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Interface iubio.readseq.BioseqWriterIface

public abstract interface BioseqWriterIface
extends iubio.readseq.BioseqIoIface

Method Index

 o close()
 o getError()
 o getOutputTranslation()
get output translation/conversion of sequence chars
 o setFeatureExtraction(Hashtable)
set list of features to extract sequence of (good only if hasdoc)
 o setMask(SeqFileInfo, String)
 o setNseq(int)
per output stream
 o setOutput(OutputStream)
 o setOutput(Writer)
 o setOutputTranslation(OutBiobaseIntf)
set output translation/conversion of sequence chars
 o setSeq(Object, int, int, String, Object, int, int)
 o setSeq(SeqFileInfo)
per sequence
 o setSeqName(String)
 o wantsDocument()
true if reader should collect documentation/features for this writer.
 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 - called at end of writeSeq() generally
 o writeSeqRecord()
write a full seq record, given setSeq()

implementation does writeRecordStart(), writeDoc(), writeSeq(), writeRecordEnd()

 o writeTrailer()

Methods

 o setOutput
 public abstract void setOutput(java.io.Writer outs)
 o setOutput
 public abstract void setOutput(java.io.OutputStream outs)
 o close
 public abstract void close() throws java.io.IOException
 o getError
 public abstract int getError()
 o wantsDocument
 public abstract boolean wantsDocument()
true if reader should collect documentation/features for this writer. false can mean speedier processing.

 o setNseq
 public abstract void setNseq(int nsequences)
per output stream

 o writeHeader
 public abstract void writeHeader() throws java.io.IOException
 o writeTrailer
 public abstract void writeTrailer()
 o setSeq
 public abstract boolean setSeq(iubio.readseq.SeqFileInfo si)
per sequence

 o setMask
 public abstract boolean setMask(iubio.readseq.SeqFileInfo si,
                                 java.lang.String masktag)
 o setSeq
 public abstract 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 abstract void setSeqName(java.lang.String name)
 o setFeatureExtraction
 public abstract void setFeatureExtraction(java.util.Hashtable featurelist)
set list of features to extract sequence of (good only if hasdoc)

 o getOutputTranslation
 public abstract iubio.readseq.OutBiobaseIntf getOutputTranslation()
get output translation/conversion of sequence chars

 o setOutputTranslation
 public abstract void setOutputTranslation(iubio.readseq.OutBiobaseIntf tester)
set output translation/conversion of sequence chars

 o writeSeqRecord
 public abstract void writeSeqRecord() throws java.io.IOException
write a full seq record, given setSeq()

implementation does writeRecordStart(), writeDoc(), writeSeq(), writeRecordEnd()

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

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

 o writeSeq
 public abstract void writeSeq()
write sequence data, when all seq is known from setSeq()

 o writeSeqEnd
 public abstract void writeSeqEnd()
end of seq before newline or end of record - called at end of writeSeq() generally

 o writeRecordEnd
 public abstract void writeRecordEnd()
end of seq record


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