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Class iubio.readseq.Readseq

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

public class Readseq
extends java.lang.Object
implements java.util.Enumeration
Readseq is public wrapper for classes of BioseqReader & BioseqWriter ancestry


Variable Index

 o kInputStringKey
special flag for readlist()
 o verbose
 o version

Constructor Index

 o Readseq()
 o Readseq(int)

Method Index

 o allresults()
 o allSeqs()
 o atresult()
 o canread()
 o canReadMore()
 o checkInList(FastVector, String)
 o checkInString(String)
 o checkInString(String, String)
 o close()
 o eof()
 o getBioseqFormat()
 o getFormat()
 o getFormatName()
 o getInfo()
 o getInput()
 o getReader()
 o hasMoreElements()
 o initIfNeeded(String)
 o isKnownFormat()
 o isMydata()
 o list(Writer)
 o moreresults()
 o nextElement()
 o nextSeq()
 o nresults()
 o readAt(int)
 o readInit()
 o readInit(String)
 o readlist(Enumeration)
 o readlist(Enumeration, String)
 o readlist(FastVector)
Read a FastVector list of inputs: File, URL, InputStream, String of (File,URL,Data) -- moved here from readseqapp for handy usage
 o readlist(FastVector, String)
 o readNext()
 o readTo(BioseqWriterIface)
 o readTo(BioseqWriterIface, boolean)
 o readToOld(BioseqWriterIface, boolean)
 o readToPair(BioseqWriterIface, BioseqWriterIface, boolean)
 o removeresults()
 o restartresults()
 o result()
 o setExtractRange(SeqRange)
 o setFeatureExtraction(Hashtable, SeqRange)
 o setFormat(int)
 o setFormatTestor(Testseq)
 o setInput(byte[])
 o setInput(char[])
 o setInput(File)
input setters -
 o setInput(InputStream)
 o setInput(OpenString)
 o setInput(Reader)
 o setInput(String)
 o setInput(URL)
 o setInputFormat(int)
 o setInputObject(Object)
 o setInputObjectChecked(Object)
 o setWriteMask(boolean)
 o writeSeqTo(SeqFileInfo, BioseqWriterIface, BioseqWriterIface)

Variables

 o version
 public static java.lang.String version
 o kInputStringKey
 public static java.lang.String kInputStringKey
special flag for readlist()

 o verbose
 public boolean verbose

Constructors

 o Readseq
 public Readseq()
 o Readseq
 public Readseq(int format)

Methods

 o getInput
 public java.io.Reader getInput()
 o setInput
 public void setInput(java.io.File f) throws java.io.IOException
input setters - @see readlist( FastVector inlist)

 o setInput
 public void setInput(java.io.Reader in) throws java.io.IOException
 o setInput
 public void setInput(java.io.InputStream in) throws java.io.IOException
 o setInput
 public void setInput(java.net.URL url) throws java.io.IOException
 o setInput
 public void setInput(java.lang.String s) throws java.io.IOException
 o setInput
 public void setInput(flybase.OpenString s) throws java.io.IOException
 o setInput
 public void setInput(byte b[]) throws java.io.IOException
 o setInput
 public void setInput(char c[]) throws java.io.IOException
 o setInputObject
 public java.lang.String setInputObject(java.lang.Object inob) throws java.io.IOException
 o setInputObjectChecked
 public java.lang.String setInputObjectChecked(java.lang.Object inob) throws java.io.IOException
 o close
 public void close() throws java.io.IOException
 o setFormatTestor
 public void setFormatTestor(iubio.readseq.Testseq testor)
 o isMydata
 public final boolean isMydata()
 o setInputFormat
 public void setInputFormat(int formatID)
 o isKnownFormat
 public boolean isKnownFormat()
 o canread
 public boolean canread()
 o getInfo
 public final iubio.readseq.SeqFileInfo getInfo()
 o getFormat
 public final int getFormat()
 o setFormat
 public void setFormat(int format)
 o getFormatName
 public java.lang.String getFormatName()
 o getReader
 public iubio.readseq.BioseqReaderIface getReader()
 o getBioseqFormat
 public iubio.readseq.BioseqFormat getBioseqFormat()
 o eof
 public boolean eof()
 o checkInString
 public final java.lang.Object checkInString(java.lang.String ins)
 o checkInString
 public java.lang.Object checkInString(java.lang.String ins,
                                       java.lang.String stringDataKey)
 o checkInList
 public void checkInList(flybase.FastVector inlist,
                         java.lang.String stringDataKey)
 o 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

 o readlist
 public final void readlist(java.util.Enumeration inlist)
 o readlist
 public void readlist(flybase.FastVector inlist,
                      java.lang.String stringDataKey)
 o readlist
 public void readlist(java.util.Enumeration inlist,
                      java.lang.String stringDataKey)
 o nextSeq
 public final iubio.readseq.SeqFileInfo nextSeq()
 o allSeqs
 public iubio.readseq.SeqFileInfo[] allSeqs()
 o result
 public final java.lang.Object result()
 o moreresults
 public final boolean moreresults()
 o atresult
 public final int atresult()
 o nresults
 public final int nresults()
 o allresults
 public final java.util.Vector allresults()
 o restartresults
 public final void restartresults()
 o removeresults
 public final void removeresults()
 o hasMoreElements
 public boolean hasMoreElements()
 o nextElement
 public java.lang.Object nextElement()
 o initIfNeeded
 public void initIfNeeded(java.lang.String defname)
 o readInit
 public final boolean readInit()
 o readInit
 public boolean readInit(java.lang.String defname)
 o canReadMore
 public boolean canReadMore()
 o readAt
 public iubio.readseq.SeqFileInfo readAt(int atEntry) throws java.io.IOException
 o readNext
 public boolean readNext() throws java.io.IOException
 o setFeatureExtraction
 public void setFeatureExtraction(java.util.Hashtable featurelist,
                                  iubio.bioseq.SeqRange featSubrange)
 o setExtractRange
 public void setExtractRange(iubio.bioseq.SeqRange exSubrange)
 o writeSeqTo
 public void writeSeqTo(iubio.readseq.SeqFileInfo si,
                        iubio.readseq.BioseqWriterIface seqwriter,
                        iubio.readseq.BioseqWriterIface docwriter) throws java.io.IOException
 o setWriteMask
 public void setWriteMask(boolean turnon)
 o readTo
 public boolean readTo(iubio.readseq.BioseqWriterIface writer) throws java.io.IOException
 o readToOld
 public boolean readToOld(iubio.readseq.BioseqWriterIface writer,
                          boolean writeWrapper) throws java.io.IOException
 o readTo
 public boolean readTo(iubio.readseq.BioseqWriterIface seqwriter,
                       boolean writeWrapper) throws java.io.IOException
 o readToPair
 public boolean readToPair(iubio.readseq.BioseqWriterIface seqwriter,
                           iubio.readseq.BioseqWriterIface docwriter,
                           boolean writeWrapper) throws java.io.IOException
 o list
 public void list(java.io.Writer out)

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