public class XTGEventReader extends AbstractXMLEventReader<XMLReaderStreamDataProvider<XTGEventReader>> implements XTGConstants
This reader supports reading pyhlogenetic trees and nested annotations. Reading scale bar and legend information
is not supported. In order to serialize the hierarchical structure of node and branch tags,
according events are fired at the end of a node or the start of a new node, depending on what happens first.
This avoids buffering large amounts of data longer than necessary.
Predefined elements as well as attributes are represented by metaevents. If necessary these events are grouped by
ResourceMetadataEvents. Textual or decimal annotation values (according to the is_decimal attribute}
are parsed to the according Java objects.
ReadWriteParameterNames#KEY_ALLOW_DEFAULT_NAMESPACEReadWriteParameterNames#KEY_LOGGERINTERNAL_USE_NAMESPACE, TAG_PARENT_OF_ROOTALIGN_LEFT, ALIGN_RIGHT, ALIGN_TREE_WIDTH, ATTR_ADAPTER_ID, ATTR_ADAPTER_NAME, ATTR_ADAPTER_PURPOSE, ATTR_ALIGN_TO_SUBTREE, ATTR_ANCHOR_0, ATTR_ANCHOR_1, ATTR_BG_COLOR, ATTR_BOTTOM, ATTR_BRANCH_LENGTH, ATTR_BRANCH_LENGTH_SCALE, ATTR_CAPTION_LINK_TYPE, ATTR_CAPTION_TYPE, ATTR_CONSTANT_WIDTH, ATTR_DECIMAL_FORMAT, ATTR_EDGE_RADIUS, ATTR_FONT_FAMILY, ATTR_HEIGHT, ATTR_ICON, ATTR_ICON_FILLED, ATTR_ICON_HEIGHT, ATTR_ICON_WIDTH, ATTR_ID, ATTR_LABEL_ABOVE, ATTR_LABEL_HEIGHT, ATTR_LABEL_SPACING, ATTR_LABEL_WIDTH, ATTR_LEFT, ATTR_LEGEND_POS, ATTR_LEGEND_SPACING, ATTR_LEGEND_STYLE, ATTR_LINE_COLOR, ATTR_LINE_NO, ATTR_LINE_POS, ATTR_LINE_WIDTH, ATTR_LOCALE_COUNTRY, ATTR_LOCALE_LANG, ATTR_LOCALE_VARIANT, ATTR_MIN_BRANCH_LENGTH, ATTR_MIN_SPACE_ABOVE, ATTR_MIN_SPACE_BELOW, ATTR_MIN_TREE_DISTANCE, ATTR_PIE_CAPTION, ATTR_PIE_COLOR, ATTR_POSITION_LABELS_TO_LEFT, ATTR_RIGHT, ATTR_SCALE_BAR_ALIGN, ATTR_SCALE_BAR_DISTANCE, ATTR_SCALE_BAR_HEIGHT, ATTR_SCALE_BAR_INCREASE, ATTR_SCALE_BAR_LONG_INTERVAL, ATTR_SCALE_BAR_SMALL_INTERVAL, ATTR_SCALE_BAR_START, ATTR_SCALE_BAR_WIDTH, ATTR_SHOW_INTERNAL_LINES, ATTR_SHOW_NULL_LINES, ATTR_SHOW_ROOTED, ATTR_SHOW_SCALE_BAR, ATTR_SHOW_TITLE, ATTR_TEXT, ATTR_TEXT_COLOR, ATTR_TEXT_HEIGHT, ATTR_TEXT_IS_DECIMAL, ATTR_TEXT_ORIENTATION, ATTR_TEXT_STYLE, ATTR_TOP, ATTR_UNIQUE_NAME, ATTR_WIDTH, BRANCH_LENGTH_UNITS, DATA_TYPE_COLOR, DATA_TYPE_LEGEND_STYLE, DATA_TYPE_PIE_CHART_LABEL_CAPTION_LINK_TYPE, DATA_TYPE_PIE_CHART_LABEL_CAPTION_TYPE, DATA_TYPE_SCALE_BAR_ALIGNMENT, DATA_TYPE_SCALE_VALUE, DATA_TYPE_TEXT_ORIENTATION, DEPRECATED_VALUE_LEAVES_ADAPTER, FULL_SCHEMA_LOCATION, MILLIMETERS, NAMESPACE_URI, ORIENT_DOWN, ORIENT_HORIZONTAL, ORIENT_UP, PRE_LEGEND_ANCHOR, PREDICATE_BRANCH_CONSTANT_WIDTH, PREDICATE_BRANCH_MIN_LENGTH, PREDICATE_BRANCH_MIN_SPACE_