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A

AbstractDataSource - class softparsmap.AbstractDataSource.: Extending this class will facilitate creating a tag instance that is needed for any class to be installed and used by the property file.
AbstractDataSource() - Constructor for class softparsmap.AbstractDataSource
AbstractEdgeType - class softparsmap.AbstractEdgeType.: Extending this class will facilitate creating a tag instance that is needed for any class to be installed and used by the property file.
AbstractEdgeType() - Constructor for class softparsmap.AbstractEdgeType
AbstractFamilyGroup - class softparsmap.AbstractFamilyGroup.: Extending this class will facilitate creating a tag instance that is needed for any class to be installed and used by the property file.
AbstractFamilyGroup() - Constructor for class softparsmap.AbstractFamilyGroup
AbstractInparalogous - class softparsmap.AbstractInparalogous.: Extending this class will facilitate creating a tag instance that is needed for any class to be installed and used by the property file.
AbstractInparalogous() - Constructor for class softparsmap.AbstractInparalogous
AbstractSequenceData - class softparsmap.AbstractSequenceData.: If the sequences are stored in one file this class can be extended and used together with the class DataSourceXmlGenData.
AbstractSequenceData() - Constructor for class softparsmap.AbstractSequenceData
AbstractStringNodeConverter - class softparsmap.AbstractStringNodeConverter.
AbstractStringNodeConverter() - Constructor for class softparsmap.AbstractStringNodeConverter
AbstractTreeParser - class softparsmap.AbstractTreeParser.: Extending this class will facilitate creating a tag instance that is needed for any class to be installed and used by the property file.
AbstractTreeParser() - Constructor for class softparsmap.AbstractTreeParser
AttributeConverter - interface ooc.AttributeConverter.: Instances implementing this interface are responsible for converting attribute values to Java instances.
AttributeConverterAbstract - class ooc.AttributeConverterAbstract.
AttributeConverterAbstract() - Constructor for class ooc.AttributeConverterAbstract
AttributeConverterAbstract(boolean, boolean) - Constructor for class ooc.AttributeConverterAbstract
AttributeConverterAttributeClass - class ooc.AttributeConverterAttributeClass.
AttributeConverterAttributeClass(boolean, boolean) - Constructor for class ooc.AttributeConverterAttributeClass
AttributeConverterBigDecimal - class ooc.AttributeConverterBigDecimal.
AttributeConverterBigDecimal() - Constructor for class ooc.AttributeConverterBigDecimal
AttributeConverterBoolean - class ooc.AttributeConverterBoolean.
AttributeConverterBoolean() - Constructor for class ooc.AttributeConverterBoolean
AttributeConverterBoolean(boolean, boolean, boolean) - Constructor for class ooc.AttributeConverterBoolean
AttributeConverterDouble - class ooc.AttributeConverterDouble.
AttributeConverterDouble() - Constructor for class ooc.AttributeConverterDouble
AttributeConverterFloat - class ooc.AttributeConverterFloat.
AttributeConverterFloat() - Constructor for class ooc.AttributeConverterFloat
AttributeConverterInstance - class ooc.AttributeConverterInstance.
AttributeConverterInstance() - Constructor for class ooc.AttributeConverterInstance
AttributeConverterInstance(boolean, boolean) - Constructor for class ooc.AttributeConverterInstance
AttributeConverterInstanceThis - class ooc.AttributeConverterInstanceThis.
AttributeConverterInstanceThis(boolean, boolean) - Constructor for class ooc.AttributeConverterInstanceThis
AttributeConverterInteger - class ooc.AttributeConverterInteger.
AttributeConverterInteger() - Constructor for class ooc.AttributeConverterInteger
AttributeConverterList - class ooc.AttributeConverterList.
AttributeConverterList() - Constructor for class ooc.AttributeConverterList
AttributeConverterList(boolean, boolean, AttributeConverter, String) - Constructor for class ooc.AttributeConverterList
AttributeConverterLong - class ooc.AttributeConverterLong.
AttributeConverterLong() - Constructor for class ooc.AttributeConverterLong
AttributeConverterMethod - class ooc.AttributeConverterMethod.
AttributeConverterMethod() - Constructor for class ooc.AttributeConverterMethod
AttributeConverterNumber - class ooc.AttributeConverterNumber.
AttributeConverterNumber() - Constructor for class ooc.AttributeConverterNumber
AttributeConverterShort - class ooc.AttributeConverterShort.
AttributeConverterShort() - Constructor for class ooc.AttributeConverterShort
AttributeConverterString - class ooc.AttributeConverterString.
AttributeConverterString() - Constructor for class ooc.AttributeConverterString
AttributeConverterString(boolean, boolean) - Constructor for class ooc.AttributeConverterString
AttributeConverterStringList - class ooc.AttributeConverterStringList.
AttributeConverterStringList(boolean, boolean, String) - Constructor for class ooc.AttributeConverterStringList
AttributeConverterStringOption - class ooc.AttributeConverterStringOption.
AttributeConverterStringOption() - Constructor for class ooc.AttributeConverterStringOption
AttributeConverterStringOption(boolean, boolean, boolean) - Constructor for class ooc.AttributeConverterStringOption
AttributeConverterTag - class ooc.AttributeConverterTag.
AttributeConverterTag() - Constructor for class ooc.AttributeConverterTag
AttributeConverterTag(boolean, boolean) - Constructor for class ooc.AttributeConverterTag
AttributeConverterTagIdRef - class ooc.AttributeConverterTagIdRef.
AttributeConverterTagIdRef(boolean, boolean) - Constructor for class ooc.AttributeConverterTagIdRef
add(Object) - Method in class softparsmap.ChildSet: Adding an object.
add(Object) - Method in class softparsmap.SortedCollection
addAll(Collection) - Method in class softparsmap.SortedCollection
addChild(Node) - Method in class softparsmap.Node: Adds a child under this parent and sets the child's parent as this node.
addContext(SourceContext) - Method in class ooc.Container: Add the given context to this container.
addDuplication(int) - Method in class softparsmap.Mutation: Adds duplications to this mutation.
addError(Tag, String) - Method in class ooc.TagErrorHandler
addError(TagAttribute, String) - Method in class ooc.TagErrorHandler
addError(TagError) - Method in class ooc.TagErrorHandler
addError(OocException) - Method in class ooc.TagErrorHandler
addError(NotValidException) - Method in class ooc.TagErrorHandler
addLoss(int) - Method in class softparsmap.Mutation: Adds loss to this mutation.
addSequence(GeneLeaf) - Method in class softparsmap.SpeciesLeaf: Adds a given sequence.
addSequence(EdgeType, int) - Method in class softparsmap.SpeciesLeaf: Add a sequence with the the given edge type and label.
afterCompute(FamilyGroup) - Method in class softparsmap.ComputeCompareGeneTrees
afterCompute(boolean) - Method in class softparsmap.ComputeFamilyGroup: This method is called after all families from the family group have been computed.
afterCompute(FamilyGroup) - Method in class softparsmap.ComputeFamilyGroupPair: This method is called after all families from the family group have been computed.
afterCompute(boolean) - Method in class softparsmap.ComputeFamilyNumbers: Prints the set with family numbers.
afterParsing(TreeStructureParser, String, Node) - Method in class softparsmap.AbstractStringNodeConverter
afterParsing(TreeStructureParser, String, Node) - Method in class softparsmap.StringGeneNodeConverterSchreiberMapLabel
afterParsing(TreeStructureParser, String, Node) - Method in interface softparsmap.StringNodeConverter
afterWork(Tag, Object, Dependencies) - Method in class ooc.InstanceConstructorAbstract
afterWork(Tag, Object, Dependencies) - Method in class ooc.InstanceConstructorInjector
afterWork(Tag, Object, Dependencies) - Method in class ooc.InstanceConstructorInjectorSetup
afterWork(Tag, Object, Dependencies) - Method in class ooc.InstanceConstructorReflection
allLeavesIsFromSameSpecies(GeneNode) - Method in class softparsmap.AbstractInparalogous
allLeavesIsFromSameSpecies(GeneNode) - Method in interface softparsmap.Inparalogous: Returns true if all gene leaves are coming from the same species.

