A B C D E F G H I L M N O P R S T U W

A

acp - Variable in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
Average Conditional Probability (ACP) is suggested as an appropriate measure of global prediction accuracy (Burset and Guigo, 1996).
acp - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.GenePredicter
average conditional probability of geneprediction program
addToTreeMap(MyTreeMap, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.util.biotools.BioTools
AddToTreeMap method creates a binary tree of locateable objects sorted by their start location.
allArguments - Static variable in class uk.ac.sanger.psu.gfmerge.GFMerge
SimpleArg object which contains all command line parameters
allArguments - Variable in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
object which contains all command line parameters
allArguments - Variable in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureOverlapAnalysis
SimpleArg object which contains all command line arguments
allArguments - Variable in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis
SimpleArg object which contains all command line arguments
allArguments - Variable in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
Object which contains all command line arguments
analysisObjArr - Variable in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
ArrayList which contains analysis objects (CDnaSpliceSiteAnalysis, CDnaOverlapAnalysis, BlastOverlapAnalysis, TotalExonLengthAnalysis, GeneModelLengthAnalysis, AvgCondProbAnalysis)
annotatedTrainSet - Variable in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
annotation of training set (for acp calculation)
arrListOfBlastRegions - Variable in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
ArrayList of Blast regions
arrListOfCDnaRegions - Variable in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
ArrayList of cDNA regions
arrListOfFeatRegions - Variable in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureOverlapAnalysis
ArrayList of SimFeature regions
arrListOfFeatRegions - Variable in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis
ArrayList of SimFeature regions (cDNA, Blast)
arrListOfGMRegions - Variable in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
ArrayList of genemodels from which low scoring genemodels are removed during analysis
arrListOfGMRegions - Variable in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureOverlapAnalysis
ArrayList of genemodel regions
arrListOfGMRegions - Variable in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis
ArrayList of genemodels
arrListOfGMRegions - Variable in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
ArrayList of genemodel regions
arrListOfGMRegions_org - Variable in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
ArrayList of genemodel regions which contains all of the original gene models
AvgCondProbAnalysis - class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.AvgCondProbAnalysis.
Analysis class which calculates the high scoring path in a clustered sequence using the average conditional probability
AvgCondProbAnalysis(ArrayList, SimpleArg) - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.AvgCondProbAnalysis
constructor of AvgCondProbAnalysis objects
AvgCondProbAnalysisTools - class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.AvgCondProbAnalysisTools.
class which contains all computing tools for AvgCondProbAnalysis
AvgCondProbAnalysisTools() - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.AvgCondProbAnalysisTools
 

B

BasicFeatureAnalysis - class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis.
abstract class from which feature analysis class are derived
BasicFeatureAnalysis(ArrayList, SimpleArg) - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
constructor of abstract BasicFeatureClass, contains partial implementation of constructors of derived classes
BasicFeatureAnalysisAble - interface uk.ac.sanger.psu.gfmerge.analysis.BasicFeatureAnalysisAble.
interface for all feature analysis classes
BasicFeatureAnalysisTools - class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.BasicFeatureAnalysisTools.
class which contains basic computing tools which are used by derived classes
BasicFeatureAnalysisTools() - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.BasicFeatureAnalysisTools
 
BioTools - class uk.ac.sanger.psu.gfmerge.util.biotools.BioTools.
class BioTools contains basic processing tools within GFMerge.
BioTools() - Constructor for class uk.ac.sanger.psu.gfmerge.util.biotools.BioTools
 
blastFile - Variable in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
blast file which is used for evidence of correct predictions (EMBL format).
BlastOverlapAnalysis - class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BlastOverlapAnalysis.
Analysis class which calculates the high scoring path in a clustered sequence using the Blast overlap on the exon level
BlastOverlapAnalysis(ArrayList, ArrayList, SimpleArg) - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BlastOverlapAnalysis
constructor for BlastOverlapAnalysis objects