ABOVE, PREDICATE_BRANCH_MIN_SPACE_BELOW, PREDICATE_COLUMN_ID, PREDICATE_DATA_ID, PREDICATE_DATA_ID_VALUE, PREDICATE_DATA_IDS, PREDICATE_DECIMAL_FORMAT, PREDICATE_DOCUMENT_MARGIN, PREDICATE_EDGE_RADIUS, PREDICATE_FONT_FAMILY, PREDICATE_GLOBAL_FORMATS, PREDICATE_GLOBAL_FORMATS_ALIGN_TO_SUBTREE, PREDICATE_GLOBAL_FORMATS_BG_COLOR, PREDICATE_GLOBAL_FORMATS_BRANCH_LENGTH_SCALE, PREDICATE_GLOBAL_FORMATS_POSITION_LABELS_TO_LEFT, PREDICATE_GLOBAL_FORMATS_SHOW_ROOTED, PREDICATE_GLOBAL_FORMATS_SHOW_SCALE_BAR, PREDICATE_HEIGHT, PREDICATE_ICON_LABEL, PREDICATE_ICON_LABEL_ICON, PREDICATE_ICON_LABEL_ICON_FILLED, PREDICATE_INVISIBLE_DATA, PREDICATE_IS_DECIMAL, PREDICATE_LABEL_ABOVE, PREDICATE_LABEL_LINE_NO, PREDICATE_LABEL_LINE_POS, PREDICATE_LABEL_MARGIN, PREDICATE_LEAF_MARGIN, PREDICATE_LEGEND, PREDICATE_LEGEND_ANCHOR_0, PREDICATE_LEGEND_ANCHOR_1, PREDICATE_LEGEND_MARGIN, PREDICATE_LEGEND_MIN_TREE_DISTANCE, PREDICATE_LEGEND_ORIENTATION, PREDICATE_LEGEND_POSITION, PREDICATE_LEGEND_SPACING, PREDICATE_LEGEND_STYLE, PREDICATE_LINE_COLOR, PREDICATE_LINE_WIDTH, PREDICATE_LOCALE_COUNTRY, PREDICATE_LOCALE_LANG, PREDICATE_LOCALE_VARIANT, PREDICATE_MARGIN_BOTTOM, PREDICATE_MARGIN_LEFT, PREDICATE_MARGIN_RIGHT, PREDICATE_MARGIN_TOP, PREDICATE_NODE_BRANCH_DATA_ADAPTERS, PREDICATE_NODE_BRANCH_DATA_ADAPTERS_ADAPTER, PREDICATE_NODE_BRANCH_DATA_ADAPTERS_ADAPTER_ID, PREDICATE_NODE_BRANCH_DATA_ADAPTERS_ADAPTER_NAME, PREDICATE_NODE_BRANCH_DATA_ADAPTERS_ADAPTER_PURPOSE, PREDICATE_NODE_UNIQUE_NAME, PREDICATE_PIE_CAPTION, PREDICATE_PIE_CHART_LABEL, PREDICATE_PIE_CHART_LABEL_CAPTION_LINK_TYPE, PREDICATE_PIE_CHART_LABEL_CAPTION_TYPE, PREDICATE_PIE_CHART_LABEL_INTERNAL_LINES, PREDICATE_PIE_CHART_LABEL_NULL_LINES, PREDICATE_PIE_CHART_LABEL_SHOW_TITLE, PREDICATE_PIE_COLOR, PREDICATE_SCALE_BAR, PREDICATE_SCALE_BAR_ALIGN, PREDICATE_SCALE_BAR_INCREASING, PREDICATE_SCALE_BAR_LONG_INTERVAL, PREDICATE_SCALE_BAR_SMALL_INTERVAL, PREDICATE_SCALE_BAR_START_LEFT, PREDICATE_SCALE_BAR_TREE_DISTANCE, PREDICATE_TEXT, PREDICATE_TEXT_COLOR, PREDICATE_TEXT_HEIGHT, PREDICATE_TEXT_LABEL, PREDICATE_TEXT_STYLE, PREDICATE_WIDTH, STYLE_BOLD, STYLE_BRACE, STYLE_BRACKET, STYLE_ITALIC, STYLE_UNDERLINE, TAG_ADAPTER, TAG_BRANCH, TAG_DOCUMENT_MARGIN, TAG_GLOBAL_FORMATS, TAG_HIDDEN_DATA, TAG_ICON_LABEL, TAG_LABEL_MARGIN, TAG_LEAF_MARGIN, TAG_LEGEND, TAG_LEGEND_MARGIN, TAG_NODE, TAG_NODE_BRANCH_DATA_ADAPTERS, TAG_PIE_CHART_ID, TAG_PIE_CHART_IDS, TAG_PIE_CHART_LABEL, TAG_ROOT, TAG_SCALE_BAR, TAG_TEXT_LABEL, TAG_TREE, VALUE_ADAPTER_PURPOSE_PREFIX, VALUE_LEAVES_ADAPTER, VALUE_SUPPORT_VALUES_ADAPTER, VERSION, XTG, XTG_DATA_TYPE_NAMESPACE, XTG_FORMAT_NAME, XTG_NAMESPACE_PREFIX, XTG_PREDICATE_NAMESPACEATTRIBUTE_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| Constructor and Description |
