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Class iubio.readseq.BioseqReader

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

public abstract class BioseqReader
extends java.lang.Object
implements iubio.readseq.BioseqReaderIface

Variable Index

 o lineEnd
 o messageapp
 o tempFile
 o verbose

Constructor Index

 o BioseqReader()
 o BioseqReader(Reader)

Method Index

 o copyto(SeqFileInfo)
 o doRead()
 o endOfFile()
 o endOfSequence()
 o formatID()
 o getInput()
 o getline()
 o getlineBuf()
 o getNseq()
 o getReadChunkSize()
 o message(String)
 o readOne(int)
 o readTo(BioseqWriterIface, int)
 o reset()
 o resetSeq()
 o setChoice(int)
 o setFormatID(int)
 o setInput(InputStream)
 o setInput(Reader)
 o setReadChunkSize(int)
 o setSkipDocs(boolean)
 o skipPastHeader(int)
 o ungetline()

Variables

 o tempFile
 public static java.lang.String tempFile
 o verbose
 public static boolean verbose
 o lineEnd
 public static java.lang.String lineEnd
 o messageapp
 public static iubio.readseq.MessageApp messageapp

Constructors

 o BioseqReader
 public BioseqReader()
 o BioseqReader
 public BioseqReader(java.io.Reader ins)

Methods

 o message
 public static void message(java.lang.String s)
 o setChoice
 public void setChoice(int seqchoice)
 o formatID
 public int formatID()
 o setFormatID
 public void setFormatID(int id)
 o getInput
 public java.io.Reader getInput()
 o setInput
 public void setInput(java.io.InputStream ins)
 o setInput
 public void setInput(java.io.Reader ins)
 o doRead
 public void doRead() throws java.io.IOException
 o getNseq
 public int getNseq()
 o getReadChunkSize
 public int getReadChunkSize()
 o setReadChunkSize
 public void setReadChunkSize(int chunksize)
 o resetSeq
 public void resetSeq()
 o skipPastHeader
 public void skipPastHeader(int skiplines)
 o copyto
 public void copyto(iubio.readseq.SeqFileInfo si)
 o setSkipDocs
 public void setSkipDocs(boolean turnon)
 o readTo
 public void readTo(iubio.readseq.BioseqWriterIface writer,
                    int skipHeaderLines) throws java.io.IOException
 o readOne
 public iubio.readseq.SeqFileInfo readOne(int whichEntry) throws java.io.IOException
 o endOfSequence
 public boolean endOfSequence()
 o endOfFile
 public boolean endOfFile()
 o ungetline
 public void ungetline()
 o reset
 public void reset()
 o getlineBuf
 public void getlineBuf() throws java.io.IOException
 o getline
 public flybase.OpenString getline() throws java.io.IOException

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