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Class iubio.readseq.BioseqWriter

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

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

Variable Index

 o checksumTime
 o checksumTotal
 o gJavaChecksum
 o gShortChecksum
 o kNocountsymbols
 o summer

Constructor Index

 o BioseqWriter()

Method Index

 o calculateChecksum(Bioseq, int, int, Checksum)
 o close()
 o CRC32checksum(Bioseq, int, int)
 o formatID()
 o GCGchecksum(Bioseq, int, int)
 o getChecksum()
 o getError()
 o getOpts()
 o getOutput()
 o getOutputTranslation()
 o getReverseComplement()
 o setChecksum(boolean)
 o setFeatureExtraction(Hashtable)
 o setFeatureSubrange(SeqRange)
 o setFormatID(int)
 o setMask(SeqFileInfo, String)
 o setNseq(int)
 o setOpts(WriteseqOpts)
 o setOutput(OutputStream)
 o setOutput(Writer)
 o setOutputTranslation(OutBiobaseIntf)
 o setReverseComplement(boolean)
 o setSeq(Object, int, int, String, Object, int, int)
 o setSeq(SeqFileInfo)
 o setSeqName(String)
 o setSeqPart(int)
 o wantsDocument()
 o writeDoc()
 o writeHeader()
 o writeRecordEnd()
 o writeRecordStart()
 o writeSeq()
 o writeSeqEnd()
 o writeSeqRecord()
 o writeTrailer()
 o ZipChecksum(Bioseq, int, int, Checksum)

Variables

 o gJavaChecksum
 public static boolean gJavaChecksum
 o gShortChecksum
 public static boolean gShortChecksum
 o summer
 public static java.util.zip.Checksum summer
 o kNocountsymbols
 public static java.lang.String kNocountsymbols
 o checksumTotal
 public static long checksumTotal
 o checksumTime
 public static long checksumTime

Constructors

 o BioseqWriter
 public BioseqWriter()

Methods

 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 setOpts
 public void setOpts(iubio.readseq.WriteseqOpts newopts)
 o getOpts
 public iubio.readseq.WriteseqOpts getOpts()
 o formatID
 public int formatID()
 o setFormatID
 public void setFormatID(int id)
 o getOutput
 public java.io.Writer getOutput()
 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 setOutputTranslation
 public void setOutputTranslation(iubio.readseq.OutBiobaseIntf tester)
 o getOutputTranslation
 public iubio.readseq.OutBiobaseIntf getOutputTranslation()
 o setNseq
 public void setNseq(int nsequences)
 o writeHeader
 public void writeHeader() throws java.io.IOException
 o writeTrailer
 public void writeTrailer()
 o writeDoc
 public void writeDoc()
 o writeSeq
 public void writeSeq()
 o writeSeqEnd
 public void writeSeqEnd()
 o writeRecordEnd
 public void writeRecordEnd()
 o writeRecordStart
 public void writeRecordStart()
 o writeSeqRecord
 public void writeSeqRecord() throws java.io.IOException
 o setFeatureExtraction
 public void setFeatureExtraction(java.util.Hashtable featurelist)
 o setFeatureSubrange
 public void setFeatureSubrange(iubio.bioseq.SeqRange extractSubrange)
 o wantsDocument
 public boolean wantsDocument()
 o setMask
 public boolean setMask(iubio.readseq.SeqFileInfo si,
                        java.lang.String masktag)
 o setSeq
 public boolean setSeq(iubio.readseq.SeqFileInfo si)
 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 getError
 public int getError()
 o calculateChecksum
 public static long calculateChecksum(iubio.bioseq.Bioseq seq,
                                      int offset,
                                      int seqlen,
                                      java.util.zip.Checksum summer)
 o ZipChecksum
 public static long ZipChecksum(iubio.bioseq.Bioseq seq,
                                int offset,
                                int seqlen,
                                java.util.zip.Checksum summer)
 o CRC32checksum
 public static long CRC32checksum(iubio.bioseq.Bioseq seq,
                                  int offset,
                                  int seqlen)
 o GCGchecksum
 public static long GCGchecksum(iubio.bioseq.Bioseq seq,
                                int offset,
                                int seqlen)

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