B

beforeCompute(FamilyGroup) - Method in class softparsmap.ComputeCompareGeneTrees
beforeCompute(boolean) - Method in class softparsmap.ComputeFamilyGroup: This method is called before any family from the family group is computed.
beforeCompute(FamilyGroup) - Method in class softparsmap.ComputeFamilyGroupPair: This method is called before any family from the family group is computed.
beforeCompute(boolean) - Method in class softparsmap.ComputeFamilyNumbers: Creating the set where all family numbers are stored.
beforeParsing(TreeStructureParser, String, Node) - Method in class softparsmap.AbstractStringNodeConverter
beforeParsing(TreeStructureParser, String, Node) - Method in class softparsmap.StringGeneNodeConverterSchreiberLabel
beforeParsing(TreeStructureParser, String, Node) - Method in class softparsmap.StringGeneNodeConverterSchreiberMapLabel
beforeParsing(TreeStructureParser, String, Node) - Method in class softparsmap.StringGeneNodeConverterStringTemplate
beforeParsing(TreeStructureParser, String, Node) - Method in interface softparsmap.StringNodeConverter

C

CharsetFileWriter - class softparsmap.CharsetFileWriter.: This class makes it easier to write data to file using a specified charset.
CharsetFileWriter(String) - Constructor for class softparsmap.CharsetFileWriter
CharsetFileWriter(File) - Constructor for class softparsmap.CharsetFileWriter
CharsetFileWriter(File, String) - Constructor for class softparsmap.CharsetFileWriter
ChildIterator - class softparsmap.ChildIterator.: This child iterator will take into account that some of a the edges in a gene tree might be collapsed and therefore skip those nodes.
ChildIterator(GeneNode) - Constructor for class softparsmap.ChildIterator: This iterator needs a gene node.
ChildIterator(GeneNode, boolean) - Constructor for class softparsmap.ChildIterator: This iterator needs a gene node and it is possible to store weak edges that are skipped when stepping through the children of the gene node.
ChildSet - class softparsmap.ChildSet.: This set is used as child set for gene trees and as well as for species trees.
ChildSet() - Constructor for class softparsmap.ChildSet: Construct an empty child set.
ChildSet(int) - Constructor for class softparsmap.ChildSet: Set the start capacity.
Compute - class softparsmap.Compute.: This program is used to compute a task.
Compute() - Constructor for class softparsmap.Compute
ComputeCompareGeneTrees - class softparsmap.ComputeCompareGeneTrees.: This program is used to compare the topology of gene trees from two family groups.
ComputeCompareGeneTrees() - Constructor for class softparsmap.ComputeCompareGeneTrees
ComputeFamilyGroup - class softparsmap.ComputeFamilyGroup.: This program is used when computing a task on a specified family group.
ComputeFamilyGroup() - Constructor for class softparsmap.ComputeFamilyGroup
ComputeFamilyGroupPair - class softparsmap.ComputeFamilyGroupPair.: This program is used when computing a task on a pair of family groups.
ComputeFamilyGroupPair() - Constructor for class softparsmap.ComputeFamilyGroupPair
ComputeFamilyNumbers - class softparsmap.ComputeFamilyNumbers.: Will print the numbers of the family group.
ComputeFamilyNumbers() - Constructor for class softparsmap.ComputeFamilyNumbers
ComputeMap - class softparsmap.ComputeMap.: This task will map species from the species tree to the the nodes of the gene tree for all families in a given family group.
ComputeMap() - Constructor for class softparsmap.ComputeMap
ComputeMapInfo - class softparsmap.ComputeMapInfo.: This task will map species from the species tree to the the nodes of the gene tree for all families in a given family group.
ComputeMapInfo() - Constructor for class softparsmap.ComputeMapInfo
ComputeRoot - class softparsmap.ComputeRoot.: This task will root unrooted gene trees by minimizing duplications and loss.
ComputeRoot() - Constructor for class softparsmap.ComputeRoot
Container - class ooc.Container.: The container.
Container() - Constructor for class ooc.Container: Constructs an container with only the Jooc descriptor loaded.
Container(SourceContext) - Constructor for class ooc.Container: Constructs an container with only the Jooc descriptor loaded.
Container(File) - Constructor for class ooc.Container: Constructs a container using a file descriptor.
Container(String) - Constructor for class ooc.Container: Constructs the container and then loads given source, looking for it in the classpath, current directory, and as a file.
characters(char[], int, int) - Method in class ooc.TagParser
childToParent - Variable in class softparsmap.DataSourceIndexXmlNcbiTaxonomy: This map contain the tree and is created from the file nodes.dmp.
clear() - Method in class softparsmap.SortedCollection
clone() - Method in interface ooc.Template
cloneFamily() - Method in class softparsmap.Family: Returns a copy of this family.
cloneNode() - Method in class softparsmap.GeneLeaf
cloneNode() - Method in class softparsmap.GeneNode: Returns a copy of this GeneNode.
cloneTree() - Method in class softparsmap.GeneNode: Returns a copy of this subtree.
close() - Method in class softparsmap.CharsetFileWriter
collapseEdges() - Method in class softparsmap.GeneNode: Collapsing all edges in this subtree where the collapsed flag is set.
collapsedEdges() - Method in class softparsmap.GeneNode: Return all nodes in the subtree where their collapse flag is set to true.
compare(Object, Object) - Method in class softparsmap.PreferredTreeStandard
compareTo(Object) - Method in class softparsmap.Family: Compare the family number between this and a second family.
compareTo(Object) - Method in class softparsmap.GeneLeaf
compareTo(Object) - Method in class softparsmap.Node: Returns this label number minus the given nodes label number.
computeFamily(Family, FamilyGroup, boolean) - Method in class softparsmap.ComputeCompareGeneTrees
computeFamily(Family, boolean) - Method in class softparsmap.ComputeFamilyGroup: Compute a family.
computeFamily(Family, FamilyGroup, boolean) - Method in class softparsmap.ComputeFamilyGroupPair: Compute a family.
computeFamily(Family, boolean) - Method in class softparsmap.ComputeFamilyNumbers: Store the family number in the set.
computeFamily(Family, boolean) - Method in class softparsmap.ComputeMap
computeFamily(Family, boolean) - Method in class softparsmap.ComputeMapInfo
computeFamily(Family, boolean) - Method in class softparsmap.ComputeRoot
computeLca(Set) - Static method in class softparsmap.SpeciesNode: Returns the last common ancestor of the given set of species nodes.
computeLca(SpeciesNode, SpeciesNode) - Static method in class softparsmap.SpeciesNode: Returns the last common ancestor of the two given species nodes.
computeTask() - Method in class softparsmap.Compute: Is called by main method to run task.
computeTask() - Method in class softparsmap.ComputeFamilyGroup
computeTask() - Method in class softparsmap.ComputeFamilyGroupPair
constructInstance(Tag, InstanceHolder, Dependencies) - Method in interface ooc.InstanceConstructor: Constructing a tag instance using the given tag and InstanceHolder.
constructInstance(Tag, InstanceHolder, Dependencies) - Method in class ooc.InstanceConstructorAbstract
constructReference(Tag, Dependencies) - Method in class ooc.InstanceConstructorAbstract
constructReference(Tag, Dependencies) - Method in class ooc.InstanceConstructorReflection
contains(Object) - Method in class softparsmap.SortedCollection
containsAll(Collection) - Method in class softparsmap.SortedCollection
containsInstance(Tag) - Method in interface ooc.InstanceHolder: Returns true if a tag instance is available for given tag, else false.
containsInstance(Tag) - Method in class ooc.InstanceHolderPrimitive
containsInstance(Tag) - Method in class ooc.InstanceHolderSingleton
containsKey(Object) - Method in interface ooc.Dependencies: Returns true if the key exists in this map.
containsKey(Object) - Method in class ooc.LinkedTagInstance
containsTag(String) - Method in class ooc.Container: Returns true if this container has a tag with the given tag id, else false.
containsTag(String) - Method in class ooc.SourceTagHolder: Returns true if this holder or any imported holder contains the tag with the given tag id, else false.
convert(String, String, Tag, TagAttribute, Dependencies) - Method in interface ooc.AttributeConverter: Return the java instance constructed using the attribute at hand.
convert(String, String, Tag, TagAttribute, Dependencies) - Method in class ooc.AttributeConverterAbstract
convert(String, String, Tag, TagAttribute, Dependencies) - Method in class ooc.AttributeConverterInstanceThis
convertCoreFromLeaf(Node, Object) - Method in class softparsmap.StringGeneNodeConverterDupSpe
convertCoreFromLeaf(Node, Object) - Method in class softparsmap.StringGeneNodeConverterLabel
convertCoreFromLeaf(Node, Object) - Method in class softparsmap.StringGeneNodeConverterNcbiNamesColumn
convertCoreFromLeaf(Node, Object) - Method in class softparsmap.StringGeneNodeConverterSchreiberLabel
convertCoreFromLeaf(Node, Object) - Method in class softparsmap.StringGeneNodeConverterSequenceDataXml
convertCoreFromLeaf(Node, Object) - Method in class softparsmap.StringNodeConverterMapInfo
convertCoreFromLeaf(Node, Object) - Method in class softparsmap.StringNodeConverterStringTemplate
convertCoreFromNode(Node, Object) - Method in class softparsmap.StringGeneNodeConverterDupSpe
convertCoreFromNode(Node, Object) - Method in class softparsmap.StringGeneNodeConverterLabel
convertCoreFromNode(Node, Object) - Method in class softparsmap.StringGeneNodeConverterNcbiNamesColumn
convertCoreFromNode(Node, Object) - Method in class softparsmap.StringGeneNodeConverterSchreiberLabel
convertCoreFromNode(Node, Object) - Method in class softparsmap.StringGeneNodeConverterSequenceDataXml
convertCoreFromNode(Node, Object) - Method in class softparsmap.StringNodeConverterMapInfo
convertCoreFromNode(Node, Object) - Method in class softparsmap.StringNodeConverterStringTemplate
convertCoreToLeaf(String, Object) - Method in class softparsmap.StringGeneNodeConverterDupSpe
convertCoreToLeaf(String, Object) - Method in class softparsmap.StringGeneNodeConverterLabel
convertCoreToLeaf(String, Object) - Method in class softparsmap.StringGeneNodeConverterSchreiberLabel
convertCoreToLeaf(String, Object) - Method in class softparsmap.StringNodeConverterMapInfo
convertCoreToLeaf(String, Object) - Method in class softparsmap.StringNodeConverterStringTemplate
convertCoreToNode(String, Object) - Method in class softparsmap.StringGeneNodeConverterDupSpe
convertCoreToNode(String, Object) - Method in class softparsmap.StringGeneNodeConverterLabel
convertCoreToNode(String, Object) - Method in class softparsmap.StringGeneNodeConverterSchreiberLabel
convertCoreToNode(String, Object) - Method in class softparsmap.StringNodeConverterMapInfo
convertCoreToNode(String, Object) - Method in class softparsmap.StringNodeConverterStringTemplate
convertFromLeaf(Node, Object) - Method in interface softparsmap.StringNodeConverter
convertFromLeaf(Node, Object) - Method in class softparsmap.StringNodeConverterStringTemplate
convertFromNode(Node, Object) - Method in interface softparsmap.StringNodeConverter
convertFromNode(Node, Object) - Method in class softparsmap.StringNodeConverterStringTemplate
convertToLeaf(String, Object) - Method in interface softparsmap.StringNodeConverter
convertToLeaf(String, Object) - Method in class softparsmap.StringNodeConverterStringTemplate
convertToNode(String, Object) - Method in interface softparsmap.StringNodeConverter
convertToNode(String, Object) - Method in class softparsmap.StringNodeConverterStringTemplate
convertToNotValid() - Method in class ooc.OocException
convertWrapt(String, String, Tag, TagAttribute, Dependencies) - Method in class ooc.AttributeConverterAbstract
convertWrapt(String, String, Tag, TagAttribute, Dependencies) - Method in class ooc.AttributeConverterBoolean
convertWrapt(String, String, Tag, TagAttribute, Dependencies) - Method in class ooc.AttributeConverterInstance
convertWrapt(String, String, Tag, TagAttribute, Dependencies) - Method in class ooc.AttributeConverterInstanceThis
convertWrapt(String, String, Tag, TagAttribute, Dependencies) - Method in class ooc.AttributeConverterList
convertWrapt(String, String, Tag, TagAttribute, Dependencies) - Method in class ooc.AttributeConverterMethod
convertWrapt(String, String, Tag, TagAttribute, Dependencies) - Method in class ooc.AttributeConverterNumber
convertWrapt(String, String, Tag, TagAttribute, Dependencies) - Method in class ooc.AttributeConverterString
convertWrapt(String, String, Tag, TagAttribute, Dependencies) - Method in class ooc.AttributeConverterStringList
convertWrapt(String, String, Tag, TagAttribute, Dependencies) - Method in class ooc.AttributeConverterTag
countDuplications() - Method in class softparsmap.GeneNode: Returns the number of duplications in this subtree.
countGeneLosses() - Method in class softparsmap.GeneNode: Returns the number of losses in this subtree.
countMutation() - Method in class softparsmap.GeneNode: Returns the number of duplications and losses in this subtree.
countStrongEdges() - Method in class softparsmap.GeneNode: Counting the number of strong edges in this subtree.
createSource(String) - Method in interface ooc.SourceContext: Returns a newly created source from which tags can be parsed.
createSource(String) - Method in class ooc.SourceContextClassPath
createSource(String) - Method in class ooc.SourceContextDirectory
createSource(String) - Method in class ooc.SourceContextFile
createTagError() - Method in class ooc.NotValidException
createTagTree(SourceTagHolder) - Static method in class ooc.TagParser: Static methods