C

calcAcp(Sequence, Sequence) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GenePredicter
method which retrieves average conditional probability from PredAccuracy object.
calcACP(Sequence, Sequence) - Method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
method which calculates ACP (average conditional probability).
calcArrListOfBlastRegions(SimpleArg) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
method which creates ArrayList of Blast regions
calcArrListOfCDnaRegions(SimpleArg) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
method which creates ArrayList of cDNA regions
calcArrListOfGMRegions(ArrayList, SimpleArg) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
method which calulates prediction objects
calcCDnaSpliceSiteGmScore(MyTreeMap, MyTreeMap, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.CDnaSpliceSiteAnalysisTools
method which calculates the score of a gm.
calcExonTotalOverlap(Exon, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which calculates total cDNA overlap on genemodel exon level.
calcGmCompTotalOverlap(FeatureComponentAble, HashMap, boolean) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
 
calcGmLongestOverlap(int, boolean, GeneModel, ArrayList, boolean) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which calculates longest overlap for a single genemodel.
calcGmTotalExIntOverlap(int, boolean, GeneModel, ArrayList, boolean) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
 
calcGmTotalOverlap(int, boolean, GeneModel, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which calculates total cDNA/single Blast protein overlap for a single genemodel.
calcHashOfLongestFeatOverlap(int, boolean, HashMap, boolean) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which calculates hash of longest feature overlap.
calcHashOfScoredOverlap(HashMap, boolean) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which calculates scored overlap of genemodels.
calcHashOfTotalOverlap(int, boolean, HashMap, boolean) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which calculates hash of total cDNA overlap for genemodels.
calcHighScoringPath(HashMap, boolean) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.tools.HighScoringPath
 
calcMergedFeatureTable() - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
method which is called from getMergedFeatureTable if variable mergedFeatureTableArr is null.
calcTotalLocationLength(Location) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which accumulates total overlap length of exons/introns by aggregating sublocations of a compound overlap.
cDnaBoundaries - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.RecordGmCDna
splice site of a cDNA feature (either start or end position)
cDNAFile - Variable in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
cDNA file which is used for evidence of correct predictions (EMBL format).
CDnaOverlapAnalysis - class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.CDnaOverlapAnalysis.
Analysis class which calculates the high scoring path in a clustered sequence using the cDNA overlap on the exon level
CDnaOverlapAnalysis(ArrayList, ArrayList, SimpleArg) - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.CDnaOverlapAnalysis
constructor for CDnaOverlapAnalysis objects
CDnaSpliceSiteAnalysis - class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.CDnaSpliceSiteAnalysis.
Analysis class which calculates the high scoring path in a clustered sequence using a cDNA splice sites scoring system
CDnaSpliceSiteAnalysis(ArrayList, ArrayList, SimpleArg) - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.CDnaSpliceSiteAnalysis
constructor for CDnaSpliceSiteAnalysis objects
CDnaSpliceSiteAnalysisTools - class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.CDnaSpliceSiteAnalysisTools.
class which contains computing tools for CDnaSpliceSiteAnalysis.
CDnaSpliceSiteAnalysisTools() - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.CDnaSpliceSiteAnalysisTools
 
checkArguments() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
method which checks arguments (briefly)
checkFeatPosInTree(int, int, MyTreeMap) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.CDnaSpliceSiteAnalysisTools
method which checks whether position is in tree or not.
compSeq(int, ArrayList, ArrayList, ArrayList, ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
method which compares two sequences for matches and overlaps.
considerCDnaStrand - Variable in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
switch for strand consideration of cDNA.
copyArrOfFeatRegions(ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
method which does a deep copy of an region array, it keeps the references to the genemodel objects
countNucleotides(HashMap, int, StringBuffer, StringBuffer) - Static method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
method which counts TP,TN,FP,FN bases.
createAnalysisObjArr(ArrayList, ArrayList, ArrayList, SimpleArg) - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
method which generated an ArrayList of analysis objects (CDnaSpliceSiteAnalysis, CDnaOverlapAnalysis, BlastOverlapAnalysis, TotalExonLengthAnalysis, GeneModelLengthAnalysis, AvgCondProbAnalysis)
createGeneFinderObjects(SimpleArg) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
methode which creates genefinder objects and calculates their accuracy
createNewSeqOfPickedGms(Sequence, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.util.biotools.BioTools
method which creates sequence object of a sequence and picked genemodels.
createPredictionObjects(SimpleArg, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
method which creates Prediction objects
createSimFeatObjects(String, MyTreeMap) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
method which creates similarity feature objects (cDNA, Blast), puts them in a MyTreeMap object and returns this tree map
createTreeOfGMs(ArrayList, MyTreeMap) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
method which creates a tree structure of genemodels which are sorted by their minimum location

