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Interface iubio.readseq.BioseqReaderIface
- public abstract interface BioseqReaderIface
- extends iubio.readseq.BioseqIoIface
-
kListSequences
- flag for setChoice() to return only list of sequence IDs
-
copyto(SeqFileInfo)
- copy last read sequence to storage record
-
doRead()
- read next sequence to internal data
-
endOfFile()
- end of sequence input stream was reached
-
getNseq()
- get total number of sequences read
may not be valid till all data read,
or return number of current sequence after doRead()
-
readOne(int)
- read one sequence to SeqFileInfo structure
-
readTo(BioseqWriterIface, int)
- reads all of sequence entries in stream, writing to writer
for piping from one format to another
-
reset()
- reset input stream for re-read (interleaved formats)
-
resetSeq()
- reset sequence storage for new sequence
-
setChoice(int)
- select which sequence to read
-
setInput(Reader)
- set input stream
-
skipPastHeader(int)
- skip past non-sequence info at top of stream
kListSequences
public static final int kListSequences
- flag for setChoice() to return only list of sequence IDs
setInput
public abstract void setInput(java.io.Reader ins)
- set input stream
endOfFile
public abstract boolean endOfFile()
- end of sequence input stream was reached
reset
public abstract void reset()
- reset input stream for re-read (interleaved formats)
resetSeq
public abstract void resetSeq()
- reset sequence storage for new sequence
setChoice
public abstract void setChoice(int seqchoice)
- select which sequence to read
- Parameters:
- seqchoice - - index from 1 of sequence in stream
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()
doRead
public abstract void doRead() throws java.io.IOException
- read next sequence to internal data
- See Also:
- setChoice
copyto
public abstract void copyto(iubio.readseq.SeqFileInfo si)
- copy last read sequence to storage record
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
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
readOne
public abstract iubio.readseq.SeqFileInfo readOne(int whichEntry) throws java.io.IOException
- read one sequence to SeqFileInfo structure
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