info.bioinfweb.treegraph.document.io.xtg
Class XTGReader

java.lang.Object
  info.bioinfweb.treegraph.document.io.AbstractDocumentReader
      info.bioinfweb.treegraph.document.io.xtg.XTGReader

All Implemented Interfaces:

DocumentReader, XTGConstants

public class XTGReader
extends AbstractDocumentReader
implements XTGConstants

Reads the TreeGraph 2 specific XML format (*.xtg).
If the document contains additional (not defined tags) they are ignored. Note that they can not tranfered to the internal data structure and therefor a not written back to a document generated with TreeGraph 2.
If defined attrubutes are missing in the document, standard values are used.

Author:

Ben Stöver

Field Summary

private XMLEventReader

reader

Fields inherited from class info.bioinfweb.treegraph.document.io.AbstractDocumentReader

document

Fields inherited from interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants

ALIGN_LEFT, ALIGN_RIGHT, ALIGN_TREE_WIDTH, ATTR_BG_COLOR, ATTR_BOTTOM, ATTR_BRANCH_LENGTH, ATTR_BRANCH_LENGTH_SCALE, ATTR_CONSTANT_WIDTH, ATTR_DECIMAL_FORMAT, ATTR_EDGE_RADIUS, ATTR_FONT_FAMILY, ATTR_HEIGHT, ATTR_HORIZ_LABEL_SPACING, ATTR_ID, ATTR_LABEL_ABOVE, ATTR_LABEL_BLOCK_DISTANCE, 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_LONG_INTERVAL, ATTR_MIN_BRANCH_LENGTH, ATTR_MIN_SPACE_ABOVE, ATTR_MIN_SPACE_BELOW, ATTR_MIN_TREE_DISTANCE, ATTR_RIGHT, ATTR_SCALE_BAR_ALIGN, ATTR_SCALE_BAR_DISTANCE, ATTR_SCALE_BAR_HEIGHT, ATTR_SCALE_BAR_INCREASE, ATTR_SCALE_BAR_START, ATTR_SCALE_BAR_WIDTH, ATTR_SHOW_ROOTED, ATTR_SHOW_SCALE_BAR, ATTR_SMALL_INTERVAL, ATTR_TEXT, ATTR_TEXT_COLOR, ATTR_TEXT_HEIGHT, ATTR_TEXT_IS_DECIMAL, ATTR_TEXT_ORIENTATION, ATTR_TEXT_STYLE, ATTR_TOP, ATTR_UNIQUE_NAME, ATTR_VERT_LABEL_SPACING, ATTR_WIDTH, BRANCH_LENGTH_UNITS, MILLIMETERS, ORIENT_DOWN, ORIENT_HORIZONTAL, ORIENT_UP, PRE_LEGEND_ANCHOR, STYLE_BOLD, STYLE_BRACE, STYLE_BRACKET, STYLE_ITALIC, STYLE_UNDERLINE, TAG_BRANCH, TAG_DOC_MARGIN, TAG_GLOBAL_FORMATS, TAG_GLOBAL_LABEL_FORMATS, TAG_GLOBAL_LEGEND_FORMATS, TAG_HIDDEN_DATA, TAG_ICON_LABEL, TAG_LABEL_BLOCK_MARGIN, TAG_LEAF_MARGIN, TAG_LEGEND, TAG_LEGEND_MARGIN, TAG_MIN_DOC_DIM, TAG_NODE, TAG_NODE_MARGIN, TAG_ROOT, TAG_SCALE_BAR, TAG_TEXT_LABEL, TAG_TREE

Constructor Summary

XTGReader()