D

debug - Variable in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
debugging mode.
Debug - class uk.ac.sanger.psu.gfmerge.util.debug.Debug.
class which contains debugging methods.
debug_101(int, SimpleArg) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging Command line arguments Debugging mode 101 - pre processing -
debug_102_1(int, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging GenePredicter and Prediction objects Debugging mode 102 - pre processing -
debug_102_2(int, String, String) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debug Prediction objects in GFMerge Debugging mode 102 - pre processing -
debug_102_3(int, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debug GeneModel objects in GFMerge Debugging mode 102 - pre processing -
debug_103(int, String, MyTreeMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging MyTreeMap for GMs and Blast hits Debugging mode 103 - pre processing -
debug_104(int, ArrayList, MyTreeMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging regions of gene models Debugging mode 104 - pre processing -
debug_105(int, String, MyTreeMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging MyTreeMap for cDNA hits Debugging mode 105 - pre processing -
debug_106(int, String, ArrayList, MyTreeMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging regions of cDNA/Blast hits Debugging mode 106 - pre processing -
debug_201(int, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging hash of by cDNAs overlapped gms Debugging mode 201 - cDNA splice site -
debug_202_1 - Static variable in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
 
debug_202_2 - Static variable in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
 
debug_202(int, GeneModel, boolean, MyTreeMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging CDnaSpliceSite - PostionTree Debugging mode 202 - cDNA splice site -
debug_203(int, String, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging hash of cDNA scored gms Debugging mode 203 - cDNA splice site -
debug_204(int, String, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging hash of high scoring path Debugging mode 204 - cDNA splice site -
debug_205(int, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging cleaned array of gm regions without lowscoring gms Debugging mode 205 - cDNA splice site -
debug_301(int, String, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging HashMap of genemodels pointing to total feature overlap Debugging mode 301 (203) - cDNA overlap -
debug_302(int, String, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging hash of cDNA overlap scored gms Debugging mode 302 (203) - cDNA overlap -
debug_401(int, String, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging HashMap of gms pointing to array of overlapping features Debugging mode 401 - Blast overlap -
debug_402(int, String, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging HashMap of exons pointing to array of overlapping features Debugging mode 402 - Blast overlap -
debug_403(int, GeneModel, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging HashMap protein hash for a single gene model Debugging mode 403 - Blast overlap -
debug_404(int, GeneModel, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging HashMap of proteins pointing to overlap length Debugging mode 404 - Blast overlap -
debug_405(int, GeneModel, String, long) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging length of longest protein overlap of single gm Debugging mode 405 - Blast overlap -
debug_501(int, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging hash of by equality scored gene models Debugging mode 501
debug_701(int, String, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.util.debug.Debug
Debugging array of analyzed genemodels Debugging mode 701 - general debugging -
Debug() - Constructor for class uk.ac.sanger.psu.gfmerge.util.debug.Debug
 
doConsiderCDnaStrand() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
accessor method which returns switch for cDNA strand consideration.
doesBoundaryOverlapCDnaIntron(int, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.CDnaSpliceSiteAnalysisTools
method which checks if genemodel boundary is overlapping a cDNA intron.
doesPosOverlapSimFeatures(int, int, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.CDnaSpliceSiteAnalysisTools
method which returns true if given position overlaps a object in SimFeature ArrayList.
doFileOfRemovedGms() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
accessor method returns switch whether removed genemodels should be saved to file or not.
doHelp(int) - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
Stub for providing help on usage
done - Variable in class uk.ac.sanger.psu.gfmerge.util.getopt.GetOpt
Internal flag - whether we are done all the options
DONE - Static variable in class uk.ac.sanger.psu.gfmerge.util.getopt.GetOpt
Public constant for "no more options" XXX should switch to hasNext()/next() pattern.

