Package softparsmap

Interface Summary

DataSource	This interface is responsible of providing the package with data regarding species trees and gene sequences.
EdgeType	This interface is used to define different properties of an edge in a gene tree.
FamilyGroup	This interface represents a set of gene families and it is responsible of providing these families for a certain task.
Inparalogous	This interface is responsible of handling inparalogous.
SequenceData	This interface is responsible of providing the package with all relevant sequence data.
StringNodeConverter
TreeParser	This interface is used to parse in and out trees.
TreeStructureParser

Class Summary

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.
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.
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.
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.
AbstractSequenceData	If the sequences are stored in one file this class can be extended and used together with the class DataSourceXmlGenData.
AbstractStringNodeConverter
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.
CharsetFileWriter	This class makes it easier to write data to file using a specified charset.
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.
ChildSet	This set is used as child set for gene trees and as well as for species trees.
Compute	This program is used to compute a task.
ComputeCompareGeneTrees	This program is used to compare the topology of gene trees from two family groups.
ComputeFamilyGroup	This program is used when computing a task on a specified family group.
ComputeFamilyGroupPair	This program is used when computing a task on a pair of family groups.
ComputeFamilyNumbers	Will print the numbers of the family group.
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.
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.
ComputeRoot	This task will root unrooted gene trees by minimizing duplications and loss.
DataSourceIndexXmlNcbiTaxonomy	Index for data source DataSourceXmlNcbiTaxonomy.
DataSourceXmlNcbiTaxonomy	This data source can be used when the sequence database is an XML document.
Family	This class represents a gene family.
FamilyGroupTreesInFiles	This family group assume that there is one file per family and that the family number can be found in the file name.
FamilyGroupTreesInFilesInfoPerRow
FilePointerPart	This class points to a block of bytes in a file.
GeneLeaf	Defines a gene leaf in a gene tree.
GeneNode	Defines a gene node in a gene tree.
InferMutation	This program is used to infer duplication and loss for small gene and species trees typed at the prompt.
InparalogousStandard	The comparator created below will decide which sequence that will be chosen.
MuNode	This class contains the code that implements the soft interpretation of gene duplication and loss.
Mutation	This class contains the result from inferring gene duplications and loss.
Node	Define common behavior for gene and species nodes and trees.
PreferredTree	Classes extending this abstract class are used by task ComputeRoot to choose the preferred gene tree.
PreferredTreeStandard
PrintTree	This program will print a tree.
PropertyFile	This class will parse the XML property file and give access to its corresponding classes.
SequenceDataXml	This class is used by DataSourceXmlNcbiTaxonomy to extract sequence data from one file in XML-format.
SortedCollection	This is a sorted collection.
SpeciesLeaf	Defines a species leaf in a species tree.
SpeciesNode	Defines a species node in a species tree.
Split	For a tree T=(V,E), let d=(L1,L2) be a split iff L1, L2 [subset_of] L(T), |L1 [cut] L2|=0, L1 [union] L2 = L(T), and there exists an edge e [in] E so if removed we get two tree graphs T1 and T2 where L1 [subset_of] L(T1) and L2 [subset_of].
StandardEdgeType	This is a edge type that can me configured within limits.
StringGeneNodeConverterDupSpe
StringGeneNodeConverterLabel
StringGeneNodeConverterNcbiNamesColumn
StringGeneNodeConverterSchreiberLabel
StringGeneNodeConverterSchreiberMapLabel
StringGeneNodeConverterSequenceDataXml
StringGeneNodeConverterStringTemplate
StringNodeConverterMapInfo
StringNodeConverterStringTemplate
StringTemplate	This class can extract string information from a string template or create a string given a template and data.
TreeParserDual	This parser uses two complementary parts to parse in and out trees.
TreeParserNewick	This parser will parse the Newick format.
TreeStructureParserLeafList
TreeStructureParserSchreiber
TreeStructureParserSchreiberInfoIn
TreeTextBlock	A help class to print trees in an easy to understand format.

Exception Summary

FatalException

A fatal exception.