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Class iubio.readseq.XmlSeqWriter
java.lang.Object
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+----iubio.readseq.XmlSeqWriter
- public class XmlSeqWriter
- extends java.lang.Object
- implements iubio.readseq.BioseqWriterIface
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dtdUrl
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includeDTD
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showErrors
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XmlSeqWriter()
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close()
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formatID()
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getChecksum()
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getDTD(String)
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getError()
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getNseq()
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getOutputTranslation()
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getReverseComplement()
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seqLen()
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setChecksum(boolean)
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setFeatureExtraction(Hashtable)
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setFormatID(int)
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setMask(SeqFileInfo, String)
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setNseq(int)
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setOutput(OutputStream)
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setOutput(Writer)
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setOutputTranslation(OutBiobaseIntf)
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setReverseComplement(boolean)
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setSeq(Object, int, int, String, Object, int, int)
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setSeq(SeqFileInfo)
- per sequence
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setSeqName(String)
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setSeqPart(int)
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wantsDocument()
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writeDoc()
- write documentation for record, form where all doc is known from setSeq()
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writeHeader()
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writeRecordEnd()
- end of seq record
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writeRecordStart()
- start of sequence record, initialize per seq, subclasses customize as needed
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writeSeq()
- write sequence data, when all seq is known from setSeq()
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writeSeqEnd()
- end of seq before newline or end of record
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writeSeqRecord()
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writeTrailer()
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showErrors
public boolean showErrors
includeDTD
public static boolean includeDTD
dtdUrl
public static java.lang.String dtdUrl
XmlSeqWriter
public XmlSeqWriter()
formatID
public int formatID()
setFormatID
public void setFormatID(int id)
getChecksum
public boolean getChecksum()
setChecksum
public void setChecksum(boolean turnon)
getReverseComplement
public boolean getReverseComplement()
setReverseComplement
public void setReverseComplement(boolean turnon)
setOutput
public final void setOutput(java.io.OutputStream outs)
setOutput
public void setOutput(java.io.Writer outs)
close
public void close() throws java.io.IOException
getError
public int getError()
setOutputTranslation
public void setOutputTranslation(iubio.readseq.OutBiobaseIntf tester)
getOutputTranslation
public iubio.readseq.OutBiobaseIntf getOutputTranslation()
setFeatureExtraction
public void setFeatureExtraction(java.util.Hashtable featurelist)
wantsDocument
public boolean wantsDocument()
seqLen
public int seqLen()
getNseq
public int getNseq()
setNseq
public void setNseq(int nsequences)
getDTD
public java.lang.String getDTD(java.lang.String rezname)
writeHeader
public void writeHeader() throws java.io.IOException
writeTrailer
public void writeTrailer()
setSeq
public boolean setSeq(iubio.readseq.SeqFileInfo si)
- per sequence
setMask
public boolean setMask(iubio.readseq.SeqFileInfo si,
java.lang.String masktag)
setSeq
public boolean setSeq(java.lang.Object seqob,
int offset,
int length,
java.lang.String seqname,
java.lang.Object seqdoc,
int atseq,
int basepart)
setSeqName
public void setSeqName(java.lang.String name)
setSeqPart
public void setSeqPart(int basepart)
writeSeqRecord
public void writeSeqRecord() throws java.io.IOException
writeSeq
public void writeSeq()
- write sequence data, when all seq is known from setSeq()
writeSeqEnd
public void writeSeqEnd()
- end of seq before newline or end of record
writeRecordStart
public void writeRecordStart()
- start of sequence record, initialize per seq, subclasses customize as needed
writeRecordEnd
public void writeRecordEnd()
- end of seq record
writeDoc
public void writeDoc()
- write documentation for record, form where all doc is known from setSeq()
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