E

Exon - class uk.ac.sanger.psu.gfmerge.datacomp.Exon.
class Exon is representing an biological exon which is a sublocation of a feature.
Exon(GFMergeFeature, Location) - Constructor for class uk.ac.sanger.psu.gfmerge.datacomp.Exon
constructor for Exon object
ExonAble - interface uk.ac.sanger.psu.gfmerge.datacomp.ExonAble.
interface for exons.
exons - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
ArrayList of exon within a genemodel
exonType - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.Exon
typesafe enumeration of the Exon type
ExonType - class uk.ac.sanger.psu.gfmerge.datacomp.ExonType.
This typesafe enumeration construct replaces primitive constants with a set of static final object references encapsulated in this class that restricts further instantiation.
ExonType(String) - Constructor for class uk.ac.sanger.psu.gfmerge.datacomp.ExonType
 

F

feature - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
BioJava feature object
FeatureAnalysis - class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis.
Abstract class which contains partial implementation of derived analysis classes
FeatureAnalysis(ArrayList, ArrayList, SimpleArg) - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis
constructor of abstract FeatureAnalysis class, contains partial implementation of constructors of derived analysis classes
FeatureComponent - class uk.ac.sanger.psu.gfmerge.datacomp.FeatureComponent.
abstract class which contains the basic implementation of gene components (Intron, Exon).
FeatureComponent(GFMergeFeature, Location) - Constructor for class uk.ac.sanger.psu.gfmerge.datacomp.FeatureComponent
constructor which contains the basic implementation for genemodel components
FeatureComponentAble - interface uk.ac.sanger.psu.gfmerge.datacomp.FeatureComponentAble.
interface for gene components
FeatureOverlapAnalysis - class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureOverlapAnalysis.
Abstract class which contains partial implementation of derived overlap analysis classes
FeatureOverlapAnalysis(ArrayList, ArrayList, SimpleArg) - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureOverlapAnalysis
constructor of abstract FeatureOverlapAnalysis class, contains partial implementation of constructors of derived overlap analysis classes
FeatureOverlapAnalysisTools - class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools.
class which contains basic overlap computing tools which are used by derived overlap analysis classes (cDNA, Blast)
FeatureOverlapAnalysisTools() - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
 
filename - Variable in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
filename of output file.
fileOfRemovedGms - Variable in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
switch for output of a file containt all removed genemodels as well as a file of each analysis level with the removed genemodels.
find(LocateAble, HashMap, MyTreeMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.biotools.BioTools
Find method contains recursive search for regions.
findLongestProteinOverlap(HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which finds longest protein overlap.
findOverlappingFeatInFeatReg(boolean, GeneModel, GFMergeRegion) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.BasicFeatureAnalysisTools
method wich finds overlapping features for gm in feature region
findOverlaps(LocateAble, MyTreeMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.biotools.BioTools
FindOverlaps method returns all overlapping objects in tree of objects.
fn - Variable in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
attribute records the number of false negative bases (bases which are predicted to be non-coding but are coding in the annotation).
fp - Variable in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
attribute records the number of false positive bases (bases which are predicted to be coding but are non-coding in the annotation).
fuzzyBoundaries - Variable in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
allowed difference between genemodel and cDNA splice site to be assigned as correct splice site.

G

GeneModel - class uk.ac.sanger.psu.gfmerge.datacomp.GeneModel.
class is representing a genemodel.
GeneModel(Prediction, StrandedFeature) - Constructor for class uk.ac.sanger.psu.gfmerge.datacomp.GeneModel
constructor for GeneModel objects.
GeneModelAble - interface uk.ac.sanger.psu.gfmerge.datacomp.GeneModelAble.
interface for GeneModel.
GeneModelLengthAnalysis - class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.GeneModelLengthAnalysis.
Analysis class which calculates the high scoring path in a clustered sequence using the genemodel length (exon + intron length) as a scoring system
GeneModelLengthAnalysis(ArrayList, SimpleArg) - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.GeneModelLengthAnalysis
constructor for GeneModelLengthAnalysis objects
GeneModelLengthAnalysisTools - class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.GeneModelLengthAnalysisTools.
class which contains computing tools for CDnaSpliceSiteAnalysis.
GeneModelLengthAnalysisTools() - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.GeneModelLengthAnalysisTools
 
