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Class iubio.readseq.BioseqWriter
java.lang.Object
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+----iubio.readseq.BioseqWriter
- public class BioseqWriter
- extends java.lang.Object
- implements iubio.readseq.BioseqWriterIface
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checksumTime
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checksumTotal
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gJavaChecksum
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gShortChecksum
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kNocountsymbols
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summer
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BioseqWriter()
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calculateChecksum(Bioseq, int, int, Checksum)
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close()
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CRC32checksum(Bioseq, int, int)
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formatID()
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GCGchecksum(Bioseq, int, int)
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getChecksum()
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getError()
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getOpts()
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getOutput()
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getOutputTranslation()
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getReverseComplement()
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setChecksum(boolean)
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setFeatureExtraction(Hashtable)
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setFeatureSubrange(SeqRange)
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setFormatID(int)
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setMask(SeqFileInfo, String)
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setNseq(int)
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setOpts(WriteseqOpts)
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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)
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setSeqName(String)
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setSeqPart(int)
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wantsDocument()
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writeDoc()
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writeHeader()
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writeRecordEnd()
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writeRecordStart()
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writeSeq()
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writeSeqEnd()
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writeSeqRecord()
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writeTrailer()
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ZipChecksum(Bioseq, int, int, Checksum)
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gJavaChecksum
public static boolean gJavaChecksum
gShortChecksum
public static boolean gShortChecksum
summer
public static java.util.zip.Checksum summer
kNocountsymbols
public static java.lang.String kNocountsymbols
checksumTotal
public static long checksumTotal
checksumTime
public static long checksumTime
BioseqWriter
public BioseqWriter()
getChecksum
public boolean getChecksum()
setChecksum
public void setChecksum(boolean turnon)
getReverseComplement
public boolean getReverseComplement()
setReverseComplement
public void setReverseComplement(boolean turnon)
setOpts
public void setOpts(iubio.readseq.WriteseqOpts newopts)
getOpts
public iubio.readseq.WriteseqOpts getOpts()
formatID
public int formatID()
setFormatID
public void setFormatID(int id)
getOutput
public java.io.Writer getOutput()
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
setOutputTranslation
public void setOutputTranslation(iubio.readseq.OutBiobaseIntf tester)
getOutputTranslation
public iubio.readseq.OutBiobaseIntf getOutputTranslation()
setNseq
public void setNseq(int nsequences)
writeHeader
public void writeHeader() throws java.io.IOException
writeTrailer
public void writeTrailer()
writeDoc
public void writeDoc()
writeSeq
public void writeSeq()
writeSeqEnd
public void writeSeqEnd()
writeRecordEnd
public void writeRecordEnd()
writeRecordStart
public void writeRecordStart()
writeSeqRecord
public void writeSeqRecord() throws java.io.IOException
setFeatureExtraction
public void setFeatureExtraction(java.util.Hashtable featurelist)
setFeatureSubrange
public void setFeatureSubrange(iubio.bioseq.SeqRange extractSubrange)
wantsDocument
public boolean wantsDocument()
setMask
public boolean setMask(iubio.readseq.SeqFileInfo si,
java.lang.String masktag)
setSeq
public boolean setSeq(iubio.readseq.SeqFileInfo si)
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)
getError
public int getError()
calculateChecksum
public static long calculateChecksum(iubio.bioseq.Bioseq seq,
int offset,
int seqlen,
java.util.zip.Checksum summer)
ZipChecksum
public static long ZipChecksum(iubio.bioseq.Bioseq seq,
int offset,
int seqlen,
java.util.zip.Checksum summer)
CRC32checksum
public static long CRC32checksum(iubio.bioseq.Bioseq seq,
int offset,
int seqlen)
GCGchecksum
public static long GCGchecksum(iubio.bioseq.Bioseq seq,
int offset,
int seqlen)
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