D

DataSource - interface softparsmap.DataSource.: This interface is responsible of providing the package with data regarding species trees and gene sequences.
DataSourceIndexXmlNcbiTaxonomy - class softparsmap.DataSourceIndexXmlNcbiTaxonomy.: Index for data source DataSourceXmlNcbiTaxonomy.
DataSourceIndexXmlNcbiTaxonomy() - Constructor for class softparsmap.DataSourceIndexXmlNcbiTaxonomy: Constructor creates empty maps.
DataSourceXmlNcbiTaxonomy - class softparsmap.DataSourceXmlNcbiTaxonomy.: This data source can be used when the sequence database is an XML document.
DataSourceXmlNcbiTaxonomy() - Constructor for class softparsmap.DataSourceXmlNcbiTaxonomy
Dependencies - interface ooc.Dependencies.: When constructing tag instances or converting attributes are dependent on instances beyond the reach of the container, these instances may be introduced using this interface.
DependenciesMapped - class ooc.DependenciesMapped.
DependenciesMapped() - Constructor for class ooc.DependenciesMapped
DependenciesMapped(Dependencies) - Constructor for class ooc.DependenciesMapped
databaseIdToFilePointerPart - Variable in class softparsmap.DataSourceIndexXmlNcbiTaxonomy: A map from the database id numbers (Integer) to a position (FilePointerPart) in the database that holds the sequence part.
databaseIdToNodesId - Variable in class softparsmap.DataSourceIndexXmlNcbiTaxonomy: A map from the database id number (Integer) to the tax id number in NCBI (Integer).
dependenciesToString(Dependencies) - Static method in class ooc.Tools
duplicatedNode() - Method in class softparsmap.GeneNode: Returns true if this node is duplicated.

E

END_PARAM - Static variable in class ooc.AttributeConverterMethod
EdgeType - interface softparsmap.EdgeType.: This interface is used to define different properties of an edge in a gene tree.
endElement(String, String, String) - Method in class ooc.TagParser
equals(Object) - Method in class softparsmap.Family: The families are the same if their family numbers are the same.
equals(Object) - Method in class softparsmap.Node: Two nodes are equal iff they have the same label.
equals(Object) - Method in class softparsmap.SortedCollection
extending(Tag) - Method in class ooc.Tag: Return true if this tag is extending the given tag.
extendingOneOrMore(Iterator) - Method in class ooc.Tag

F

Family - class softparsmap.Family.: This class represents a gene family.
Family(FamilyGroup, Integer) - Constructor for class softparsmap.Family: A family needs to know from which family group it comes from.
FamilyGroup - interface softparsmap.FamilyGroup.: This interface represents a set of gene families and it is responsible of providing these families for a certain task.
FamilyGroupTreesInFiles - class softparsmap.FamilyGroupTreesInFiles.: This family group assume that there is one file per family and that the family number can be found in the file name.
FamilyGroupTreesInFiles() - Constructor for class softparsmap.FamilyGroupTreesInFiles
FamilyGroupTreesInFilesInfoPerRow - class softparsmap.FamilyGroupTreesInFilesInfoPerRow.
FamilyGroupTreesInFilesInfoPerRow() - Constructor for class softparsmap.FamilyGroupTreesInFilesInfoPerRow
FatalException - exception softparsmap.FatalException.: A fatal exception.
FatalException(String) - Constructor for class softparsmap.FatalException: Creating a fatal exception using the description.
FatalException(String, Throwable) - Constructor for class softparsmap.FatalException: Constructing an fatal exception using an description and a cause exception.
FilePointerPart - class softparsmap.FilePointerPart.: This class points to a block of bytes in a file.
FilePointerPart(long, int) - Constructor for class softparsmap.FilePointerPart: An instance needs a pointer which points into the file and how many bytes the block consists of.
findField(Class, String, String, Tag, TagErrorHandler) - Method in class ooc.InstanceInjectorAttributeAllField
findLCA(Set) - Method in class softparsmap.Node: Find the last common ancestor in this subtree for the given set of leaves.
findLeaf(GeneLeaf) - Method in class softparsmap.GeneLeaf
findLeaf(int) - Method in class softparsmap.GeneNode: Returns the leaf with given label.
findLeaf(GeneLeaf) - Method in class softparsmap.GeneNode: Returns the leaf with the same label as given leaf.
findNode(GeneNode) - Method in class softparsmap.GeneNode: Returns the gene node that exists in this subtree and has the same label.
findNodeForUnrootedSplit(Set, Set) - Method in class softparsmap.GeneNode: Returns the gene node that harbor the split that contain the leaf set 'splitLeavesA'.
first() - Method in class softparsmap.SortedCollection
flush() - Method in class softparsmap.CharsetFileWriter