Method Summary

Document	read(File file, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes) If you want to implement file specific functionalities you should override this method.
Document	read(InputStream stream, NodeDataAdapter internalAdapter, NodeDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)
private void	readAnchor(StartElement element, Legend l, int no)
private void	readBranch(StartElement rootElement, Branch b)
private void	readDecimalFormat(TextFormats f, StartElement element, String prefix)
private void	readDistanceDimensionAttr(DistanceDimension d, StartElement element)
private void	readDistanceValueAttr(DistanceValue value, StartElement element, QName name)
private void	readDocument(StartElement rootElement)
private void	readGlobalFormats(StartElement rootElement)
private void	readGlobalLabelFormst(StartElement rootElement, GlobalFormats f)
private void	readGlobalLegendFormst(StartElement rootElement, GlobalFormats f)
private void	readHiddenData(StartElement element, HiddenDataMap list)
private void	readLabel(StartElement element, Labels labels)
private void	readLegend(StartElement element, Legends legends)
private void	readLineAttr(LineFormats f, StartElement element)
private void	readMarginAttr(Margin m, StartElement element)
private void	readScaleBar(StartElement element, ScaleBar s)
private void	readScaleValueAttr(ScaleValue value, StartElement element, QName name)
private Node	readSubtree(StartElement rootElement)
private void	readTextElementDataAttr(TextElementData data, StartElement element)
private void	readTextFormatsAttr(TextFormats f, StartElement element, String prefix)
private void	readTextStyleAttr(TextFormats f, StartElement element)
private void	readTree(StartElement rootElement)

Methods inherited from class info.bioinfweb.treegraph.document.io.AbstractDocumentReader

read, read, read, read

Methods inherited from class java.lang.Object

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

Field Detail

reader

private XMLEventReader reader

Constructor Detail

XTGReader

public XTGReader()

Method Detail

readDistanceValueAttr

private void readDistanceValueAttr(DistanceValue value,
                                   StartElement element,
                                   QName name)

readTextElementDataAttr

private void readTextElementDataAttr(TextElementData data,
                                     StartElement element)

readDistanceDimensionAttr

private void readDistanceDimensionAttr(DistanceDimension d,
                                       StartElement element)

readMarginAttr

private void readMarginAttr(Margin m,
                            StartElement element)

readGlobalLabelFormst

private void readGlobalLabelFormst(StartElement rootElement,
                                   GlobalFormats f)
                            throws XMLStreamException

Throws:

XMLStreamException

readGlobalLegendFormst

private void readGlobalLegendFormst(StartElement rootElement,
                                    GlobalFormats f)
                             throws XMLStreamException

Throws:

XMLStreamException

readGlobalFormats

private void readGlobalFormats(StartElement rootElement)
                        throws XMLStreamException

Throws:

XMLStreamException

readTextStyleAttr

private void readTextStyleAttr(TextFormats f,
                               StartElement element)

readDecimalFormat

private void readDecimalFormat(TextFormats f,
                               StartElement element,
                               String prefix)

readTextFormatsAttr

private void readTextFormatsAttr(TextFormats f,
                                 StartElement element,
                                 String prefix)

readLineAttr

private void readLineAttr(LineFormats f,
                          StartElement element)

readBranch

private void readBranch(StartElement rootElement,
                        Branch b)
                 throws XMLStreamException

Throws:

XMLStreamException

readLabel

private void readLabel(StartElement element,
                       Labels labels)

readHiddenData

private void readHiddenData(StartElement element,
                            HiddenDataMap list)

readSubtree

private Node readSubtree(StartElement rootElement)
                  throws XMLStreamException

Throws:

XMLStreamException

readScaleValueAttr

private void readScaleValueAttr(ScaleValue value,
                                StartElement element,
                                QName name)

readScaleBar

private void readScaleBar(StartElement element,
                          ScaleBar s)

readAnchor

private void readAnchor(StartElement element,
                        Legend l,
                        int no)

readLegend

private void readLegend(StartElement element,
                        Legends legends)

readTree

private void readTree(StartElement rootElement)
               throws XMLStreamException

Throws:

XMLStreamException

readDocument

private void readDocument(StartElement rootElement)
                   throws XMLStreamException

Throws:

XMLStreamException

read

public Document read(InputStream stream,
                     NodeDataAdapter internalAdapter,
                     NodeDataAdapter branchLengthsAdapter,
                     TreeSelector selector,
                     boolean translateInternalNodes)
              throws Exception

Specified by:

read in interface DocumentReader

Throws:

Exception

read

public Document read(File file,
                     NodeDataAdapter internalAdapter,
                     NodeDataAdapter branchLengthsAdapter,
                     TreeSelector selector,
                     boolean translateInternalNodes)
              throws Exception

Description copied from class: AbstractDocumentReader

If you want to implement file specific functionalities you should override this method. It is called by all other read-methods with a file as parameter.

Specified by:

read in interface DocumentReader

Overrides:

read in class AbstractDocumentReader

Throws:

Exception

See Also:

info.bioinfweb.treegraph.document.io.DocumentReader#read(java.io.File, NodeDataAdapter, int)