geneModels - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.Prediction
ArrayList of predicted genemodels on sequence
genePredicter - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.Prediction
reference to gene prediction program
GenePredicter - class uk.ac.sanger.psu.gfmerge.datacomp.GenePredicter.
class is representing a geneprediction program (its prediction).
GenePredicter(Sequence, Sequence, String) - Constructor for class uk.ac.sanger.psu.gfmerge.datacomp.GenePredicter
constructor of GenePredicter objects
genePredicterName - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.Prediction
name of gene prediction program (method tag in prediction file)
genePredicters - Variable in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
ArrayList of gene predicter objects
getAcp() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GenePredicter
accessor method which returns average conditional probability of genepredicter program.
getACP() - Method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
accessor method which returns average conditional probability value.
getAcpScoredGmHash(int, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.AvgCondProbAnalysisTools
method which returns a hash of genemodels pointing to their score
getAListOfLocs(FeatureHolder) - Static method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
method which returns ArrayList of locations when sequence is given.
getAllArguments() - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which returns the object containg all command line parameters
getAllArguments() - Method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
accessor method which returns object which contains all command line arguments
getAllPaths(TreeMap, ArrayList, HashMap, boolean) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.tools.HighScoringPath
 
getAnalysisObjArr() - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which returns ArrayList of analysis objects generated in calcAnalysisObjArr (CDnaSpliceSiteAnalysis, CDnaOverlapAnalysis, BlastOverlapAnalysis, TotalExonLengthAnalysis, GeneModelLengthAnalysis, AvgCondProbAnalysis)
getAnnotatedTrainSet_Sequence() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
accessor method which returns a sequence object of the annotated training set, used filename is stored in attribute 'annotatedTrainSet' , retrieved from command-line argument (-a)
getAnnotatedTrainSet() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
accessor method which returns the filename of the annotated training set file stored in attribute 'annotatedTrainSet', retrieved from command-line argument (-a)
getArrListOfBlastRegions() - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which return ArrayList of Blast regions
getArrListOfCDnaRegions() - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which returns ArrayList of cDNA regions
getArrListOfFeatRegions() - Method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis
accessor method which gets ArrayList of SimFeature regions (cDNA, Blast)
getArrListOfGMRegions_org() - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which returns an array list of regions which correspond to the original array used in the constructor
getArrListOfGMRegions() - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which returns ArrayList of genemodel regions
getArrListOfGMRegions() - Method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
accessor method which returns ArrayList of genemodel regions
getBlastFile() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
accessor method which returns an blast filename, retrieved from command-line argument (-b)
getCDNAFile() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
accessor method which returns an cDNA filename, retrieved from command-line argument (-c)
getCDnaScoredSpliceSiteForGm(int, int, GeneModel, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.CDnaSpliceSiteAnalysisTools
methode which calculates the score for one gm (either intron boundaries or splice sites).
getCDnaScoredSpliceSiteHash(int, int, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.CDnaSpliceSiteAnalysisTools
method which gets scored splice sites of genemodels using cDNA evidence.
getCDnaSpliceSiteScoredGmHash(int, int, boolean, ArrayList, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.CDnaSpliceSiteAnalysisTools
method which returns HashMap of genemodels pointing to their score using a cDNA splice site scoring system.
getClassName() - Method in interface uk.ac.sanger.psu.gfmerge.analysis.BasicFeatureAnalysisAble
stub for method which returns class name without package information
getClassName() - Method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
accessor method which retrieves the class name without package information
getDebug() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
accessor method which returns debug mode (int variable).
getExonHashOfOverlappedFeat(int, boolean, GeneModel, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which returns hash of exons pointing to ArrayList of overlapping features.
getExons() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeatureAble
 
getExons() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
accessor method which returns ArrayList of exons
getExonType() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.Exon
accessor method which return exon type
getExonType() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.ExonAble
 
getFeatOverlapArr(boolean, GeneModel, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.BasicFeatureAnalysisTools
method which gets overlapping features for genemodel
getFeatOverlapArrForExon(Exon, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which returns overlapping features for a single exon.
getFeatOverlapArrForGmComp(FeatureComponentAble, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
 
getFeature() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeatureAble
 
getFeature() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
accessor method which returns the appertaining StrandedFeature retrieved from file
getFeaturesFromStrand(boolean, FeatureHolder) - Static method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
method which returns featureholder of all features on either forward or reverse strand
getFN() - Method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
accessor method which returns number of false negative bases.
getFP() - Method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
accessor method which gets number of false positive bases.
getFrame() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.Exon
method which returns frame of the exon.
getFrame() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.ExonAble
 
