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Interface iubio.readseq.BioseqReaderIface

public abstract interface BioseqReaderIface
extends iubio.readseq.BioseqIoIface

Variable Index

 o kListSequences
flag for setChoice() to return only list of sequence IDs

Method Index

 o copyto(SeqFileInfo)
copy last read sequence to storage record
 o doRead()
read next sequence to internal data
 o endOfFile()
end of sequence input stream was reached
 o getNseq()
get total number of sequences read

may not be valid till all data read, or return number of current sequence after doRead()

 o readOne(int)
read one sequence to SeqFileInfo structure
 o readTo(BioseqWriterIface, int)
reads all of sequence entries in stream, writing to writer

for piping from one format to another

 o reset()
reset input stream for re-read (interleaved formats)
 o resetSeq()
reset sequence storage for new sequence
 o setChoice(int)
select which sequence to read
 o setInput(Reader)
set input stream
 o skipPastHeader(int)
skip past non-sequence info at top of stream

Variables

 o kListSequences
 public static final int kListSequences
flag for setChoice() to return only list of sequence IDs

Methods

 o setInput
 public abstract void setInput(java.io.Reader ins)
set input stream

 o endOfFile
 public abstract boolean endOfFile()
end of sequence input stream was reached

 o reset
 public abstract void reset()
reset input stream for re-read (interleaved formats)

 o resetSeq
 public abstract void resetSeq()
reset sequence storage for new sequence

 o setChoice
 public abstract void setChoice(int seqchoice)
select which sequence to read

Parameters:
seqchoice - - index from 1 of sequence in stream
 o getNseq
 public abstract int getNseq()
get total number of sequences read

may not be valid till all data read, or return number of current sequence after doRead()

 o doRead
 public abstract void doRead() throws java.io.IOException
read next sequence to internal data

See Also:
setChoice
 o copyto
 public abstract void copyto(iubio.readseq.SeqFileInfo si)
copy last read sequence to storage record

 o skipPastHeader
 public abstract void skipPastHeader(int skiplines)
skip past non-sequence info at top of stream

Parameters:
skiplines - - presumed number of lines to skip past
 o readTo
 public abstract void readTo(iubio.readseq.BioseqWriterIface writer,
                             int skipHeaderLines) throws java.io.IOException
reads all of sequence entries in stream, writing to writer

for piping from one format to another

 o readOne
 public abstract iubio.readseq.SeqFileInfo readOne(int whichEntry) throws java.io.IOException
read one sequence to SeqFileInfo structure


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