apollo.util
Class FeatureList

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList
              apollo.util.FeatureList

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess

Direct Known Subclasses:

Selection

public class FeatureList
extends java.util.ArrayList

Just a little helper class. Holds an array list of SeqFeatureIs, add more list methods as needed. This should be replaced by FeatureSet once FeatureSet is refactored, right now FeatureSet is just too heavyweight for such a lightweight activity. Once FS is refactored this should be deleted/incorporated.

See Also:

Serialized Form

Field Summary

protected static org.apache.log4j.Logger

logger

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

FeatureList()

FeatureList(boolean doUniqueCheck)
if unique check is true, check that feat doesnt already exist on adding

FeatureList(int size)

FeatureList(SeqFeatureI seqFeat, boolean addLeaves)
Create FeatureList from seqFeat.

FeatureList(java.util.Vector features)

Method Summary

boolean	add(java.lang.Object o) addFeature should be used in lieu of add.
void	addAlignable(SeqFeatureI alignable)
void	addAll(FeatureList feats) Adds all feats that are new, that it doesnt already have.
void	addAllFeatures(FeatureList feats)
void	addFeature(SeqFeatureI feat) Adds SeqFeatureI if not already in list
void	addFeaturePair(FeaturePairI featPair)
void	addVector(java.util.Vector v)
FeatureList	cloneList() Returns a FeatureList that contains seq feature clones of all features in current list.
FeatureIterator	featureIterator()
FeatureList	filterForFeaturePairs()
SeqFeatureI	first()
SeqFeatureI	getAlignable(int index)
FeatureList	getAllFeaturePairLeaves()
FeatureList	getAllLeaves() Returns a list of all the descendants of the current list that are leaves.
FeatureList	getConsolidatedFeatures() Consolidates features.
FeatureList	getFeatsWithAlignments() Filters FeatureList for features with hasAlignable==true and the Alignable hasAlignmentSequence
FeatureList	getFeatsWithinRefSeqRegion()
SeqFeatureI	getFeature(int index)
FeaturePairI	getFeaturePair(int i)
SeqFeatureI	getFeatWithName(java.lang.String name) not recursive - just gets first feature with name - null if none
FeatureList	getParents() Returns unique list of parents
RangeI	getRangeOfWholeList() Assumes feats on same strand
java.lang.String[]	getUniqueHitNames()
SeqFeatureI	last()
void	removeFeature(SeqFeatureI feat)
void	setAlignablesOnly(boolean alignablesOnly)
void	setDoUniqueCheck(boolean doUniqueCheck)
void	setFeaturePairsOnly(boolean featPairOnly) We could just have a FeaturePairList?
void	sortByStart() this is misnamed.
java.util.Vector	toVector()

Methods inherited from class java.util.ArrayList

add, addAll, addAll, clear, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, remove, removeRange, set, size, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode, iterator, listIterator, listIterator, subList

Methods inherited from class java.util.AbstractCollection

containsAll, removeAll, retainAll, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

containsAll, equals, hashCode, iterator, listIterator, listIterator, removeAll, retainAll, subList

Field Detail

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

FeatureList

public FeatureList()

FeatureList

public FeatureList(int size)

FeatureList

public FeatureList(java.util.Vector features)

FeatureList

public FeatureList(boolean doUniqueCheck)

if unique check is true, check that feat doesnt already exist on adding

FeatureList

public FeatureList(SeqFeatureI seqFeat,
                   boolean addLeaves)

Create FeatureList from seqFeat. If addLeaves is true make feat list of all leaves(descendants) of seqFeat, if addLeaves is false make a list of just the seqFeat itself

Method Detail

addFeature

public void addFeature(SeqFeatureI feat)

Adds SeqFeatureI if not already in list

setDoUniqueCheck

public void setDoUniqueCheck(boolean doUniqueCheck)

addAll

public void addAll(FeatureList feats)

Adds all feats that are new, that it doesnt already have. If we need to do addAll that doesnt guarantee uniqueness we can paramaterize

removeFeature

public void removeFeature(SeqFeatureI feat)

add

public boolean add(java.lang.Object o)

addFeature should be used in lieu of add. This is here as an override to ArrayList.add. cant call addFeature as it calls add. Ive added the constraint that it only adds feature if doesnt already have, in other words cant have redundant features. I think this is always how FeatureLists are used. If not, this can be parameterized.

Specified by:

add in interface java.util.Collection

Specified by:

add in interface java.util.List

Overrides:

add in class java.util.ArrayList

featureIterator

public FeatureIterator featureIterator()

getFeature

public SeqFeatureI getFeature(int index)

last

public SeqFeatureI last()

first

public SeqFeatureI first()

addAllFeatures

public void addAllFeatures(FeatureList feats)

getParents

public FeatureList getParents()

Returns unique list of parents

cloneList

public FeatureList cloneList()

Returns a FeatureList that contains seq feature clones of all features in current list.

toVector

public java.util.Vector toVector()

addVector

public void addVector(java.util.Vector v)

getRangeOfWholeList

public RangeI getRangeOfWholeList()

Assumes feats on same strand

getAllLeaves

public FeatureList getAllLeaves()

Returns a list of all the descendants of the current list that are leaves. Leaves are SeqFeatures with no children (eg Exons, FeaturePairs)

getAllFeaturePairLeaves

public FeatureList getAllFeaturePairLeaves()

getFeatsWithAlignments

public FeatureList getFeatsWithAlignments()

Filters FeatureList for features with hasAlignable==true and the Alignable hasAlignmentSequence

getFeatsWithinRefSeqRegion

public FeatureList getFeatsWithinRefSeqRegion()

getConsolidatedFeatures

public FeatureList getConsolidatedFeatures()

Consolidates features. eg if all exons in a transcript are in the feature list, the transcript is added and the exons are removed. Presently this is not recursive, only does one level of processing as that is all that is needed, change if need be. This stops at "holders". In other words if we have selected all the genes on a strand it will not consolidate to the FeatureSet that is the holder of all those genes.

See Also:

#FeatureSetI.isHolder

sortByStart

public void sortByStart()

this is misnamed. Its sorting by low not start

setFeaturePairsOnly

public void setFeaturePairsOnly(boolean featPairOnly)

We could just have a FeaturePairList?

addFeaturePair

public void addFeaturePair(FeaturePairI featPair)

filterForFeaturePairs

public FeatureList filterForFeaturePairs()

getFeaturePair

public FeaturePairI getFeaturePair(int i)

getUniqueHitNames

public java.lang.String[] getUniqueHitNames()

setAlignablesOnly

public void setAlignablesOnly(boolean alignablesOnly)

addAlignable

public void addAlignable(SeqFeatureI alignable)

getAlignable

public SeqFeatureI getAlignable(int index)

getFeatWithName

public SeqFeatureI getFeatWithName(java.lang.String name)

not recursive - just gets first feature with name - null if none