|---|
XTGEventReader(java.io.File file,
ReadWriteParameterMap parameters) |
XTGEventReader(java.io.InputStream stream,
ReadWriteParameterMap parameters) |
XTGEventReader(java.io.Reader reader,
ReadWriteParameterMap parameters) |
XTGEventReader(javax.xml.stream.XMLEventReader xmlReader,
ReadWriteParameterMap parameters) |
| Modifier and Type | Method and Description |
|---|---|
protected void |
fillMap() |
java.lang.String |
getFormatID()
Returns a string ID uniquely identifying the target format of this instance.
|
close, createMetaXMLEventReader, createMetaXMLStreamReader, createStreamDataProvider, getElementReader, getElementReaderMap, getEncounteredTags, getNamespaceContext, getXMLReader, isAllowDefaultNamespace, parseQName, putElementReader, readNextEventaddEventListener, fireEvent, getCurrentEventCollection, getIDManager, getLastNonCommentEvent, getParameters, getParentInformation, getPreviousEvent, getSequenceTokensEventManager, getStreamDataProvider, getUpcomingEvents, hasNextEvent, hasSpecialEventCollection, isBeforeFirstAccess, next, nextOfType, peek, removeEventListener, resetCurrentEventCollection, setCurrentEventCollectionclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitaddEventListener, getLastNonCommentEvent, getParentInformation, getPreviousEvent, hasNextEvent, next, nextOfType, peek, removeEventListenerpublic XTGEventReader(java.io.File file, ReadWriteParameterMap parameters) throws java.io.IOException, javax.xml.stream.XMLStreamException
java.io.IOExceptionjavax.xml.stream.XMLStreamExceptionpublic XTGEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters) throws java.io.IOException, javax.xml.stream.XMLStreamException
java.io.IOExceptionjavax.xml.stream.XMLStreamExceptionpublic XTGEventReader(java.io.Reader reader, ReadWriteParameterMap parameters) throws java.io.IOException, javax.xml.stream.XMLStreamException
java.io.IOExceptionjavax.xml.stream.XMLStreamExceptionpublic XTGEventReader(javax.xml.stream.XMLEventReader xmlReader, ReadWriteParameterMap parameters)
public java.lang.String getFormatID()
JPhyloIOFormatSpecificObjectJPhyloIOReaderWriterFactory.getFormatInfo(String).
Third party developers that create readers or writers for additional formats must make sure to use a globally unique
format ID. It is strongly recommended to use owned reverse domain names for this (e.g.
org.example.additionalformat).
getFormatID in interface JPhyloIOFormatSpecificObjectJPhyloIOReaderWriterFactory.getFormatInfo(String)protected void fillMap()
fillMap in class AbstractXMLEventReader<XMLReaderStreamDataProvider<XTGEventReader>>