org.geworkbench.bison.datastructure.bioobjects.sequence
Class CSAlignmentResultSet

java.lang.Object
  extended by java.util.AbstractCollection<E>
      extended by java.util.AbstractList<E>
          extended by java.util.ArrayList<T>
              extended by org.geworkbench.bison.datastructure.complex.panels.CSItemList<T>
                  extended by org.geworkbench.bison.datastructure.complex.panels.CSSequentialItemList<T>
                      extended by org.geworkbench.bison.datastructure.biocollections.CSDataSet<T>
                          extended by org.geworkbench.bison.datastructure.biocollections.CSAncillaryDataSet<DSBioObject>
                              extended by org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<DSBioObject>, java.util.Collection<DSBioObject>, java.util.List<DSBioObject>, java.util.RandomAccess, DSAncillaryDataSet<DSBioObject>, DSDataSet<DSBioObject>, DSAlignmentResultSet, DSItemList<DSBioObject>, DSDescribable, DSExtendable, DSIdentifiable, DSNamed

public class CSAlignmentResultSet
extends CSAncillaryDataSet<DSBioObject>
implements DSAlignmentResultSet

See Also:
Serialized Form

Field Summary
 
Fields inherited from class org.geworkbench.bison.datastructure.biocollections.CSDataSet
columnOrder, compatibilityLabel, dataSetProperties, description, experimentInfo, extend, file, label
 
Fields inherited from class java.util.AbstractList
modCount
 
Constructor Summary
CSAlignmentResultSet(java.lang.String resultFile, java.util.List<java.util.Vector<BlastObj>> blastDataSet, java.lang.String fastaFile, DSSequenceSet<? extends DSSequence> blastedParentdataSet, DSSequenceSet<? extends DSSequence> parentDataSet)
           
 
Method Summary
 boolean equals(java.lang.Object ads)
           
 java.util.List<java.util.Vector<BlastObj>> getBlastDataSet()
           
 DSSequenceSet<? extends DSSequence> getBlastedParentDataSet()
           
 java.io.File getDataSetFile()
           
 java.lang.String getDataSetName()
          getDataSetName
 java.io.File getFile()
          getFile
 int getHitCount()
           
 java.lang.String getSummary()
           
 boolean isDirty()
          isDirty
 void setBlastedParentDataSet(DSSequenceSet<? extends DSSequence> blastedParentDataSet)
           
 void setDataSetFile(java.io.File _file)
           
 void setDirty(boolean boolean0)
          setDirty
 
Methods inherited from class org.geworkbench.bison.datastructure.biocollections.CSAncillaryDataSet
getParentDataSet, setParent
 
Methods inherited from class org.geworkbench.bison.datastructure.biocollections.CSDataSet
addNameValuePair, addObject, allowMultipleValues, clearName, forceUniqueValue, getColumnOrder, getCompatibilityLabel, getDescription, getExperimentInformation, getID, getLabel, getObject, getValuesForName, isActive, isUniqueValue, setColumnOrder, setDescription, setExperimentInformation, setFile, setID, setLabel, toString, writeToFile
 
Methods inherited from class org.geworkbench.bison.datastructure.complex.panels.CSSequentialItemList
add, add, remove
 
Methods inherited from class org.geworkbench.bison.datastructure.complex.panels.CSItemList
addAll, clear, get, hashCode, set, setLabel
 
Methods inherited from class java.util.ArrayList
addAll, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, removeRange, size, toArray, toArray, trimToSize
 
Methods inherited from class java.util.AbstractList
iterator, listIterator, listIterator, subList
 
Methods inherited from class java.util.AbstractCollection
containsAll, removeAll, retainAll
 
Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface org.geworkbench.bison.datastructure.biocollections.DSAncillaryDataSet
getParentDataSet
 
Methods inherited from interface org.geworkbench.bison.datastructure.biocollections.DSDataSet
addObject, getColumnOrder, getCompatibilityLabel, getExperimentInformation, 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, 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
 

Constructor Detail

CSAlignmentResultSet

public CSAlignmentResultSet(java.lang.String resultFile,
                            java.util.List<java.util.Vector<BlastObj>> blastDataSet,
                            java.lang.String fastaFile,
                            DSSequenceSet<? extends DSSequence> blastedParentdataSet,
                            DSSequenceSet<? extends DSSequence> parentDataSet)
Parameters:
fileName -
inputFile -
dataSet -
Method Detail

getBlastedParentDataSet

public DSSequenceSet<? extends DSSequence> getBlastedParentDataSet()
Specified by:
getBlastedParentDataSet in interface DSAlignmentResultSet

setBlastedParentDataSet

public void setBlastedParentDataSet(DSSequenceSet<? extends DSSequence> blastedParentDataSet)

isDirty

public boolean isDirty()
isDirty

Returns:
boolean

setDirty

public void setDirty(boolean boolean0)
setDirty

Parameters:
boolean0 - boolean

getDataSetName

public java.lang.String getDataSetName()
getDataSetName

Specified by:
getDataSetName in interface DSDataSet<DSBioObject>
Overrides:
getDataSetName in class CSDataSet<DSBioObject>
Returns:
String

getBlastDataSet

public java.util.List<java.util.Vector<BlastObj>> getBlastDataSet()
Specified by:
getBlastDataSet in interface DSAlignmentResultSet

getDataSetFile

public java.io.File getDataSetFile()

setDataSetFile

public void setDataSetFile(java.io.File _file)

equals

public boolean equals(java.lang.Object ads)
Specified by:
equals in interface java.util.Collection<DSBioObject>
Specified by:
equals in interface java.util.List<DSBioObject>
Overrides:
equals in class CSItemList<DSBioObject>
Parameters:
ads - IAncillaryDataSet
Returns:
boolean

getFile

public java.io.File getFile()
getFile

Specified by:
getFile in interface DSDataSet<DSBioObject>
Overrides:
getFile in class CSDataSet<DSBioObject>
Returns:
File

getSummary

public java.lang.String getSummary()
Specified by:
getSummary in interface DSAlignmentResultSet

getHitCount

public int getHitCount()
Specified by:
getHitCount in interface DSAlignmentResultSet