G

GeneLeaf - class softparsmap.GeneLeaf.: Defines a gene leaf in a gene tree.
GeneLeaf(EdgeType, int, double) - Constructor for class softparsmap.GeneLeaf: Construct a gene leaf given an edge type, a label, and an edge value.
GeneLeaf(EdgeType, int) - Constructor for class softparsmap.GeneLeaf: Same as using the constructor GeneLeaf(edgeType, label, 1.0);
GeneNode - class softparsmap.GeneNode.: Defines a gene node in a gene tree.
GeneNode(EdgeType, int) - Constructor for class softparsmap.GeneNode: Constructs a gene node given an edge type and a label.
GeneNode(EdgeType, int, double) - Constructor for class softparsmap.GeneNode: Constructs a gene node given an edge type, edge value, and label.
get(Object) - Method in interface ooc.Dependencies: Returns the depdendency mapped to by the given key.
get(Object) - Method in class ooc.LinkedTagInstance
getAncestorIterator() - Method in class ooc.Tag
getArg(int) - Method in class softparsmap.Compute: Returns the specified argument.
getArgs() - Method in class softparsmap.Compute: Returns a list with remaining arguments.
getAttribute(String) - Method in class ooc.LinkedTagInstance: For more information see Tag.getAttribute(java.lang.String, java.lang.Object, java.lang.Object).
getAttribute(String, Object, Object) - Method in class ooc.Tag
getAttribute(String) - Method in class ooc.Tag
getAttribute(String, Dependencies) - Method in class ooc.Tag
getAttribute(Tag, Dependencies) - Method in class ooc.TagAttribute
getAttributeBoolean(String) - Method in class ooc.LinkedTagInstance: For more information see Tag.getAttributeBoolean(java.lang.String, ooc.Dependencies).
getAttributeBoolean(String, Dependencies) - Method in class ooc.Tag: Returns a parsed boolean value using method Tag.getAttribute(java.lang.String, java.lang.Object, java.lang.Object).
getAttributeBoolean(String) - Method in class ooc.Tag
getAttributeDouble(String) - Method in class ooc.LinkedTagInstance: For more information see Tag.getAttributeDouble(java.lang.String, ooc.Dependencies).
getAttributeDouble(String, Dependencies) - Method in class ooc.Tag: Returns a parsed double value using method Tag.getAttribute(java.lang.String, java.lang.Object, java.lang.Object).
getAttributeDouble(String) - Method in class ooc.Tag
getAttributeFloat(String) - Method in class ooc.LinkedTagInstance: For more information see Tag.getAttributeFloat(java.lang.String, ooc.Dependencies).
getAttributeFloat(String, Dependencies) - Method in class ooc.Tag: Returns a parsed float value using method Tag.getAttribute(java.lang.String, java.lang.Object, java.lang.Object).
getAttributeFloat(String) - Method in class ooc.Tag
getAttributeInteger(String) - Method in class ooc.LinkedTagInstance: For more information see Tag.getAttributeInteger(java.lang.String, ooc.Dependencies).
getAttributeInteger(String, Dependencies) - Method in class ooc.Tag: Returns a parsed int value using method Tag.getAttribute(java.lang.String, java.lang.Object, java.lang.Object).
getAttributeInteger(String) - Method in class ooc.Tag
getAttributeKeyIterator() - Method in class ooc.Tag
getAttributeList(String) - Method in class ooc.LinkedTagInstance: For more information see Tag.getAttributeList(java.lang.String).
getAttributeList(String) - Method in class ooc.Tag
getAttributeList(String, Dependencies) - Method in class ooc.Tag
getAttributeLong(String, Dependencies) - Method in class ooc.Tag: Returns a parsed long value using method Tag.getAttribute(java.lang.String, java.lang.Object, java.lang.Object).
getAttributeLong(String) - Method in class ooc.Tag
getAttributeName() - Method in class ooc.TagAttribute
getAttributeRef(String) - Method in class ooc.LinkedTagInstance: For more information see Tag.getAttributeRef(java.lang.String).
getAttributeRef(String) - Method in class ooc.Tag
getAttributeRef(TagAttribute) - Method in class ooc.Tag
getAttributeShort(String) - Method in class ooc.LinkedTagInstance: For more information see Tag.getAttributeShort(java.lang.String, ooc.Dependencies).
getAttributeShort(String, Dependencies) - Method in class ooc.Tag: Returns a parsed short value using method Tag.getAttribute(java.lang.String, java.lang.Object, java.lang.Object).
getAttributeShort(String) - Method in class ooc.Tag
getAttributeString(String) - Method in class ooc.LinkedTagInstance: For more information see Tag.getAttributeString(java.lang.String, ooc.Dependencies).
getAttributeString(String, Dependencies) - Method in class ooc.Tag: Returns a string using method Tag.getAttribute(java.lang.String, java.lang.Object, java.lang.Object).
getAttributeString(String) - Method in class ooc.Tag
getAttributeTag(String) - Method in class ooc.LinkedTagInstance: For more information see Tag.getAttributeTag(String name).
getAttributeTag(String, Dependencies) - Method in class ooc.Tag: Returns a Tag using method Tag.getAttribute(java.lang.String, java.lang.Object, java.lang.Object).
getAttributeTag(String) - Method in class ooc.Tag
getCharset() - Method in class softparsmap.AbstractTreeParser: Returns the name of the encoding.
getChildIterator() - Method in class ooc.LinkedTagInstance: For more information see Tag.getChildIterator(ooc.Tag).
getChildIterator(Tag) - Method in class ooc.Tag: Returns an iterator of the children of this tag such that all retained from the iterator extends superTag.
getChildIterator() - Method in class ooc.Tag: Returns an iterator of the children of this tag.
getChildIterator(Tag) - Method in class ooc.TagValidatorRestrictChildTag
getChildIterator(Tag) - Method in class ooc.TagValidatorRestrictChildTree
getChildIterator() - Method in class softparsmap.GeneNode: Returns the child iterator for this node.
getChildIteratorByName(String) - Method in class ooc.LinkedTagInstance: For more information see Tag.getChildIteratorByName(String tagName).
getChildIteratorByName(String) - Method in class ooc.Tag: Returns an iterator with child tags such that their name is as given.
getChildren() - Method in class softparsmap.GeneLeaf: Leaves can not have children so this will throw an FatalException.
getChildren() - Method in class softparsmap.Node: Returns the child set containing the children.
getChildren() - Method in class softparsmap.SpeciesLeaf: Leaves can not have children so if calling this method will throw a FatalException.
getClass(String, String, Tag, TagAttribute, TagErrorHandler) - Method in interface ooc.AttributeConverter: Returns the class of the instance converted by this attribute converter.
getClass(String, String, Tag, TagAttribute, TagErrorHandler) - Method in class ooc.AttributeConverterBigDecimal
getClass(String, String, Tag, TagAttribute, TagErrorHandler) - Method in class ooc.AttributeConverterBoolean
getClass(String, String, Tag, TagAttribute, TagErrorHandler) - Method in class ooc.AttributeConverterDouble
getClass(String, String, Tag, TagAttribute, TagErrorHandler) - Method in class ooc.AttributeConverterFloat
getClass(String, String, Tag, TagAttribute, TagErrorHandler) - Method in class ooc.AttributeConverterInstance
getClass(String, String, Tag, TagAttribute, TagErrorHandler) - Method in class ooc.AttributeConverterInstanceThis
getClass(String, String, Tag, TagAttribute, TagErrorHandler) - Method in class ooc.AttributeConverterInteger
getClass(String, String, Tag, TagAttribute, TagErrorHandler) - Method in class ooc.AttributeConverterList
getClass(String, String, Tag, TagAttribute, TagErrorHandler) - Method in class ooc.AttributeConverterLong
getClass(String, String, Tag, TagAttribute, TagErrorHandler) - Method in class ooc.AttributeConverterMethod
getClass(String, String, Tag, TagAttribute, TagErrorHandler) - Method in class ooc.AttributeConverterShort
getClass(String, String, Tag, TagAttribute, TagErrorHandler) - Method in class ooc.AttributeConverterString
getClass(String, String, Tag, TagAttribute, TagErrorHandler) - Method in class ooc.AttributeConverterStringList
getClass(String, String, Tag, TagAttribute, TagErrorHandler) - Method in class ooc.AttributeConverterTag
getClass(Tag, TagErrorHandler) - Static method in class ooc.Tools
getClass(Tag, String, Tag, TagErrorHandler) - Static method in class ooc.Tools
getClasses(Tag, List, Tag, TagErrorHandler) - Static method in class ooc.Tools
getClasses(Object[]) - Static method in class ooc.Tools
getClassesToInject(Class, Tag, Tag, Dependencies, TagErrorHandler) - Method in class ooc.InstanceInjectorMethodAbstract
getClassesToInject(Class, Tag, Tag, Dependencies, TagErrorHandler) - Method in class ooc.InstanceInjectorMethodAttributes
getClassesToInject(Class, Tag, Tag, Dependencies, TagErrorHandler) - Method in class ooc.InstanceInjectorMethodInstances
getClassesToInject(Class, Tag, Tag, Dependencies, TagErrorHandler) - Method in class ooc.InstanceInjectorTag
getCollapsedEdge() - Method in class softparsmap.GeneNode: Returns true if the node is flagged collapsed.
getComparator() - Method in class softparsmap.SortedCollection: Returns the comparator used when keeping the elements sorted.
getConstructor(Tag, Class, Class[], TagErrorHandler) - Static method in class ooc.Tools
getConstructorRef(Class, Class[]) - Static method in class ooc.Tools
getContainer() - Method in class ooc.LinkedTagInstance: Returns the tag handler from which this tag was generated.
getContainer() - Method in class ooc.SourceTagHolder
getContainer() - Method in class ooc.Tag: Returns the Container instance that this tag belong to.
getContainerTag(String) - Method in class ooc.LinkedTagInstance
getContainerTag(String) - Method in class ooc.Tag
getConverter() - Method in class ooc.TagAttribute
getDataSource() - Method in class softparsmap.AbstractFamilyGroup
getDataSource() - Method in interface softparsmap.FamilyGroup: Returns the data source that this family group is using.
getDataSource() - Method in class softparsmap.SpeciesNode: Returns the data source for this species node.
getDefaultLeafEdge() - Method in class softparsmap.AbstractEdgeType
getDefaultLeafEdge() - Method in interface softparsmap.EdgeType
getDefaultNodeEdge() - Method in class softparsmap.AbstractEdgeType
getDefaultNodeEdge() - Method in interface softparsmap.EdgeType
getDependencyMethodName() - Method in class ooc.InstanceInjectorAttribute
getDependencyMethodName() - Method in class ooc.InstanceInjectorChildInstances
getDesc(GeneNode) - Method in class softparsmap.PreferredTree: Returns the data used in the given gene tree that is used to choose the preferred tree.
getDesc(GeneNode) - Method in class softparsmap.PreferredTreeStandard
getDescendentIterator() - Method in class ooc.Tag
getDuplicatedNodes() - Method in class softparsmap.GeneNode: Returns the set of all duplicated nodes in this subtree.
getDuplication() - Method in class softparsmap.Mutation: Returns number of duplications.
getDuplicationsNode() - Method in class softparsmap.GeneNode: Returns the number of duplications this node causes given a species tree.
getEdgeType() - Method in class softparsmap.GeneNode: Returns the edge type of the edge that belong to this node.
getEdgeType() - Method in class softparsmap.TreeParserNewick: Returns the edge type that exists in the tree.
getEdgeValue() - Method in class softparsmap.GeneNode: Returns the edge value.
getErrorCount() - Method in class ooc.TagErrorHandler
getFamilies() - Method in interface softparsmap.FamilyGroup: Returns the set of Family instances that this this family group is responsible for.
getFamilies() - Method in class softparsmap.FamilyGroupTreesInFiles
getFamily() - Method in class softparsmap.GeneNode: Returns the family that this node belongs to.
getFamilyGroup() - Method in class softparsmap.Family: Returns the family group to which this family belongs.
getFamilyGroup1() - Method in class softparsmap.ComputeFamilyGroupPair
getFamilyGroup2() - Method in class softparsmap.ComputeFamilyGroupPair
getFamilyNumber() - Method in class softparsmap.Family: Returns the family number.