getFuzzyBoundariesValue() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
accessor method which returns the value of tolerance inbetween cDNA and genemodel splice sites.
getGeneModels() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.Prediction
accessor method which returns ArrayList of genemodels on sequence
getGeneModels() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.PredictionAble
 
getGenePredicter() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.Prediction
accessor method which returns genepredicter object
getGenePredicter() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.PredictionAble
 
getGenePredicterFromSequence(Sequence, String) - Static method in class uk.ac.sanger.psu.gfmerge.util.biotools.BioTools
method returns genefinder name of geneprediction if all features have the same 'method' value in the prediction file otherwise it throughs an exception.
getGenePredicterName() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.Prediction
accessor method which returns the genepredicter name in the method tag of the prediction file
getGenePredicterName() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.PredictionAble
 
getGfmFeature() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.FeatureComponentAble
 
getGfmFeature() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.FeatureComponent
accessor method which returns reference to genemodel
getGmCompHashOfOverlappedFeat(int, boolean, ArrayList, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which returns hash of gm features (exons or introns) pointing to ArrayList of overlapping features (Blast or cDNA).
getGmHashOfAbsoluteFeatOverlap(int, boolean, boolean, ArrayList, ArrayList, boolean) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which returns hash of genemodels pointing to their ABSOLUTE overlap (CDNA).
getGmHashOfEqualGms(ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.TotalExonLengthAnalysisTools
method which calculates hash of gene models pointing to number of equal gms (including the genemodel itself)
getGmHashOfLocations(ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.TotalExonLengthAnalysisTools
method which calculates hash of locations pointing to their array of gms with the same location (equal genemodels).
getGmHashOfLongestAbsoluteFeatOverlap(int, boolean, boolean, ArrayList, ArrayList, boolean) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which returns hash of gms pointing to their longest absolute overlap (BLAST).
getGmHashOfOverlappedFeat(int, boolean, ArrayList, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.BasicFeatureAnalysisTools
method which gets hash of gms pointing to ArrayList of overlapping features (returns only overlapped genemodels !!!)
getGmLengthScoredGmHash(int, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.GeneModelLengthAnalysisTools
method which returns HashMap of genemodels pointing to their score using genemodel length (intron + exon length) as scoring system.
getGmSpliceSiteTree(int, int, boolean, GeneModel, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.CDnaSpliceSiteAnalysisTools
method which creates a tree of either max or min splice sites of the genemodel and overlapping features.
getHighScoringGmRegArr(ArrayList) - Method in interface uk.ac.sanger.psu.gfmerge.analysis.BasicFeatureAnalysisAble
stub for method which returns high scoring path of genemodels on the sequence
getHighScoringGmRegArr(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.TotalExonLengthAnalysis
method which returns the high scoring path of genemodels on a sequence using the accumulated exon length as a scoring system For further details consult the documentation.
getHighScoringGmRegArr(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BlastOverlapAnalysis
method which returns the high scoring path of genemodels on a sequence using the Blast overlap on the exon level.
getHighScoringGmRegArr(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.AvgCondProbAnalysis
method which returns the high scoring path of genemodels on a sequence using the average conditional probability as scoring system
getHighScoringGmRegArr(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.GeneModelLengthAnalysis
method which returns the high scoring path of genemodels on a sequence.
getHighScoringGmRegArr(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
stub for high scoring method which returns the high scoring path of genemodels on a sequence
getHighScoringGmRegArr(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.CDnaOverlapAnalysis
method which returns the high scoring path of genemodels on a sequence using the cDNA overlap on the exon level
getHighScoringGmRegArr(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.CDnaSpliceSiteAnalysis
method which returns the high scoring path of genemodels on a sequence using a cDNA splice site scoring system
getHighScoringPath(HashMap, ArrayList, boolean) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.tools.HighScoringPath
 
getIntrons() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeatureAble
 
getIntrons() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
accessor method which returns ArrayList of introns
getLength() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeatureAble
 
getLength() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.FeatureComponentAble
 
