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Class iubio.readseq.SeqFileInfo

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

public class SeqFileInfo
extends java.lang.Object
implements java.lang.Cloneable
a lightweight class to pass seq and file info between reader/writer and others. This lacks knowledge of BioseqDoc (seqdoc). Recommended you use BioseqRecord instead of this one.


Variable Index

 o atseq
 o err
 o extradata
 o format
 o gBlanknum
 o gBlankSeqid
 o gMaskName
 o gWriteMask
 o hasmask
 o ismask
 o modtime
 o nseq
 o offset
 o seq
 o seqdoc
 o seqid
 o seqlen
 o skiplines

Constructor Index

 o SeqFileInfo()
 o SeqFileInfo(Object, int, int)

Method Index

 o checkSeqID()
 o cleanSeqID(String)
 o clone()
 o copyto(SeqFileInfo)
 o getdocObject()
 o getextraObject()
 o getID()
 o getNextBlankID()
 o getNextBlankID(String)
 o getseqObject()
 o hasdoc()
 o hasid()
 o hasmask()
 o hasseq()
 o length()
 o offset()
 o setdoc(Object)
 o setextra(Object)
 o setlength(int)
 o setoffset(int)
 o setseq(Object)
 o setSeqID(String)
 o toString()

Variables

 o gBlankSeqid
 public static java.lang.String gBlankSeqid
 o gMaskName
 public static java.lang.String gMaskName
 o gWriteMask
 public static boolean gWriteMask
 o gBlanknum
 public static int gBlanknum
 o format
 public int format
 o skiplines
 public int skiplines
 o err
 public int err
 o atseq
 public int atseq
 o nseq
 public int nseq
 o modtime
 public long modtime
 o seqlen
 public int seqlen
 o offset
 public int offset
 o ismask
 public boolean ismask
 o hasmask
 public boolean hasmask
 o seq
 public java.lang.Object seq
 o seqdoc
 public java.lang.Object seqdoc
 o seqid
 public java.lang.String seqid
 o extradata
 public java.lang.Object extradata

Constructors

 o SeqFileInfo
 public SeqFileInfo()
 o SeqFileInfo
 public SeqFileInfo(java.lang.Object seq,
                    int offset,
                    int seqlen)

Methods

 o toString
 public java.lang.String toString()
Overrides:
toString in class java.lang.Object
 o length
 public final int length()
 o setlength
 public void setlength(int len)
 o offset
 public final int offset()
 o setoffset
 public void setoffset(int off)
 o getseqObject
 public final java.lang.Object getseqObject()
 o setseq
 public void setseq(java.lang.Object seq)
 o getdocObject
 public final java.lang.Object getdocObject()
 o setdoc
 public void setdoc(java.lang.Object doc)
 o getextraObject
 public final java.lang.Object getextraObject()
 o setextra
 public void setextra(java.lang.Object doc)
 o hasseq
 public final boolean hasseq()
 o hasdoc
 public final boolean hasdoc()
 o hasid
 public final boolean hasid()
 o hasmask
 public final boolean hasmask()
 o getID
 public final java.lang.String getID()
 o setSeqID
 public final void setSeqID(java.lang.String seqid)
 o checkSeqID
 public void checkSeqID()
 o getNextBlankID
 public static java.lang.String getNextBlankID()
 o getNextBlankID
 public static java.lang.String getNextBlankID(java.lang.String id)
 o cleanSeqID
 public static java.lang.String cleanSeqID(java.lang.String s)
 o copyto
 public void copyto(iubio.readseq.SeqFileInfo si)
 o clone
 public java.lang.Object clone()
Overrides:
clone in class java.lang.Object

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