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

java.lang.Object
  extended by info.bioinfweb.treegraph.document.io.AbstractDocumentReader
      extended by 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 transfered to the internal data structure and therefor a not written back to a document generated with TreeGraph 2.
If defined attributes 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, loadLogger
 
Fields inherited from interface info.bioinfweb.treegraph.document.io.xtg.XTGConstants
ALIGN_LEFT, ALIGN_RIGHT, ALIGN_TREE_WIDTH, ATTR_ALIGN_TO_SUBTREE, 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_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_LONG_INTERVAL, ATTR_MIN_BRANCH_LENGTH, ATTR_MIN_SPACE_ABOVE, ATTR_MIN_SPACE_BELOW, ATTR_MIN_TREE_DISTANCE, 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_START, ATTR_SCALE_BAR_WIDTH, ATTR_SHOW_INTERNAL_LINES, ATTR_SHOW_NULL_LINES, 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_WIDTH, BRANCH_LENGTH_UNITS, FULL_SCHEMA_LOCATION, MILLIMETERS, NAMESPACE_URI, 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_HIDDEN_DATA, TAG_ICON_LABEL, TAG_LABEL_MARGIN, TAG_LEAF_MARGIN, TAG_LEGEND, TAG_LEGEND_MARGIN, TAG_NODE, TAG_PIE_CHART_ID, TAG_PIE_CHART_IDS, TAG_PIE_CHART_LABEL, TAG_ROOT, TAG_SCALE_BAR, TAG_TEXT_LABEL, TAG_TREE, VERSION
 
Constructor Summary
XTGReader()
           
 
Method Summary
private  void checkNameSpace(StartElement element)
          Outputs warnings about the XML namespace and sets the version of document.
 Document read(File file, LoadLogger loadLogger, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)
          If you want to implement file specific functionalities you should override this method.
 Document read(InputStream stream, LoadLogger loadLogger, NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, TreeSelector selector, boolean translateInternalNodes)
           
private  void readAnchor(StartElement rootElement, 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 readGraphicalLabelDimensions(GraphicalLabelFormats f, StartElement element)
           
private  void readHiddenData(StartElement element, HiddenDataMap list)
           
private  void readIconLabel(StartElement rootElement, Labels labels)
           
private  void readLabelData(StartElement rootElement, Label l)
          This method also reads the subelements of the root element.
private  void readLegend(StartElement rootElement, Legends legends)
           
private  void readLineAttr(LineFormats f, StartElement element)
           
private  void readMargin(Margin m, StartElement element)
           
private  void readPieChartIDs(PieChartLabel l)
           
private  void readPieChartLabel(StartElement rootElement, Labels labels)
           
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 readTextLabel(StartElement rootElement, Labels labels)
           
private  void readTextStyleAttr(TextFormats f, StartElement element)
           
private  void readTree(StartElement rootElement)
           
 
Methods inherited from class info.bioinfweb.treegraph.document.io.AbstractDocumentReader
reachElementEnd, reachElementEnd, 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)

readMargin

private void readMargin(Margin m,
                        StartElement element)
                 throws XMLStreamException
Parameters:
m -
element -
Throws:
XMLStreamException
Since:
2.0.41

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

readPieChartIDs

private void readPieChartIDs(PieChartLabel l)
                      throws XMLStreamException
Throws:
XMLStreamException

readLabelData

private void readLabelData(StartElement rootElement,
                           Label l)
                    throws XMLStreamException
This method also reads the subelements of the root element. Therefor no more attributes can be read after the call of this method.

Parameters:
rootElement -
label -
Throws:
XMLStreamException

readTextLabel

private void readTextLabel(StartElement rootElement,
                           Labels labels)
                    throws XMLStreamException
Throws:
XMLStreamException

readGraphicalLabelDimensions

private void readGraphicalLabelDimensions(GraphicalLabelFormats f,
                                          StartElement element)

readIconLabel

private void readIconLabel(StartElement rootElement,
                           Labels labels)
                    throws XMLStreamException
Throws:
XMLStreamException

readPieChartLabel

private void readPieChartLabel(StartElement rootElement,
                               Labels labels)
                        throws XMLStreamException
Throws:
XMLStreamException

readHiddenData

private void readHiddenData(StartElement element,
                            HiddenDataMap list)
                     throws XMLStreamException
Throws:
XMLStreamException

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)
                   throws XMLStreamException
Throws:
XMLStreamException

readAnchor

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

readLegend

private void readLegend(StartElement rootElement,
                        Legends legends)
                 throws XMLStreamException
Throws:
XMLStreamException

readTree

private void readTree(StartElement rootElement)
               throws XMLStreamException
Throws:
XMLStreamException

readDocument

private void readDocument(StartElement rootElement)
                   throws XMLStreamException
Throws:
XMLStreamException

checkNameSpace

private void checkNameSpace(StartElement element)
Outputs warnings about the XML namespace and sets the version of document.

Parameters:
element -

read

public Document read(InputStream stream,
                     LoadLogger loadLogger,
                     NodeBranchDataAdapter internalAdapter,
                     NodeBranchDataAdapter branchLengthsAdapter,
                     TreeSelector selector,
                     boolean translateInternalNodes)
              throws Exception
Specified by:
read in interface DocumentReader
Throws:
Exception

read

public Document read(File file,
                     LoadLogger loadLogger,
                     NodeBranchDataAdapter internalAdapter,
                     NodeBranchDataAdapter 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, NodeBranchDataAdapter, int)
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