All Packages Class Hierarchy This Package Previous Next Index
Class iubio.readseq.BioseqReader
java.lang.Object
|
+----iubio.readseq.BioseqReader
- public abstract class BioseqReader
- extends java.lang.Object
- implements iubio.readseq.BioseqReaderIface
-
lineEnd
-
-
messageapp
-
-
tempFile
-
-
verbose
-
-
BioseqReader()
-
-
BioseqReader(Reader)
-
-
copyto(SeqFileInfo)
-
-
doRead()
-
-
endOfFile()
-
-
endOfSequence()
-
-
formatID()
-
-
getInput()
-
-
getline()
-
-
getlineBuf()
-
-
getNseq()
-
-
getReadChunkSize()
-
-
message(String)
-
-
readOne(int)
-
-
readTo(BioseqWriterIface, int)
-
-
reset()
-
-
resetSeq()
-
-
setChoice(int)
-
-
setFormatID(int)
-
-
setInput(InputStream)
-
-
setInput(Reader)
-
-
setReadChunkSize(int)
-
-
setSkipDocs(boolean)
-
-
skipPastHeader(int)
-
-
ungetline()
-
tempFile
public static java.lang.String tempFile
verbose
public static boolean verbose
lineEnd
public static java.lang.String lineEnd
messageapp
public static iubio.readseq.MessageApp messageapp
BioseqReader
public BioseqReader()
BioseqReader
public BioseqReader(java.io.Reader ins)
message
public static void message(java.lang.String s)
setChoice
public void setChoice(int seqchoice)
formatID
public int formatID()
setFormatID
public void setFormatID(int id)
getInput
public java.io.Reader getInput()
setInput
public void setInput(java.io.InputStream ins)
setInput
public void setInput(java.io.Reader ins)
doRead
public void doRead() throws java.io.IOException
getNseq
public int getNseq()
getReadChunkSize
public int getReadChunkSize()
setReadChunkSize
public void setReadChunkSize(int chunksize)
resetSeq
public void resetSeq()
skipPastHeader
public void skipPastHeader(int skiplines)
copyto
public void copyto(iubio.readseq.SeqFileInfo si)
setSkipDocs
public void setSkipDocs(boolean turnon)
readTo
public void readTo(iubio.readseq.BioseqWriterIface writer,
int skipHeaderLines) throws java.io.IOException
readOne
public iubio.readseq.SeqFileInfo readOne(int whichEntry) throws java.io.IOException
endOfSequence
public boolean endOfSequence()
endOfFile
public boolean endOfFile()
ungetline
public void ungetline()
reset
public void reset()
getlineBuf
public void getlineBuf() throws java.io.IOException
getline
public flybase.OpenString getline() throws java.io.IOException
All Packages Class Hierarchy This Package Previous Next Index