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Class iubio.readseq.Readseq
java.lang.Object
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+----iubio.readseq.Readseq
- public class Readseq
- extends java.lang.Object
- implements java.util.Enumeration
Readseq is public wrapper for
classes of BioseqReader & BioseqWriter ancestry
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kInputStringKey
- special flag for readlist()
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verbose
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version
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Readseq()
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Readseq(int)
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allresults()
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allSeqs()
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atresult()
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canread()
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canReadMore()
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checkInList(FastVector, String)
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checkInString(String)
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checkInString(String, String)
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close()
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eof()
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getBioseqFormat()
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getFormat()
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getFormatName()
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getInfo()
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getInput()
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getReader()
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hasMoreElements()
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initIfNeeded(String)
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isKnownFormat()
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isMydata()
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list(Writer)
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moreresults()
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nextElement()
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nextSeq()
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nresults()
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readAt(int)
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readInit()
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readInit(String)
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readlist(Enumeration)
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readlist(Enumeration, String)
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readlist(FastVector)
- Read a FastVector list of inputs: File, URL, InputStream, String of (File,URL,Data)
-- moved here from readseqapp for handy usage
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readlist(FastVector, String)
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readNext()
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readTo(BioseqWriterIface)
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readTo(BioseqWriterIface, boolean)
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readToOld(BioseqWriterIface, boolean)
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readToPair(BioseqWriterIface, BioseqWriterIface, boolean)
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removeresults()
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restartresults()
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result()
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setExtractRange(SeqRange)
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setFeatureExtraction(Hashtable, SeqRange)
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setFormat(int)
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setFormatTestor(Testseq)
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setInput(byte[])
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setInput(char[])
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setInput(File)
- input setters -
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setInput(InputStream)
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setInput(OpenString)
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setInput(Reader)
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setInput(String)
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setInput(URL)
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setInputFormat(int)
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setInputObject(Object)
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setInputObjectChecked(Object)
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setWriteMask(boolean)
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writeSeqTo(SeqFileInfo, BioseqWriterIface, BioseqWriterIface)
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version
public static java.lang.String version
kInputStringKey
public static java.lang.String kInputStringKey
- special flag for readlist()
verbose
public boolean verbose
Readseq
public Readseq()
Readseq
public Readseq(int format)
getInput
public java.io.Reader getInput()
setInput
public void setInput(java.io.File f) throws java.io.IOException
- input setters - @see readlist( FastVector inlist)
setInput
public void setInput(java.io.Reader in) throws java.io.IOException
setInput
public void setInput(java.io.InputStream in) throws java.io.IOException
setInput
public void setInput(java.net.URL url) throws java.io.IOException
setInput
public void setInput(java.lang.String s) throws java.io.IOException
setInput
public void setInput(flybase.OpenString s) throws java.io.IOException
setInput
public void setInput(byte b[]) throws java.io.IOException
setInput
public void setInput(char c[]) throws java.io.IOException
setInputObject
public java.lang.String setInputObject(java.lang.Object inob) throws java.io.IOException
setInputObjectChecked
public java.lang.String setInputObjectChecked(java.lang.Object inob) throws java.io.IOException
close
public void close() throws java.io.IOException
setFormatTestor
public void setFormatTestor(iubio.readseq.Testseq testor)
isMydata
public final boolean isMydata()
setInputFormat
public void setInputFormat(int formatID)
isKnownFormat
public boolean isKnownFormat()
canread
public boolean canread()
getInfo
public final iubio.readseq.SeqFileInfo getInfo()
getFormat
public final int getFormat()
setFormat
public void setFormat(int format)
getFormatName
public java.lang.String getFormatName()
getReader
public iubio.readseq.BioseqReaderIface getReader()
getBioseqFormat
public iubio.readseq.BioseqFormat getBioseqFormat()
eof
public boolean eof()
checkInString
public final java.lang.Object checkInString(java.lang.String ins)
checkInString
public java.lang.Object checkInString(java.lang.String ins,
java.lang.String stringDataKey)
checkInList
public void checkInList(flybase.FastVector inlist,
java.lang.String stringDataKey)
readlist
public final void readlist(flybase.FastVector inlist)
- Read a FastVector list of inputs: File, URL, InputStream, String of (File,URL,Data)
-- moved here from readseqapp for handy usage
readlist
public final void readlist(java.util.Enumeration inlist)
readlist
public void readlist(flybase.FastVector inlist,
java.lang.String stringDataKey)
readlist
public void readlist(java.util.Enumeration inlist,
java.lang.String stringDataKey)
nextSeq
public final iubio.readseq.SeqFileInfo nextSeq()
allSeqs
public iubio.readseq.SeqFileInfo[] allSeqs()
result
public final java.lang.Object result()
moreresults
public final boolean moreresults()
atresult
public final int atresult()
nresults
public final int nresults()
allresults
public final java.util.Vector allresults()
restartresults
public final void restartresults()
removeresults
public final void removeresults()
hasMoreElements
public boolean hasMoreElements()
nextElement
public java.lang.Object nextElement()
initIfNeeded
public void initIfNeeded(java.lang.String defname)
readInit
public final boolean readInit()
readInit
public boolean readInit(java.lang.String defname)
canReadMore
public boolean canReadMore()
readAt
public iubio.readseq.SeqFileInfo readAt(int atEntry) throws java.io.IOException
readNext
public boolean readNext() throws java.io.IOException
setFeatureExtraction
public void setFeatureExtraction(java.util.Hashtable featurelist,
iubio.bioseq.SeqRange featSubrange)
setExtractRange
public void setExtractRange(iubio.bioseq.SeqRange exSubrange)
writeSeqTo
public void writeSeqTo(iubio.readseq.SeqFileInfo si,
iubio.readseq.BioseqWriterIface seqwriter,
iubio.readseq.BioseqWriterIface docwriter) throws java.io.IOException
setWriteMask
public void setWriteMask(boolean turnon)
readTo
public boolean readTo(iubio.readseq.BioseqWriterIface writer) throws java.io.IOException
readToOld
public boolean readToOld(iubio.readseq.BioseqWriterIface writer,
boolean writeWrapper) throws java.io.IOException
readTo
public boolean readTo(iubio.readseq.BioseqWriterIface seqwriter,
boolean writeWrapper) throws java.io.IOException
readToPair
public boolean readToPair(iubio.readseq.BioseqWriterIface seqwriter,
iubio.readseq.BioseqWriterIface docwriter,
boolean writeWrapper) throws java.io.IOException
list
public void list(java.io.Writer out)
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