getFirstChildTag(Tag) - Method in class ooc.Tag: Returns the first child tag extending the given name.
getFirstChildTagByName(String) - Method in class ooc.LinkedTagInstance: For more information see Tag.getFirstChildTagByName(java.lang.String).
getFirstChildTagByName(String) - Method in class ooc.Tag: Returns the first child tag with the given name.
getFirstValue(String) - Method in class softparsmap.StringTemplate: Returns the value of the first marker named as given.
getFreeGeneTree() - Method in class softparsmap.PreferredTree: Returns the free gene tree.
getGeneLossesNode() - Method in class softparsmap.GeneNode: Returns the number of gene losses this node causes given a species tree.
getGeneTree() - Method in class softparsmap.Family: Returns the gene tree.
getGeneTree(Integer) - Method in interface softparsmap.FamilyGroup: Returns the gene tree given a family number.
getGeneTree(Integer) - Method in class softparsmap.FamilyGroupTreesInFiles
getGeneTree(Integer) - Method in class softparsmap.FamilyGroupTreesInFilesInfoPerRow
getGiNumber() - Method in interface softparsmap.SequenceData: Returns the GI number.
getGiNumber() - Method in class softparsmap.SequenceDataXml
getGroupName() - Method in class softparsmap.AbstractFamilyGroup: Returns the name of the family group which is the value in the did attribute in the tag.
getGroupName() - Method in interface softparsmap.FamilyGroup: Returns the name of the family group.
getIdNumber() - Method in interface softparsmap.SequenceData: Returns the identity number for this sequence.
getIdNumber() - Method in class softparsmap.SequenceDataXml
getInparalogous(Family, GeneNode) - Method in class softparsmap.AbstractInparalogous
getInparalogous() - Method in class softparsmap.Compute: Returns a singleton instance of Inparalogous definied by attribute 'inparalogous' which this task can use regarding inparalogous.
getInparalogous(Family, GeneNode) - Method in interface softparsmap.Inparalogous: Returns a set of nodes N where all nodes n in N only have in-paralogous sequences in its subtree.
getInputStream() - Method in interface ooc.Source: Returns the input stream of this source.
getInputStream() - Method in class ooc.SourceInputStream
getInstance(Tag) - Method in interface ooc.InstanceHolder: Returns the tag available for the given tag.
getInstance(Tag) - Method in class ooc.InstanceHolderPrimitive
getInstance(Tag) - Method in class ooc.InstanceHolderSingleton
getInstanceToInject(Object, Tag, Tag, Dependencies) - Method in class ooc.InstanceInjectorMethodAbstract
getInstanceToInject(Object, Tag, Tag, Dependencies) - Method in class ooc.InstanceInjectorMethodAttributes
getInstanceToInject(Object, Tag, Tag, Dependencies) - Method in class ooc.InstanceInjectorMethodInstances
getInstanceToInject(Object, Tag, Tag, Dependencies) - Method in class ooc.InstanceInjectorTag
getInternalNodes() - Method in class softparsmap.GeneNode: Return all internal nodes in this subtree.
getL1() - Method in class softparsmap.Split: Returns the first part of this split.
getL2() - Method in class softparsmap.Split: Returns the second part of this split.
getLabel() - Method in class softparsmap.Node: Returns the label.
getLeafComparator(Family) - Method in interface softparsmap.Inparalogous: Returns a comparator that compare gene leaves.
getLeafComparator(Family) - Method in class softparsmap.InparalogousStandard: Returns a comparator that compare gene leaves.
getLeafKey() - Method in class softparsmap.StringNodeConverterMapInfo
getLeaves() - Method in class softparsmap.Node: Return the leaves of this subtree.
getLength() - Method in class softparsmap.FilePointerPart: Returns the length of the block.
getLocator() - Method in class ooc.TagParser
getLoss() - Method in class softparsmap.Mutation: Returns number of loss.
getM() - Method in class softparsmap.GeneLeaf
getM() - Method in class softparsmap.GeneNode: See the m-map in the article.
getM() - Method in class softparsmap.MuNode
getMM() - Method in class softparsmap.GeneNode: See the M-map in the article.
getMM() - Method in class softparsmap.MuNode
getMap() - Method in class softparsmap.Node: Returns a map that can be used to save any additional information associated with this node.
getMessage() - Method in class ooc.NotValidException
getMessage() - Method in class ooc.OocException
getMethod(Class, String, Class[]) - Static method in class ooc.Tools: Helpers
getMethodName() - Method in class ooc.InstanceInjectorAttribute
getMethodName() - Method in class ooc.InstanceInjectorChildInstances
getMethodName() - Method in class ooc.InstanceInjectorMethodAbstract
getMethodRef(Object, String, Object[]) - Static method in class ooc.Tools
getMethodRef(Class, String) - Static method in class ooc.Tools
getMethodRef(Class, String, Class) - Static method in class ooc.Tools
getMethodRef(Class, String, Class[]) - Static method in class ooc.Tools
getMethodRef(Class, String, String) - Static method in class ooc.Tools
getName() - Method in interface ooc.Source: Returns the name of this source.
getName() - Method in interface ooc.SourceContext: Returns the name of this source context.
getName() - Method in class ooc.SourceContextAbstract
getName() - Method in class ooc.SourceInputStream
getName() - Method in interface softparsmap.EdgeType: Returns the name of the edge type.
getName() - Method in class softparsmap.StandardEdgeType
getNcbiNamesColumn(SpeciesNode, int) - Method in class softparsmap.DataSourceXmlNcbiTaxonomy
getNcbiTagId(SpeciesNode) - Method in class softparsmap.DataSourceXmlNcbiTaxonomy
getNodeKey() - Method in class softparsmap.StringNodeConverterMapInfo
getNodes() - Method in class softparsmap.Node: Return all internal nodes and leaves in this subtree.
getNumberOfSequences() - Method in class softparsmap.Family: Returns the number of sequences of this family.
getPaintedTemplate() - Method in class softparsmap.StringTemplate: After markers have been set, calling this method will return the template with its markers painted accordingly.
getParent() - Method in class ooc.TagParser
getParent() - Method in class softparsmap.Node: Returns the parent of this node.
getParentTag() - Method in class ooc.Tag: Returns the parent tag of this tag.
getPointer() - Method in class softparsmap.FilePointerPart: Returns the pointer.
getPrintFamilyInfo() - Method in class softparsmap.Compute: If this methods returns true, Compute will print header information and more when executed.
getPropertyFile() - Method in class softparsmap.AbstractDataSource
getPropertyFile() - Method in class softparsmap.AbstractEdgeType
getPropertyFile() - Method in class softparsmap.AbstractFamilyGroup
getPropertyFile() - Method in class softparsmap.AbstractSequenceData: Returns the property file.
getPropertyFile() - Method in class softparsmap.AbstractTreeParser: Returns the property file.
getPropertyFile() - Method in class softparsmap.Compute: Returns the property file.
getPropertyFile() - Method in interface softparsmap.DataSource: Returns the property file.
getPropertyFile() - Method in interface softparsmap.EdgeType: Returns the property file.
getPropertyFile() - Method in class softparsmap.Family: Returns the property file.
getPropertyFile() - Method in interface softparsmap.FamilyGroup: Returns the property file.
getPropertyFile() - Method in class softparsmap.GeneNode: Returns the property file.
getPropertyFile() - Method in class softparsmap.SpeciesNode: Returns the property file.
getReturnType(Class, String) - Static method in class ooc.Tools
getReturnType(Class, String, Class) - Static method in class ooc.Tools
getReturnType(Class, String, Class[]) - Static method in class ooc.Tools
getRoot() - Method in class ooc.TagParser
getRoot() - Method in class softparsmap.Node: Returns the root of this tree.
getSL() - Method in class softparsmap.GeneNode: See the SL function in the article.
getSL() - Method in class softparsmap.MuNode
getSequenceData(GeneLeaf) - Method in interface softparsmap.DataSource: Returns an instance that implements the interface SequenceData for a given gene leaf.
getSequenceData(GeneLeaf) - Method in class softparsmap.DataSourceXmlNcbiTaxonomy
getSequenceLength() - Method in interface softparsmap.SequenceData: Returns the length of the sequence.
getSequenceLength() - Method in class softparsmap.SequenceDataXml
getSequences() - Method in class softparsmap.SpeciesLeaf: Returns the set of gene sequences that belongs to this species.
getShortName() - Method in interface softparsmap.EdgeType: Returns a short name of this edge type.
getShortName() - Method in class softparsmap.StandardEdgeType
getSource() - Method in class ooc.SourceTagHolder
getSourceContext() - Method in interface ooc.Source: Returns the context for this source.
getSourceContext() - Method in class ooc.SourceInputStream
getSourceLine() - Method in class ooc.Tag: Returns the number of the line of the source where this tag was parsed.
getSourceName() - Method in class ooc.SourceTagHolder
getSourceTagHolder() - Method in class ooc.Tag: Returns the source tag holder where this tag resides.
getSourceTagHolder() - Method in class ooc.TagParser
getSpeciesName(SpeciesNode) - Method in interface softparsmap.DataSource: Returns the name of the species for a given species node.
getSpeciesName(SpeciesNode) - Method in class softparsmap.DataSourceXmlNcbiTaxonomy
getSpeciesName() - Method in interface softparsmap.SequenceData: Returns the species name that harbor this sequence.
getSpeciesName() - Method in class softparsmap.SequenceDataXml
getSpeciesTree(GeneNode) - Method in interface softparsmap.DataSource: Returns the root to a species tree such that all genes found in the gene tree exist in this species tree.
getSpeciesTree(GeneNode) - Method in class softparsmap.DataSourceXmlNcbiTaxonomy
getSpeciesTree() - Method in class softparsmap.PreferredTree: Returns the rooted species tree.
getSplits() - Method in class softparsmap.Node: Returns the splits that exist in this tree.
getTag(String) - Method in class ooc.Container: Returns a tag with the given tag id.
getTag() - Method in class ooc.LinkedTagInstance: Returns the tag of this tag instance.
getTag() - Method in class ooc.NotValidException
getTag() - Method in class ooc.OocException
getTag(String) - Method in class ooc.SourceTagHolder: Returns the tag with the given tag id found in this holder or any imported holder.
getTag() - Method in class ooc.TagAttribute
getTag() - Method in interface ooc.TagError: Returns the tag in which this error was found.
getTag() - Method in class ooc.TagErrorMsg
getTagErrorHandler() - Method in class ooc.TagErrorHandlerException
getTagId() - Method in class ooc.LinkedTagInstance: For more information see Tag.getTagId().
getTagId() - Method in class ooc.Tag: Returns the value of the did attribute.
getTagInstance() - Method in class ooc.LinkedTagInstance
getTagInstance(Dependencies) - Method in class ooc.LinkedTagInstance
getTagInstance(Object, Object) - Method in class ooc.Tag
getTagInstance(Object, Object, Object, Object) - Method in class ooc.Tag
getTagInstance() - Method in class ooc.Tag
getTagInstance(Dependencies) - Method in class ooc.Tag
getTagName() - Method in class ooc.Tag: Returns the name of the tag.
getTagRef() - Method in class ooc.LinkedTagInstance: For more information see Tag.getTagRef().
getTagRef() - Method in class ooc.Tag: Returns a reference to this tag.
getTargetFile(String, Integer) - Method in class softparsmap.Compute: Returns a file given the family number and the template attribute name.
getText() - Method in class ooc.Tag: Returns the text in this tag.
getTreeParser(String) - Method in class softparsmap.Compute: Returns a parser defined by attribute 'attributeName'.
getTreeParserIn() - Method in class softparsmap.FamilyGroupTreesInFiles
getValidateCard() - Method in class ooc.TagAttribute
getValue() - Method in class ooc.TagAttribute

