String listID)

Returns a map object that translates between a Nexus name and the JPhyloIO ID of the according event.

Parameters:

type - the event type of events of the requested ID

listID - the JPhyloIO ID of the according OTU list start event

Returns:

the map

Throws:

java.lang.NullPointerException - if listID is null

getTreesTranslationTable

public NexusTranslationTable getTreesTranslationTable()

Returns the current Nexus translation table object. If none is present, a new empty instance will be created and stored in the shared information map.

Returns:

the current table

getMatrixWidthsMap

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

Returns a map object that stores the widths of all sequence matrices encountered until now. It is used by readers of set commands to determine the last column of a matrix, which may be referred by a set definition.

Returns:

the map