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Class iubio.readseq.BioseqRecord

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


Constructor Index

 o BioseqRecord()
 o BioseqRecord(Bioseq, BioseqDocImpl)
 o BioseqRecord(Bioseq, BioseqDocImpl, String)
 o BioseqRecord(SeqFileInfo)

Method Index

 o clone()
 o copyTo(SeqFileInfo)
 o extractBases(SeqRange)
 o extractFeatureBases(FeatureItem)
 o extractFeatureBases(Hashtable)
 o extractFeatureBases(Hashtable, SeqRange)
 o extractRemoveFeatureBases(boolean, Hashtable, SeqRange)
 o findFeatures(Hashtable)
 o findFeatures(Hashtable, SeqRange)
 o findFeatures(SeqRange)
 o findFeatures(String)
 o findFeatures(String[])
 o getdoc()
 o getseq()
 o getSeqFileInfo()
 o removeFeatureBases(Hashtable)
 o removeFeatureBases(Hashtable, SeqRange)
 o set(Object, Object, String)
 o toString()

Constructors

 o BioseqRecord
 public BioseqRecord()
 o BioseqRecord
 public BioseqRecord(iubio.bioseq.Bioseq seq,
                     iubio.readseq.BioseqDocImpl seqdoc)
 o BioseqRecord
 public BioseqRecord(iubio.bioseq.Bioseq seq,
                     iubio.readseq.BioseqDocImpl seqdoc,
                     java.lang.String seqid)
 o BioseqRecord
 public BioseqRecord(iubio.readseq.SeqFileInfo si)

Methods

 o set
 public void set(java.lang.Object seqob,
                 java.lang.Object docob,
                 java.lang.String id)
 o getseq
 public final iubio.bioseq.Bioseq getseq()
 o getdoc
 public final iubio.readseq.BioseqDocImpl getdoc()
 o toString
 public java.lang.String toString()
Overrides:
toString in class iubio.readseq.SeqFileInfo
 o getSeqFileInfo
 public iubio.readseq.SeqFileInfo getSeqFileInfo()
 o copyTo
 public void copyTo(iubio.readseq.SeqFileInfo si)
 o clone
 public java.lang.Object clone()
Overrides:
clone in class iubio.readseq.SeqFileInfo
 o findFeatures
 public final iubio.readseq.FeatureItem[] findFeatures(java.lang.String feature)
 o findFeatures
 public final iubio.readseq.FeatureItem[] findFeatures(java.lang.String features[])
 o findFeatures
 public final iubio.readseq.FeatureItem[] findFeatures(java.util.Hashtable wantfeatures)
 o findFeatures
 public final iubio.readseq.FeatureItem[] findFeatures(iubio.bioseq.SeqRange wantrange)
 o findFeatures
 public iubio.readseq.FeatureItem[] findFeatures(java.util.Hashtable wantfeatures,
                                                 iubio.bioseq.SeqRange wantrange)
 o extractFeatureBases
 public final iubio.bioseq.Bioseq extractFeatureBases(iubio.readseq.FeatureItem feature) throws iubio.bioseq.SeqRangeException
 o extractFeatureBases
 public final iubio.bioseq.Bioseq extractFeatureBases(java.util.Hashtable wantfeatures) throws iubio.bioseq.SeqRangeException
 o extractFeatureBases
 public final iubio.bioseq.Bioseq extractFeatureBases(java.util.Hashtable wantfeatures,
                                                      iubio.bioseq.SeqRange wantrange) throws iubio.bioseq.SeqRangeException
 o removeFeatureBases
 public final iubio.bioseq.Bioseq removeFeatureBases(java.util.Hashtable wantfeatures) throws iubio.bioseq.SeqRangeException
 o removeFeatureBases
 public final iubio.bioseq.Bioseq removeFeatureBases(java.util.Hashtable wantfeatures,
                                                     iubio.bioseq.SeqRange wantrange) throws iubio.bioseq.SeqRangeException
 o extractRemoveFeatureBases
 public iubio.bioseq.Bioseq extractRemoveFeatureBases(boolean extract,
                                                      java.util.Hashtable wantfeatures,
                                                      iubio.bioseq.SeqRange wantrange) throws iubio.bioseq.SeqRangeException
 o extractBases
 public iubio.bioseq.Bioseq extractBases(iubio.bioseq.SeqRange range) throws iubio.bioseq.SeqRangeException

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