H

hasAncestorTags() - Method in class ooc.Tag
hasAttributeConverter(String) - Method in class ooc.Tag
hasAttributeValue(String) - Method in class ooc.LinkedTagInstance: For more information see Tag.hasAttributeValue(java.lang.String).
hasAttributeValue(String) - Method in class ooc.Tag
hasChildTag(Tag) - Method in class ooc.Tag
hasChildTagByName(String) - Method in class ooc.LinkedTagInstance: For more information see Tag.hasChildTagByName(java.lang.String).
hasChildTagByName(String) - Method in class ooc.Tag: Returns true if there exists a child tag with the given name, else false.
hasChildTags() - Method in class ooc.LinkedTagInstance: For more information see Tag.hasChildTags().
hasChildTags() - Method in class ooc.Tag: Returns true if this tag has child tags.
hasChildren() - Method in class softparsmap.Node: Returns true if this node has children, else false.
hasConverter() - Method in class ooc.TagAttribute
hasDescendentTags() - Method in class ooc.Tag
hasErrors() - Method in class ooc.TagErrorHandler
hasFailedValidation(Tag) - Method in class ooc.TagErrorHandler
hasFamily() - Method in class softparsmap.GeneNode: Returns true if this node has a family.
hasM() - Method in class softparsmap.GeneNode: Returns true if M has been set.
hasMM() - Method in class softparsmap.GeneNode: Returns true if the M-map has been set.
hasMarker(String) - Method in class softparsmap.StringTemplate: Returns true if the marker exists in the template.
hasMethodName() - Method in class ooc.InstanceInjectorMethodAbstract
hasNext() - Method in class softparsmap.ChildIterator: See Iterator.java
hasParentTag() - Method in class ooc.Tag: Returns true if this tag has a parent tag, else false.
hasSL() - Method in class softparsmap.GeneNode: Returns true if SL has been set.
hasTag() - Method in class ooc.LinkedTagInstance: Returns true if this tag instance has a tag.
hashCode() - Method in class softparsmap.Family: Returns the hash code and it has to agree with Family.equals(java.lang.Object).
hashCode() - Method in class softparsmap.Node: Returns the label value.
hashCode() - Method in class softparsmap.SortedCollection
holdInstance(Tag, Object) - Method in interface ooc.InstanceHolder: Adds a tag instance to this holder given the tag and the instance.
holdInstance(Tag, Object) - Method in class ooc.InstanceHolderPrimitive
holdInstance(Tag, Object) - Method in class ooc.InstanceHolderSingleton

