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## edu.msu.cme.rdp.classifier.rrnaclassifier
Class TreeFileParser

    java.lang.Object
      org.xml.sax.helpers.DefaultHandler
          edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParser

All Implemented Interfaces:
  org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler

     class TreeFileParser

extends org.xml.sax.helpers.DefaultHandler

A parser to parse a reader containing taxonomic training information. Note: The first TreeNode is the root TreeNode.

Field Summary
`private HierarchyTree` | `root`
`private java.util.Stack` | `treeNodeStack`

Constructor Summary
`TreeFileParser()` Creates a new instance of TreeFileParser.

Method Summary
`(package private) HierarchyTree` | `createTree(java.io.Reader in, HierarchyVersion version)` Reads from a reader that contains the information for each treenode.
`void` | `endElement(java.lang.String str, java.lang.String str1, java.lang.String str2)`
`void` | `error(org.xml.sax.SAXParseException e)`
`private void` | `load(java.lang.String document)`
`void` | `startElement(java.lang.String namespaceURI, java.lang.String lName, java.lang.String qName, org.xml.sax.Attributes attrs)`

Methods inherited from class org.xml.sax.helpers.DefaultHandler
`characters, endDocument, endPrefixMapping, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, skippedEntity, startDocument, startPrefixMapping, unparsedEntityDecl, warning`

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Field Detail

### treeNodeStack

    private java.util.Stack treeNodeStack

### root

    private HierarchyTree root

Constructor Detail

### TreeFileParser

    TreeFileParser()

  Creates a new instance of TreeFileParser.

Method Detail

### createTree

    HierarchyTree createTree(java.io.Reader in,
                             HierarchyVersion version)
                       throws java.io.IOException,
                              TrainingDataException

  Reads from a reader that contains the information for each treenode. Creates all the HierarchyTrees and returns the root of the trees. Note: The first TreeNode is the root TreeNode. The version information should be obtained from the other files first.

  Throws:
    `java.io.IOException`
    `TrainingDataException`

### load

    private void load(java.lang.String document)
               throws TrainingDataException,
                      java.io.IOException

  Throws:
    `TrainingDataException`
    `java.io.IOException`

### startElement

    public void startElement(java.lang.String namespaceURI,
                             java.lang.String lName,
                             java.lang.String qName,
                             org.xml.sax.Attributes attrs)
                      throws org.xml.sax.SAXException

  Specified by:
    `startElement` in interface `org.xml.sax.ContentHandler`
  Overrides:
    `startElement` in class `org.xml.sax.helpers.DefaultHandler`
  Throws:
    `org.xml.sax.SAXException`

### endElement

    public void endElement(java.lang.String str,
                           java.lang.String str1,
                           java.lang.String str2)
                    throws org.xml.sax.SAXException

  Specified by:
    `endElement` in interface `org.xml.sax.ContentHandler`
  Overrides:
    `endElement` in class `org.xml.sax.helpers.DefaultHandler`
  Throws:
    `org.xml.sax.SAXException`

### error

    public void error(org.xml.sax.SAXParseException e)
               throws org.xml.sax.SAXException

  Specified by:
    `error` in interface `org.xml.sax.ErrorHandler`
  Overrides:
    `error` in class `org.xml.sax.helpers.DefaultHandler`
  Throws:
    `org.xml.sax.SAXException`

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