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Class iubio.readseq.SeqFileInfo
java.lang.Object
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+----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.
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atseq
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err
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extradata
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format
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gBlanknum
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gBlankSeqid
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gMaskName
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gWriteMask
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hasmask
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ismask
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modtime
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nseq
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offset
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seq
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seqdoc
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seqid
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seqlen
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skiplines
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SeqFileInfo()
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SeqFileInfo(Object, int, int)
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checkSeqID()
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cleanSeqID(String)
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clone()
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copyto(SeqFileInfo)
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getdocObject()
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getextraObject()
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getID()
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getNextBlankID()
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getNextBlankID(String)
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getseqObject()
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hasdoc()
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hasid()
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hasmask()
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hasseq()
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length()
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offset()
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setdoc(Object)
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setextra(Object)
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setlength(int)
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setoffset(int)
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setseq(Object)
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setSeqID(String)
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toString()
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gBlankSeqid
public static java.lang.String gBlankSeqid
gMaskName
public static java.lang.String gMaskName
gWriteMask
public static boolean gWriteMask
gBlanknum
public static int gBlanknum
format
public int format
skiplines
public int skiplines
err
public int err
atseq
public int atseq
nseq
public int nseq
modtime
public long modtime
seqlen
public int seqlen
offset
public int offset
ismask
public boolean ismask
hasmask
public boolean hasmask
seq
public java.lang.Object seq
seqdoc
public java.lang.Object seqdoc
seqid
public java.lang.String seqid
extradata
public java.lang.Object extradata
SeqFileInfo
public SeqFileInfo()
SeqFileInfo
public SeqFileInfo(java.lang.Object seq,
int offset,
int seqlen)
toString
public java.lang.String toString()
- Overrides:
- toString in class java.lang.Object
length
public final int length()
setlength
public void setlength(int len)
offset
public final int offset()
setoffset
public void setoffset(int off)
getseqObject
public final java.lang.Object getseqObject()
setseq
public void setseq(java.lang.Object seq)
getdocObject
public final java.lang.Object getdocObject()
setdoc
public void setdoc(java.lang.Object doc)
getextraObject
public final java.lang.Object getextraObject()
setextra
public void setextra(java.lang.Object doc)
hasseq
public final boolean hasseq()
hasdoc
public final boolean hasdoc()
hasid
public final boolean hasid()
hasmask
public final boolean hasmask()
getID
public final java.lang.String getID()
setSeqID
public final void setSeqID(java.lang.String seqid)
checkSeqID
public void checkSeqID()
getNextBlankID
public static java.lang.String getNextBlankID()
getNextBlankID
public static java.lang.String getNextBlankID(java.lang.String id)
cleanSeqID
public static java.lang.String cleanSeqID(java.lang.String s)
copyto
public void copyto(iubio.readseq.SeqFileInfo si)
clone
public java.lang.Object clone()
- Overrides:
- clone in class java.lang.Object
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