I

InferMutation - class softparsmap.InferMutation.: This program is used to infer duplication and loss for small gene and species trees typed at the prompt.
InferMutation() - Constructor for class softparsmap.InferMutation
Inparalogous - interface softparsmap.Inparalogous.: This interface is responsible of handling inparalogous.
InparalogousStandard - class softparsmap.InparalogousStandard.: The comparator created below will decide which sequence that will be chosen.
InparalogousStandard() - Constructor for class softparsmap.InparalogousStandard
InstanceConstructor - interface ooc.InstanceConstructor.: Used by the Container in order to construct instances.
InstanceConstructorAbstract - class ooc.InstanceConstructorAbstract.
InstanceConstructorAbstract() - Constructor for class ooc.InstanceConstructorAbstract
InstanceConstructorInjector - class ooc.InstanceConstructorInjector.
InstanceConstructorInjector() - Constructor for class ooc.InstanceConstructorInjector
InstanceConstructorInjectorSetup - class ooc.InstanceConstructorInjectorSetup.
InstanceConstructorInjectorSetup() - Constructor for class ooc.InstanceConstructorInjectorSetup
InstanceConstructorReflection - class ooc.InstanceConstructorReflection.
InstanceConstructorReflection() - Constructor for class ooc.InstanceConstructorReflection
InstanceHolder - interface ooc.InstanceHolder.: Keeping track of the life cycle of the instance after construction.
InstanceHolderPrimitive - class ooc.InstanceHolderPrimitive.
InstanceHolderPrimitive() - Constructor for class ooc.InstanceHolderPrimitive
InstanceHolderSingleton - class ooc.InstanceHolderSingleton.
InstanceHolderSingleton() - Constructor for class ooc.InstanceHolderSingleton
InstanceInjector - interface ooc.InstanceInjector.: Injects instances into tag instances.
InstanceInjectorAbstract - class ooc.InstanceInjectorAbstract.
InstanceInjectorAbstract() - Constructor for class ooc.InstanceInjectorAbstract
InstanceInjectorAbstractIfNull - class ooc.InstanceInjectorAbstractIfNull.
InstanceInjectorAbstractIfNull() - Constructor for class ooc.InstanceInjectorAbstractIfNull
InstanceInjectorAttribute - class ooc.InstanceInjectorAttribute.
InstanceInjectorAttribute() - Constructor for class ooc.InstanceInjectorAttribute
InstanceInjectorAttributeAll - class ooc.InstanceInjectorAttributeAll.
InstanceInjectorAttributeAll() - Constructor for class ooc.InstanceInjectorAttributeAll
InstanceInjectorAttributeAllField - class ooc.InstanceInjectorAttributeAllField.
InstanceInjectorAttributeAllField() - Constructor for class ooc.InstanceInjectorAttributeAllField
InstanceInjectorChildInstances - class ooc.InstanceInjectorChildInstances.
InstanceInjectorChildInstances() - Constructor for class ooc.InstanceInjectorChildInstances
InstanceInjectorChildTemplates - class ooc.InstanceInjectorChildTemplates.
InstanceInjectorChildTemplates() - Constructor for class ooc.InstanceInjectorChildTemplates
InstanceInjectorDependency - class ooc.InstanceInjectorDependency.
InstanceInjectorDependency() - Constructor for class ooc.InstanceInjectorDependency
InstanceInjectorGroup - class ooc.InstanceInjectorGroup.
InstanceInjectorGroup() - Constructor for class ooc.InstanceInjectorGroup
InstanceInjectorMethodAbstract - class ooc.InstanceInjectorMethodAbstract.
InstanceInjectorMethodAbstract() - Constructor for class ooc.InstanceInjectorMethodAbstract
InstanceInjectorMethodAttributes - class ooc.InstanceInjectorMethodAttributes.
InstanceInjectorMethodAttributes() - Constructor for class ooc.InstanceInjectorMethodAttributes
InstanceInjectorMethodChildTagsAttributes - class ooc.InstanceInjectorMethodChildTagsAttributes.
InstanceInjectorMethodChildTagsAttributes() - Constructor for class ooc.InstanceInjectorMethodChildTagsAttributes
InstanceInjectorMethodInstances - class ooc.InstanceInjectorMethodInstances.
InstanceInjectorMethodInstances() - Constructor for class ooc.InstanceInjectorMethodInstances
InstanceInjectorParentInstance - class ooc.InstanceInjectorParentInstance.
InstanceInjectorParentInstance() - Constructor for class ooc.InstanceInjectorParentInstance
InstanceInjectorTag - class ooc.InstanceInjectorTag.
InstanceInjectorTag() - Constructor for class ooc.InstanceInjectorTag
InstanceSetup - interface ooc.InstanceSetup.: Initiates the new tag instance after construction.
InstanceSetupAttribute - class ooc.InstanceSetupAttribute.
InstanceSetupAttribute() - Constructor for class ooc.InstanceSetupAttribute
InstanceSetupMethod - class ooc.InstanceSetupMethod.
InstanceSetupMethod() - Constructor for class ooc.InstanceSetupMethod
ignoreCase() - Method in class ooc.AttributeConverterStringOption
inferMutation(GeneNode, boolean, Inparalogous) - Method in class softparsmap.SpeciesNode: Infers duplications and loss using this species subtree.
initiate() - Method in interface softparsmap.DataSource: Called by the program ComputeFamilyGroup or ComputeFamilyGroupPair once if the method Compute.initiateDataSource() returns true, else it is not called at all.
initiate() - Method in class softparsmap.DataSourceXmlNcbiTaxonomy
initiateDataSource() - Method in class softparsmap.Compute: Returns true if the data source should be initiated.
inject(Object, Tag, Tag, Dependencies) - Method in interface ooc.InstanceInjector: Injects the instance into the tag instance.
inject(Object, Tag, Tag, Dependencies) - Method in class ooc.InstanceInjectorAttribute
inject(Object, Tag, Tag, Dependencies) - Method in class ooc.InstanceInjectorAttributeAll
inject(Object, Tag, Tag, Dependencies) - Method in class ooc.InstanceInjectorAttributeAllField
inject(Object, Tag, Tag, Dependencies) - Method in class ooc.InstanceInjectorChildInstances
inject(Object, Tag, Tag, Dependencies) - Method in class ooc.InstanceInjectorChildTemplates
inject(Object, Tag, Tag, Dependencies) - Method in class ooc.InstanceInjectorDependency
inject(Object, Tag, Tag, Dependencies) - Method in class ooc.InstanceInjectorGroup
inject(Object, Tag, Tag, Dependencies) - Method in class ooc.InstanceInjectorMethodAbstract
inject(Object, Tag, Tag, Dependencies) - Method in class ooc.InstanceInjectorMethodChildTagsAttributes
inject(Object, Tag, Tag, Dependencies) - Method in class ooc.InstanceInjectorParentInstance
injectValueIfNull() - Method in class ooc.InstanceInjectorAbstractIfNull
insertSpeciesTreeSplits() - Method in class softparsmap.GeneNode: Insert splits from the species tree if it does not increase the minimum number of duplications and gene loss.
invokeMethod(Object, String) - Static method in class ooc.Tools
invokeMethod(Object, String, Object) - Static method in class ooc.Tools
invokeMethod(Object, String, Object[]) - Static method in class ooc.Tools
invokeStaticMethod(Class, String, Object[]) - Static method in class ooc.Tools
isBelow(SpeciesNode) - Method in class softparsmap.SpeciesNode: Returns true if this node is below given node.
isBinaryTree() - Method in class softparsmap.GeneLeaf
isBinaryTree() - Method in class softparsmap.Node: Return true if the subtree where this node is the root is binary, else false.
isCompleteSequence() - Method in interface softparsmap.SequenceData: Returns true if the sequence is complete, otherwise false.
isCompleteSequence() - Method in class softparsmap.SequenceDataXml
isConsistentWith(Node) - Method in class softparsmap.Node: Returns true if this tree is consistent with the given tree.
isConsistentWith(Split) - Method in class softparsmap.Split: Returns true if this split is consistent with the given split.
isEdgeWeak(GeneNode) - Method in interface softparsmap.EdgeType: Returns true if the edge value for the gene node is weak, else false.
isEdgeWeak() - Method in class softparsmap.GeneNode: Returns true if the edge for this node is weak, else false.
isEdgeWeak() - Method in class softparsmap.MuNode
isEdgeWeak(GeneNode) - Method in class softparsmap.StandardEdgeType
isEmpty() - Method in class softparsmap.SortedCollection
isLeaf(Node) - Method in class softparsmap.AbstractStringNodeConverter
isLeaf(Node) - Method in interface softparsmap.StringNodeConverter
isMutable() - Method in interface ooc.Dependencies: Returns true if this dependency map is mutable, else false;
isMutable() - Method in class ooc.DependenciesMapped
isMutable() - Method in class ooc.LinkedTagInstance
isOnSameRootPath(SpeciesNode) - Method in class softparsmap.SpeciesNode: Returns true if this node and the given node is on the same root path.
isRoot() - Method in class softparsmap.Node: Returns true if this node is the root of the tree.
isSame(Mutation) - Method in class softparsmap.Mutation: Returns true if the given mutation is the same as this.
isSourceInContext(String) - Method in interface ooc.SourceContext: Returns true if the given source exists in this contexts.
isSourceInContext(String) - Method in class ooc.SourceContextClassPath
isSourceInContext(String) - Method in class ooc.SourceContextDirectory
isSourceInContext(String) - Method in class ooc.SourceContextFile
isTagAbstract() - Method in class ooc.Tag
isWorse(Mutation) - Method in class softparsmap.Mutation: Returns true if this is worse then the given mutation.
iterator() - Method in class softparsmap.SortedCollection

J

joinEdges(GeneNode, GeneNode) - Method in interface softparsmap.EdgeType: Returns the edge value retained when joining the edges of the two gene nodes.
joinEdges(GeneNode, GeneNode) - Method in class softparsmap.StandardEdgeType

K

keySet() - Method in interface ooc.Dependencies: Returns the the key set mapping to the instances in this dependency map.
keySet() - Method in class ooc.LinkedTagInstance

L

LinkedTagInstance - class ooc.LinkedTagInstance.: This class contains mehtods mapped from class Tag in order to facilitate usage of the tag instance.
LinkedTagInstance() - Constructor for class ooc.LinkedTagInstance: Constructs an instance without any arguments.
last() - Method in class softparsmap.SortedCollection
loadSource(String) - Method in class ooc.Container: Loading the given source.
loadSource(String, String) - Method in class ooc.Container: Loading the given source.
loadSource(Source) - Method in class ooc.Container: Loading the given source.

M

MAX_SIZE - Static variable in class ooc.TagErrorHandler
METHOD_CLASS_SEPARATOR_ID - Static variable in class ooc.AttributeConverterMethod
MuNode - class softparsmap.MuNode.: This class contains the code that implements the soft interpretation of gene duplication and loss.
Mutation - class softparsmap.Mutation.: This class contains the result from inferring gene duplications and loss.
Mutation(int, int) - Constructor for class softparsmap.Mutation: Creating a mutation given duplications and loss.
main(String[]) - Static method in class ooc.Print
main(String[]) - Static method in class ooc.Validate
main(String[]) - Static method in class softparsmap.Compute: The main method called to do a task.
main(String[]) - Static method in class softparsmap.DataSourceXmlNcbiTaxonomy
main(String[]) - Static method in class softparsmap.InferMutation
main(String[]) - Static method in class softparsmap.PrintTree
methodExists(Class, String) - Static method in class ooc.Tools
methodExists(Class, String, Class) - Static method in class ooc.Tools
methodExists(Class, String, Class[]) - Static method in class ooc.Tools
methodExistsNumberParameters(Class, String, int) - Static method in class ooc.Tools
minimizeMutation(GeneNode, boolean, Inparalogous) - Method in class softparsmap.SpeciesNode: Returns a list of rooted gene trees.
moveNextSequence() - Method in class softparsmap.AbstractSequenceData: Move to next sequence in file.
moveNextSequence() - Method in class softparsmap.SequenceDataXml

