All Packages Class Hierarchy This Package Previous Next Index
Interface iubio.readseq.BioseqWriterIface
- public abstract interface BioseqWriterIface
- extends iubio.readseq.BioseqIoIface
-
close()
-
-
getError()
-
-
getOutputTranslation()
- get output translation/conversion of sequence chars
-
setFeatureExtraction(Hashtable)
- set list of features to extract sequence of (good only if hasdoc)
-
setMask(SeqFileInfo, String)
-
-
setNseq(int)
- per output stream
-
setOutput(OutputStream)
-
-
setOutput(Writer)
-
-
setOutputTranslation(OutBiobaseIntf)
- set output translation/conversion of sequence chars
-
setSeq(Object, int, int, String, Object, int, int)
-
-
setSeq(SeqFileInfo)
- per sequence
-
setSeqName(String)
-
-
wantsDocument()
- true if reader should collect documentation/features for this writer.
-
writeDoc()
- write documentation for record, form where all doc is known from setSeq()
-
writeHeader()
-
-
writeRecordEnd()
- end of seq record
-
writeRecordStart()
- start of sequence record, initialize per seq, subclasses customize as needed
-
writeSeq()
- write sequence data, when all seq is known from setSeq()
-
writeSeqEnd()
- end of seq before newline or end of record - called at end of writeSeq() generally
-
writeSeqRecord()
- write a full seq record, given setSeq()
implementation does writeRecordStart(), writeDoc(), writeSeq(), writeRecordEnd()
-
writeTrailer()
-
setOutput
public abstract void setOutput(java.io.Writer outs)
setOutput
public abstract void setOutput(java.io.OutputStream outs)
close
public abstract void close() throws java.io.IOException
getError
public abstract int getError()
wantsDocument
public abstract boolean wantsDocument()
- true if reader should collect documentation/features for this writer.
false can mean speedier processing.
setNseq
public abstract void setNseq(int nsequences)
- per output stream
writeHeader
public abstract void writeHeader() throws java.io.IOException
writeTrailer
public abstract void writeTrailer()
setSeq
public abstract boolean setSeq(iubio.readseq.SeqFileInfo si)
- per sequence
setMask
public abstract boolean setMask(iubio.readseq.SeqFileInfo si,
java.lang.String masktag)
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)
setSeqName
public abstract void setSeqName(java.lang.String name)
setFeatureExtraction
public abstract void setFeatureExtraction(java.util.Hashtable featurelist)
- set list of features to extract sequence of (good only if hasdoc)
getOutputTranslation
public abstract iubio.readseq.OutBiobaseIntf getOutputTranslation()
- get output translation/conversion of sequence chars
setOutputTranslation
public abstract void setOutputTranslation(iubio.readseq.OutBiobaseIntf tester)
- set output translation/conversion of sequence chars
writeSeqRecord
public abstract void writeSeqRecord() throws java.io.IOException
- write a full seq record, given setSeq()
implementation does writeRecordStart(), writeDoc(), writeSeq(), writeRecordEnd()
writeRecordStart
public abstract void writeRecordStart()
- start of sequence record, initialize per seq, subclasses customize as needed
writeDoc
public abstract void writeDoc()
- write documentation for record, form where all doc is known from setSeq()
writeSeq
public abstract void writeSeq()
- write sequence data, when all seq is known from setSeq()
writeSeqEnd
public abstract void writeSeqEnd()
- end of seq before newline or end of record - called at end of writeSeq() generally
writeRecordEnd
public abstract void writeRecordEnd()
- end of seq record
All Packages Class Hierarchy This Package Previous Next Index