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Class iubio.readseq.BioseqRecord
java.lang.Object
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+----iubio.readseq.SeqFileInfo
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+----iubio.readseq.BioseqRecord
- public class BioseqRecord
- extends iubio.readseq.SeqFileInfo
BioseqRecord, like SeqFileInfo is an object to join seq and seqdoc objects.
It also includes some manipulations for managing features of sequences
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BioseqRecord()
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BioseqRecord(Bioseq, BioseqDocImpl)
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BioseqRecord(Bioseq, BioseqDocImpl, String)
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BioseqRecord(SeqFileInfo)
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clone()
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copyTo(SeqFileInfo)
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extractBases(SeqRange)
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extractFeatureBases(FeatureItem)
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extractFeatureBases(Hashtable)
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extractFeatureBases(Hashtable, SeqRange)
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extractRemoveFeatureBases(boolean, Hashtable, SeqRange)
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findFeatures(Hashtable)
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findFeatures(Hashtable, SeqRange)
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findFeatures(SeqRange)
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findFeatures(String)
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findFeatures(String[])
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getdoc()
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getseq()
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getSeqFileInfo()
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removeFeatureBases(Hashtable)
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removeFeatureBases(Hashtable, SeqRange)
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set(Object, Object, String)
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toString()
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BioseqRecord
public BioseqRecord()
BioseqRecord
public BioseqRecord(iubio.bioseq.Bioseq seq,
iubio.readseq.BioseqDocImpl seqdoc)
BioseqRecord
public BioseqRecord(iubio.bioseq.Bioseq seq,
iubio.readseq.BioseqDocImpl seqdoc,
java.lang.String seqid)
BioseqRecord
public BioseqRecord(iubio.readseq.SeqFileInfo si)
set
public void set(java.lang.Object seqob,
java.lang.Object docob,
java.lang.String id)
getseq
public final iubio.bioseq.Bioseq getseq()
getdoc
public final iubio.readseq.BioseqDocImpl getdoc()
toString
public java.lang.String toString()
- Overrides:
- toString in class iubio.readseq.SeqFileInfo
getSeqFileInfo
public iubio.readseq.SeqFileInfo getSeqFileInfo()
copyTo
public void copyTo(iubio.readseq.SeqFileInfo si)
clone
public java.lang.Object clone()
- Overrides:
- clone in class iubio.readseq.SeqFileInfo
findFeatures
public final iubio.readseq.FeatureItem[] findFeatures(java.lang.String feature)
findFeatures
public final iubio.readseq.FeatureItem[] findFeatures(java.lang.String features[])
findFeatures
public final iubio.readseq.FeatureItem[] findFeatures(java.util.Hashtable wantfeatures)
findFeatures
public final iubio.readseq.FeatureItem[] findFeatures(iubio.bioseq.SeqRange wantrange)
findFeatures
public iubio.readseq.FeatureItem[] findFeatures(java.util.Hashtable wantfeatures,
iubio.bioseq.SeqRange wantrange)
extractFeatureBases
public final iubio.bioseq.Bioseq extractFeatureBases(iubio.readseq.FeatureItem feature) throws iubio.bioseq.SeqRangeException
extractFeatureBases
public final iubio.bioseq.Bioseq extractFeatureBases(java.util.Hashtable wantfeatures) throws iubio.bioseq.SeqRangeException
extractFeatureBases
public final iubio.bioseq.Bioseq extractFeatureBases(java.util.Hashtable wantfeatures,
iubio.bioseq.SeqRange wantrange) throws iubio.bioseq.SeqRangeException
removeFeatureBases
public final iubio.bioseq.Bioseq removeFeatureBases(java.util.Hashtable wantfeatures) throws iubio.bioseq.SeqRangeException
removeFeatureBases
public final iubio.bioseq.Bioseq removeFeatureBases(java.util.Hashtable wantfeatures,
iubio.bioseq.SeqRange wantrange) throws iubio.bioseq.SeqRangeException
extractRemoveFeatureBases
public iubio.bioseq.Bioseq extractRemoveFeatureBases(boolean extract,
java.util.Hashtable wantfeatures,
iubio.bioseq.SeqRange wantrange) throws iubio.bioseq.SeqRangeException
extractBases
public iubio.bioseq.Bioseq extractBases(iubio.bioseq.SeqRange range) throws iubio.bioseq.SeqRangeException
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