N

NAME - Static variable in class ooc.SourceContextClassPath: Contains the default name of this context which is 'classpath'.
NAME - Static variable in class ooc.SourceContextDirectory: Contains the default name of this context which is 'current_directory'.
NAME - Static variable in class ooc.SourceContextFile: The name of this context is 'file'.
Node - class softparsmap.Node.: Define common behavior for gene and species nodes and trees.
Node(int) - Constructor for class softparsmap.Node: Constructs a gene node with given label.
NotValidException - exception ooc.NotValidException.: This exception will be thrown when a tag or attribute is not valid.
NotValidException(Tag, TagAttribute, String) - Constructor for class ooc.NotValidException
NotValidException(Tag) - Constructor for class ooc.NotValidException
NotValidException(Tag, Exception) - Constructor for class ooc.NotValidException
NotValidException(Tag, String) - Constructor for class ooc.NotValidException
NotValidException(TagAttribute, String) - Constructor for class ooc.NotValidException
NotValidException(TagAttribute, String, Exception) - Constructor for class ooc.NotValidException
NotValidException(Tag, String, Exception) - Constructor for class ooc.NotValidException
needsValidateCard() - Method in interface ooc.AttributeConverter: Returns true if the attribute must have a validation card, else false.
needsValidateCard() - Method in class ooc.AttributeConverterAbstract
needsValue() - Method in interface ooc.AttributeConverter: Returns true if the attribute must have a value, else false.
needsValue() - Method in class ooc.AttributeConverterAbstract
newFilePointerPartCurrent() - Method in class softparsmap.AbstractSequenceData: Returns a new FilePointerPart on current position in the file.
newFilePointerPartCurrent() - Method in class softparsmap.SequenceDataXml
newInstance(Tag, Class, Object[]) - Static method in class ooc.Tools
next() - Method in class softparsmap.ChildIterator: See Iterator.java
nextLeaf(EdgeType) - Static method in class softparsmap.GeneLeaf: Returns a new leaf with an unique label.
nextLeafS(DataSource, int) - Static method in class softparsmap.SpeciesLeaf: Returns a species leaf with a unique label and with one sequence.
nextLeafS(DataSource) - Static method in class softparsmap.SpeciesLeaf: Returns a species leaf with a unique label.
nextNode(EdgeType, double) - Static method in class softparsmap.GeneNode: Returns the next unique node with edge with give value and edge type.
nextNode(EdgeType) - Static method in class softparsmap.GeneNode: Return the next unique node with given edge type.
nextNodeS(DataSource) - Static method in class softparsmap.SpeciesNode: Return the next unique labeled species node.
nextUnique() - Static method in class softparsmap.Node: Returns the next unique integer.
nodesIdToNamesFilePointer - Variable in class softparsmap.DataSourceIndexXmlNcbiTaxonomy: A map from NCBI's tax id's (Integer) to file pointer into the file names.dmp such that when reading one line from that position will get the name row for that species.
nullFilter(String) - Method in class ooc.TagParser
numChildren() - Method in class softparsmap.Node: Returns the number of children this node has.
numberArgs() - Method in class softparsmap.Compute: Returns the number of remaining arguments.

O

OocException - exception ooc.OocException.: This exception will be thrown when a fatal error has occured.
OocException(Tag) - Constructor for class ooc.OocException
OocException(Tag, Throwable) - Constructor for class ooc.OocException
OocException(Tag, String) - Constructor for class ooc.OocException
OocException(TagAttribute, String) - Constructor for class ooc.OocException
OocException(TagAttribute, String, Throwable) - Constructor for class ooc.OocException
OocException(Tag, String, Throwable) - Constructor for class ooc.OocException
ooc - package ooc

P

PreferredTree - class softparsmap.PreferredTree.: Classes extending this abstract class are used by task ComputeRoot to choose the preferred gene tree.
PreferredTree() - Constructor for class softparsmap.PreferredTree
PreferredTreeStandard - class softparsmap.PreferredTreeStandard.
PreferredTreeStandard() - Constructor for class softparsmap.PreferredTreeStandard
Print - class ooc.Print.: This program will create the container and print the tag instance to the standard output.
Print() - Constructor for class ooc.Print
PrintTree - class softparsmap.PrintTree.: This program will print a tree.
PrintTree() - Constructor for class softparsmap.PrintTree
PropertyFile - class softparsmap.PropertyFile.: This class will parse the XML property file and give access to its corresponding classes.
PropertyFile(File) - Constructor for class softparsmap.PropertyFile: Construct the instance using a file.
PropertyFile(String) - Constructor for class softparsmap.PropertyFile: Construct the instance from a file in the classpath.
paintTemplate(String) - Method in class softparsmap.StringTemplate: If the value matches the template the markers will be set to corresponding values.
paintTemplateWithMarkerNames() - Method in class softparsmap.StringTemplate: Sets the markers with their own names.
parseIn(InputStream) - Method in class softparsmap.AbstractTreeParser
parseIn(Node, InputStream) - Method in class softparsmap.AbstractTreeParser
parseIn(String) - Method in class softparsmap.AbstractTreeParser
parseIn(Node, String) - Method in class softparsmap.AbstractTreeParser
parseIn(InputStream) - Method in interface softparsmap.TreeParser: Returns the root of the parsed tree.
parseIn(String) - Method in interface softparsmap.TreeParser: Returns the root of the parsed tree.
parseIn(Node, InputStream) - Method in interface softparsmap.TreeParser: Adding information to the existing tree.
parseIn(Node, String) - Method in interface softparsmap.TreeParser: Adding information to the existing tree.
parseIn(String) - Method in class softparsmap.TreeParserDual
parseIn(Node, String) - Method in class softparsmap.TreeParserDual
parseIn(String) - Method in class softparsmap.TreeParserNewick
parseIn(Node, String) - Method in class softparsmap.TreeParserNewick
parseNewick(DataSource, String) - Static method in class softparsmap.SpeciesNode: Parse a string in Neiwck format with gene sequences in the inner bracket.
parseOut(OutputStream, Node) - Method in class softparsmap.AbstractTreeParser
parseOut(Node) - Method in class softparsmap.AbstractTreeParser
parseOut(OutputStream, Node) - Method in interface softparsmap.TreeParser: This method will parse out the tree to the output stream.
parseOut(Node) - Method in interface softparsmap.TreeParser: This method will parse out the tree to a string.
parseOut(Node) - Method in class softparsmap.TreeParserDual
parseOut(Node) - Method in class softparsmap.TreeParserNewick
parseSequence(RandomAccessFile, FilePointerPart) - Method in class softparsmap.AbstractSequenceData: Parse in a sequence given a the file and pointer.
parseSequence(RandomAccessFile, FilePointerPart) - Method in class softparsmap.SequenceDataXml
parseStructureIn(String, StringNodeConverter) - Method in interface softparsmap.TreeStructureParser
parseStructureIn(Node, String, StringNodeConverter) - Method in interface softparsmap.TreeStructureParser
parseStructureIn(String, StringNodeConverter) - Method in class softparsmap.TreeStructureParserLeafList
parseStructureIn(Node, String, StringNodeConverter) - Method in class softparsmap.TreeStructureParserLeafList
parseStructureIn(String, StringNodeConverter) - Method in class softparsmap.TreeStructureParserSchreiber
parseStructureIn(Node, String, StringNodeConverter) - Method in class softparsmap.TreeStructureParserSchreiber
parseStructureIn(String, StringNodeConverter) - Method in class softparsmap.TreeStructureParserSchreiberInfoIn
parseStructureIn(Node, String, StringNodeConverter) - Method in class softparsmap.TreeStructureParserSchreiberInfoIn
parseStructureOut(Node, StringNodeConverter) - Method in interface softparsmap.TreeStructureParser
parseStructureOut(Node, StringNodeConverter) - Method in class softparsmap.TreeStructureParserLeafList
parseStructureOut(Node, StringNodeConverter) - Method in class softparsmap.TreeStructureParserSchreiber
parseStructureOut(Node, StringNodeConverter) - Method in class softparsmap.TreeStructureParserSchreiberInfoIn
print(PrintStream, String) - Method in interface ooc.TagError: Prints a description of the error to the given stream.
print(PrintStream) - Method in class ooc.TagErrorHandler
print(PrintStream, String) - Method in class ooc.TagErrorMsg
pruneOneChildNodes() - Method in class softparsmap.GeneLeaf
pruneOneChildNodes() - Method in class softparsmap.GeneNode: Collapsing all internal nodes with only one child node.
pruneOneChildNodes() - Method in class softparsmap.Node: Remove all internal nodes with only one child.
pruneOneChildNodes() - Method in class softparsmap.SpeciesLeaf
put(Object, Object) - Method in interface ooc.Dependencies: Add a new dependency into this map and return the old one, if any.
put(Object, Object) - Method in class ooc.LinkedTagInstance

R

ROOT_NODES_MAP_KEY - Static variable in class softparsmap.TreeStructureParserSchreiber
remove(Object) - Method in interface ooc.Dependencies: Remove the key-value pair from this depedency map.
remove(Object) - Method in class ooc.LinkedTagInstance
remove() - Method in class softparsmap.ChildIterator: This method can not be used and a FatalException will be thrown if called.
remove(Object) - Method in class softparsmap.SortedCollection
removeAll(Collection) - Method in class softparsmap.SortedCollection
removeBeforeSaving() - Method in class softparsmap.AbstractInparalogous
removeBeforeSaving() - Method in interface softparsmap.Inparalogous: Returns true iff inparalogous are removed before saving the final gene tree.
removeChild(Node) - Method in class softparsmap.Node: Remove the child from this parent and set the child's parent to null.
removeInparalogous(Family, GeneNode) - Method in class softparsmap.AbstractInparalogous
removeInparalogous(Family, GeneNode) - Method in interface softparsmap.Inparalogous: Removes all inparalogous in the gene tree.
removeWhileMinimizingMutation() - Method in class softparsmap.AbstractInparalogous
removeWhileMinimizingMutation() - Method in interface softparsmap.Inparalogous: Returns true iff inparalogous are removed after each mid point re-root, before duplications and loss is counted, else false.
reroot() - Method in class softparsmap.GeneNode: Re-rooting the gene tree that this gene tree is a part of, using midpoint re-rooting.
rerootThis() - Method in class softparsmap.GeneLeaf
rerootThis() - Method in class softparsmap.GeneNode: Re-rooting the gene tree that this node is a part of.
resolveUncertainties(GeneNode) - Method in class softparsmap.GeneNode: Try to resolve all uncertainties in this rooted gene tree using the original unrooted gene tree.
retainAll(Collection) - Method in class softparsmap.SortedCollection
rootedEquals(GeneNode) - Method in class softparsmap.GeneLeaf
rootedEquals(GeneNode) - Method in class softparsmap.GeneNode: Returns true if this subtrees have the same rooted topology as the given subtree.