umms.core.scripture.BuildScriptureCoordinateSpace Class Reference

Collaboration diagram for umms.core.scripture.BuildScriptureCoordinateSpace:

Public Member Functions
	BuildScriptureCoordinateSpace (File bamFile, String genomeDir)
	BuildScriptureCoordinateSpace (File bamFile, String genomeDir, String outputName, boolean forceStrandedness, TranscriptionRead st, ArgumentMap argMap)
	BuildScriptureCoordinateSpace (File bamFile, String genomeDir, String outputName, boolean forceStrandedness, TranscriptionRead strand, String chr, ArgumentMap argMap)
Map< String, Collection< Gene > >	getPaths ()

Static Public Member Functions
static void	write (String save, Map< String, Collection< Gene >> rtrn) throws IOException
static void	memoryStats ()
static boolean	compatible (Annotation assembly, Annotation read)
static double[]	l2a (List< Double > list)
static Map< Gene, Set< Gene > >	getIsoformMap (Collection< Gene > genes)
static boolean	isoformMapContains (Map< Gene, Set< Gene >> isoformMap, Gene gene)
static Collection< Gene >	getOverlappingGenes (Gene gene, Collection< Gene > allGenes, double minPctOverlap)
static Collection< Gene >	getOverlappingGenes (Gene gene, IntervalTree< Gene > allGenesTree, double minPctOverlap)
static boolean	hasAnOverlappingGene (Gene gene, IntervalTree< Gene > allGenesTree, double minPctOverlap)
static void	main (String[] args) throws IOException

Constructor & Destructor Documentation

umms.core.scripture.BuildScriptureCoordinateSpace.BuildScriptureCoordinateSpace	(	File	bamFile,
		String	genomeDir
	)

Here is the caller graph for this function:

umms.core.scripture.BuildScriptureCoordinateSpace.BuildScriptureCoordinateSpace	(	File	bamFile,
		String	genomeDir,
		String	outputName,
		boolean	forceStrandedness,
		TranscriptionRead	st,
		ArgumentMap	argMap
	)

Parameters

bamFile
threshold
genomeDir
outputName
forceStrandedness

Here is the call graph for this function:

umms.core.scripture.BuildScriptureCoordinateSpace.BuildScriptureCoordinateSpace	(	File	bamFile,
		String	genomeDir,
		String	outputName,
		boolean	forceStrandedness,
		TranscriptionRead	strand,
		String	chr,
		ArgumentMap	argMap
	)

Parameters

bamFile
threshold
genomeDir
outputName
forceStrandedness
chr

Here is the call graph for this function:

Member Function Documentation

static boolean umms.core.scripture.BuildScriptureCoordinateSpace.compatible ( Annotation  assembly, Annotation  read  )

static

Parameters

iter
workingAssemblies
strand

Returns

Parameters

iter
workingAssemblies
strand

Returns

Returns true is the exon is a subset of the assembly AND the exon does not match an exon of the assembly

Parameters

assembly
exon

Returns

Here is the call graph for this function:

static Map<Gene,Set<Gene> > umms.core.scripture.BuildScriptureCoordinateSpace.getIsoformMap ( Collection< Gene >  genes )

static

Parameters

genes

Returns

Here is the call graph for this function:

static Collection<Gene> umms.core.scripture.BuildScriptureCoordinateSpace.getOverlappingGenes ( Gene  gene, Collection< Gene >  allGenes, double  minPctOverlap  )

static

Parameters

gene
allGenes
minPctOverlap

Returns

TODO: optimize using interval tree

Here is the call graph for this function:

Here is the caller graph for this function:

static Collection<Gene> umms.core.scripture.BuildScriptureCoordinateSpace.getOverlappingGenes ( Gene  gene, IntervalTree< Gene >  allGenesTree, double  minPctOverlap  )

static

returns a collection of genes in the interval tree that overlap this gene with atleast minPctOverlap and in the same orientation

Parameters

gene
allGenesTree
minPctOverlap

Returns

Here is the call graph for this function:

Map<String, Collection<Gene> > umms.core.scripture.BuildScriptureCoordinateSpace.getPaths

(

)

Here is the caller graph for this function:

static boolean umms.core.scripture.BuildScriptureCoordinateSpace.hasAnOverlappingGene ( Gene  gene, IntervalTree< Gene >  allGenesTree, double  minPctOverlap  )

static

Returns true if has an overlapping gene with atleast minPctOverlap and in the same orientationin the interval tree

Parameters

gene
allGenesTree
minPctOverlap

Returns

Here is the call graph for this function:

static boolean umms.core.scripture.BuildScriptureCoordinateSpace.isoformMapContains ( Map< Gene, Set< Gene >>  isoformMap, Gene  gene  )

static

Here is the caller graph for this function:

static double [] umms.core.scripture.BuildScriptureCoordinateSpace.l2a ( List< Double >  list )

static

Converts a list to an array

Parameters

list

Returns

static void umms.core.scripture.BuildScriptureCoordinateSpace.main ( String[]  args ) throws IOException

static

Here is the call graph for this function:

static void umms.core.scripture.BuildScriptureCoordinateSpace.memoryStats ( )

static

static void umms.core.scripture.BuildScriptureCoordinateSpace.write ( String  save, Map< String, Collection< Gene >>  rtrn  ) throws IOException

static

Here is the caller graph for this function:

---

The documentation for this class was generated from the following file:

• java/umms/core/scripture/BuildScriptureCoordinateSpace.java