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Class iubio.readseq.XmlSeqWriter

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

public class XmlSeqWriter
extends java.lang.Object
implements iubio.readseq.BioseqWriterIface

Variable Index

 o dtdUrl
 o includeDTD
 o showErrors

Constructor Index

 o XmlSeqWriter()

Method Index

 o close()
 o formatID()
 o getChecksum()
 o getDTD(String)
 o getError()
 o getNseq()
 o getOutputTranslation()
 o getReverseComplement()
 o seqLen()
 o setChecksum(boolean)
 o setFeatureExtraction(Hashtable)
 o setFormatID(int)
 o setMask(SeqFileInfo, String)
 o setNseq(int)
 o setOutput(OutputStream)
 o setOutput(Writer)
 o setOutputTranslation(OutBiobaseIntf)
 o setReverseComplement(boolean)
 o setSeq(Object, int, int, String, Object, int, int)
 o setSeq(SeqFileInfo)
per sequence
 o setSeqName(String)
 o setSeqPart(int)
 o wantsDocument()
 o writeDoc()
write documentation for record, form where all doc is known from setSeq()
 o writeHeader()
 o writeRecordEnd()
end of seq record
 o writeRecordStart()
start of sequence record, initialize per seq, subclasses customize as needed
 o writeSeq()
write sequence data, when all seq is known from setSeq()
 o writeSeqEnd()
end of seq before newline or end of record
 o writeSeqRecord()
 o writeTrailer()

Variables

 o showErrors
 public boolean showErrors
 o includeDTD
 public static boolean includeDTD
 o dtdUrl
 public static java.lang.String dtdUrl

Constructors

 o XmlSeqWriter
 public XmlSeqWriter()

Methods

 o formatID
 public int formatID()
 o setFormatID
 public void setFormatID(int id)
 o getChecksum
 public boolean getChecksum()
 o setChecksum
 public void setChecksum(boolean turnon)
 o getReverseComplement
 public boolean getReverseComplement()
 o setReverseComplement
 public void setReverseComplement(boolean turnon)
 o setOutput
 public final void setOutput(java.io.OutputStream outs)
 o setOutput
 public void setOutput(java.io.Writer outs)
 o close
 public void close() throws java.io.IOException
 o getError
 public int getError()
 o setOutputTranslation
 public void setOutputTranslation(iubio.readseq.OutBiobaseIntf tester)
 o getOutputTranslation
 public iubio.readseq.OutBiobaseIntf getOutputTranslation()
 o setFeatureExtraction
 public void setFeatureExtraction(java.util.Hashtable featurelist)
 o wantsDocument
 public boolean wantsDocument()
 o seqLen
 public int seqLen()
 o getNseq
 public int getNseq()
 o setNseq
 public void setNseq(int nsequences)
 o getDTD
 public java.lang.String getDTD(java.lang.String rezname)
 o writeHeader
 public void writeHeader() throws java.io.IOException
 o writeTrailer
 public void writeTrailer()
 o setSeq
 public boolean setSeq(iubio.readseq.SeqFileInfo si)
per sequence

 o setMask
 public boolean setMask(iubio.readseq.SeqFileInfo si,
                        java.lang.String masktag)
 o setSeq
 public boolean setSeq(java.lang.Object seqob,
                       int offset,
                       int length,
                       java.lang.String seqname,
                       java.lang.Object seqdoc,
                       int atseq,
                       int basepart)
 o setSeqName
 public void setSeqName(java.lang.String name)
 o setSeqPart
 public void setSeqPart(int basepart)
 o writeSeqRecord
 public void writeSeqRecord() throws java.io.IOException
 o writeSeq
 public void writeSeq()
write sequence data, when all seq is known from setSeq()

 o writeSeqEnd
 public void writeSeqEnd()
end of seq before newline or end of record

 o writeRecordStart
 public void writeRecordStart()
start of sequence record, initialize per seq, subclasses customize as needed

 o writeRecordEnd
 public void writeRecordEnd()
end of seq record

 o writeDoc
 public void writeDoc()
write documentation for record, form where all doc is known from setSeq()


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