org.geworkbench.bison.datastructure.biocollections.sequences
Interface DSSequenceSet<T extends DSSequence>

All Superinterfaces:
java.lang.Cloneable, java.util.Collection<T>, DSDataSet<T>, DSDescribable, DSExtendable, DSIdentifiable, DSItemList<T>, DSNamed, java.lang.Iterable<T>, java.util.List<T>, java.util.RandomAccess, java.io.Serializable
All Known Implementing Classes:
CSSequenceSet

public interface DSSequenceSet<T extends DSSequence>
extends java.util.RandomAccess, java.lang.Cloneable, java.io.Serializable, DSDataSet<T>, java.util.List<T>

Version:
$Id: DSSequenceSet.java 7487 2011-02-24 14:48:09Z zji $
Author:
John Watkinson

Method Summary
 void addASequence(T sequence)
           
 DSItemList<? extends DSGeneMarker> getMarkerList()
           
 int[] getMatchIndex()
           
 int getMaxLength()
           
 int[] getReverseIndex()
           
 T getSequence(int i)
           
 int getSequenceNo()
           
 boolean isDNA()
           
 void setMatchIndex(int[] matchIndex)
           
 void setReverseIndex(int[] reverseIndex)
           
 
Methods inherited from interface org.geworkbench.bison.datastructure.biocollections.DSDataSet
addObject, getColumnOrder, getCompatibilityLabel, getDataSetName, getExperimentInformation, getFile, getObject, isActive, setColumnOrder, setExperimentInformation, setFile, writeToFile
 
Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSDescribable
getDescription, setDescription
 
Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSNamed
getLabel, setLabel
 
Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSExtendable
addNameValuePair, allowMultipleValues, clearName, forceUniqueValue, getValuesForName, isUniqueValue
 
Methods inherited from interface org.geworkbench.bison.datastructure.complex.panels.DSItemList
get
 
Methods inherited from interface java.util.List
add, add, addAll, addAll, clear, contains, containsAll, equals, get, hashCode, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, retainAll, set, size, subList, toArray, toArray
 
Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSIdentifiable
getID, setID
 

Method Detail

addASequence

void addASequence(T sequence)

getSequenceNo

int getSequenceNo()

getSequence

T getSequence(int i)

getMaxLength

int getMaxLength()

isDNA

boolean isDNA()

setMatchIndex

void setMatchIndex(int[] matchIndex)

setReverseIndex

void setReverseIndex(int[] reverseIndex)

getMarkerList

DSItemList<? extends DSGeneMarker> getMarkerList()

getMatchIndex

int[] getMatchIndex()

getReverseIndex

int[] getReverseIndex()