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