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Class iubio.readseq.XmlSeqReader

java.lang.Object
   |
   +----iubio.readseq.XmlSeqReader

public class XmlSeqReader
extends java.lang.Object
implements iubio.readseq.BioseqReaderIface, iubio.readseq.BioseqDocVals, org.xml.sax.EntityResolver, org.xml.sax.DTDHandler, org.xml.sax.DocumentHandler, org.xml.sax.ErrorHandler

Variable Index

 o readChunkSize
 o showErrors

Constructor Index

 o XmlSeqReader()

Method Index

 o characters(char[], int, int)
 o copyto(SeqFileInfo)
 o doRead()
 o endDocument()
 o endElement(String)
 o endOfFile()
 o error(SAXParseException)
 o fatalError(SAXParseException)
 o formatID()
 o getNseq()
 o ignorableWhitespace(char[], int, int)
 o notationDecl(String, String, String)
 o processingInstruction(String, String)
 o readOne(int)
 o readTo(BioseqWriterIface, int)
 o reset()
 o resetSeq()
 o resolveEntity(String, String)
 o seqLen()
 o setChoice(int)
 o setDocumentLocator(Locator)
 o setFormatID(int)
 o setInput(Reader)
 o setSeqName(String)
 o skipPastHeader(int)
 o startDocument()
 o startElement(String, AttributeList)
 o unparsedEntityDecl(String, String, String, String)
 o warning(SAXParseException)

Variables

 o showErrors
 public boolean showErrors
 o readChunkSize
 public static int readChunkSize

Constructors

 o XmlSeqReader
 public XmlSeqReader()

Methods

 o formatID
 public int formatID()
 o setFormatID
 public void setFormatID(int id)
 o seqLen
 public int seqLen()
 o getNseq
 public int getNseq()
 o setChoice
 public void setChoice(int seqchoice)
 o setInput
 public void setInput(java.io.Reader ins)
 o doRead
 public void doRead() throws java.io.IOException
 o readTo
 public void readTo(iubio.readseq.BioseqWriterIface writer,
                    int skipHeaderLines) throws java.io.IOException
 o readOne
 public iubio.readseq.SeqFileInfo readOne(int whichEntry) throws java.io.IOException
 o endOfFile
 public boolean endOfFile()
 o reset
 public void reset()
 o skipPastHeader
 public void skipPastHeader(int skiplines)
 o copyto
 public void copyto(iubio.readseq.SeqFileInfo si)
 o setSeqName
 public void setSeqName(java.lang.String name)
 o resetSeq
 public void resetSeq()
 o error
 public void error(org.xml.sax.SAXParseException e) throws org.xml.sax.SAXException
 o fatalError
 public void fatalError(org.xml.sax.SAXParseException e) throws org.xml.sax.SAXException
 o warning
 public void warning(org.xml.sax.SAXParseException e) throws org.xml.sax.SAXException
 o startDocument
 public void startDocument() throws org.xml.sax.SAXException
 o endDocument
 public void endDocument() throws org.xml.sax.SAXException
 o startElement
 public void startElement(java.lang.String name,
                          org.xml.sax.AttributeList atts) throws org.xml.sax.SAXException
 o endElement
 public void endElement(java.lang.String name) throws org.xml.sax.SAXException
 o characters
 public void characters(char ch[],
                        int start,
                        int length) throws org.xml.sax.SAXException
 o ignorableWhitespace
 public void ignorableWhitespace(char ch[],
                                 int start,
                                 int length) throws org.xml.sax.SAXException
 o processingInstruction
 public void processingInstruction(java.lang.String target,
                                   java.lang.String data) throws org.xml.sax.SAXException
 o resolveEntity
 public org.xml.sax.InputSource resolveEntity(java.lang.String publicId,
                                              java.lang.String systemId) throws org.xml.sax.SAXException
 o notationDecl
 public void notationDecl(java.lang.String name,
                          java.lang.String publicId,
                          java.lang.String systemId)
 o unparsedEntityDecl
 public void unparsedEntityDecl(java.lang.String name,
                                java.lang.String publicId,
                                java.lang.String systemId,
                                java.lang.String notationName)
 o setDocumentLocator
 public void setDocumentLocator(org.xml.sax.Locator locator)

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