getLength() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
accessor method which returns the length of the feature
getLength() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.FeatureComponent
method which returns length of genemodel component
getLocateable() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeRegion
accessor method which returns ArrayList of overlapping features in cluster
getLocation() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeRegion
accessor method which returns location of the cluster
getLocation() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.LocateAble
stub which returns Location
getLocation() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
accessor method which returns Location of the BioJava feature
getLocation() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.FeatureComponent
accessor method which returns Location of genemodel component
getMaxObjectFound() - Method in class uk.ac.sanger.psu.gfmerge.util.algotools.MyTreeMap
accessor method which returns max length seen.
getMergedFeatureTable() - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
method which returns an array list of regions only containing the genemodels which have been picked during the process of scoring
getName() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GenePredicter
accessor method which returns name of genepredicter.
getNonOverlappingObjs(ArrayList, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.tools.HighScoringPath
 
GetOpt - class uk.ac.sanger.psu.gfmerge.util.getopt.GetOpt.
A class to implement UNIX-style (single-character) command arguments
GetOpt(String) - Constructor for class uk.ac.sanger.psu.gfmerge.util.getopt.GetOpt
 
getopt(String[]) - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.GetOpt
Return one argument.
getOptInd() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.GetOpt
Retrieve the option index
getOutputFilename() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
accessor method which returns an output filename, retrieved from command-line argument (-f)
getPathScore(ArrayList, HashMap, boolean) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.tools.HighScoringPath
 
getPositionForPosTree(boolean, FeatureComponentAble) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.CDnaSpliceSiteAnalysisTools
method which returns position of exon boundary for position tree.
getPredictedTrainSet_Sequences() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
accessor method which returns an array list of sequence objects containing predictions on the training set of different gene predicters, used filename are stored in attribute 'predictedTrainSet' , retrieved from command-line argument (-t)
getPredictedTrainSet() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
accessor method which returns an array list of filenames of predictions from different gene prediction programs on the training set, retrieved from command-line argument (-t)
getPrediction() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.GeneModelAble
 
getPrediction() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GeneModel
accessor method which returns reference to prediction object.
getPredictions_Sequences() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
accessor method which returns an array list of sequence objects containing predictions of different gene predicters, used filename are stored in attribute 'predictions' , retrieved from command-line argument (-p)
getPredictions() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
accessor method which returns an array list of filenames of predictions, stored in attribute 'predictions', retrieved from command-line argument (-p)
getPredictions() - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which returns an array list of prediction objects
getProteinHash(int, GeneModel, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which returns protein hash.
getProteinID(GFMergeFeature) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which returns the protein ID of a feature.
getProteinOverlapHash(int, boolean, GeneModel, HashMap, boolean) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which returns hash map of proteins pointing to overlap length.
getRemovedFeatures(ArrayList, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.tools.SavScoreInBioFeat
 
getSeq(String) - Static method in class uk.ac.sanger.psu.gfmerge.util.io.GFMergeInput
method which returns a BioJava SequenceIterator.
getSequence() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.Prediction
accessor method which return BioJava sequence object
getSequence() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.PredictionAble
 
getSingleProteinOverlap(int, boolean, GeneModel, ArrayList, boolean) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which returns single protein overlap for a genemodel.
getStrand() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.StrandAble
 
getStrand() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
accessor method which returns Strand of the BioJava feature
getTlExLengthScoredGmHash(int, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.TotalExonLengthAnalysisTools
method which returns total exon length of a genemodel.
getTN() - Method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
accessor method which returns number of true negative bases.
getTotalExonLength() - Method in interface uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeatureAble
 
getTotalExonLength() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
accessor method which returns total exon length of the feature
getTotalExonLengthScore(GeneModel, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.TotalExonLengthAnalysisTools
method which calculates score for a genemodel using the total exon length as scoring system.
getTP() - Method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
accessor method which returns number of true positive bases.
getTreeScore(MyTreeMap, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.CDnaSpliceSiteAnalysisTools
method which calculates the score of a tree.
GFMerge - class uk.ac.sanger.psu.gfmerge.GFMerge.
class which contains the logic of the program GFMerge
GFMerge_Analysis - class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis.
class which wraps analysis of gene predictions
GFMerge_Analysis(SimpleArg) - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
constructor of GFMerge_Analysis objects
GFMerge() - Constructor for class uk.ac.sanger.psu.gfmerge.GFMerge
 
GFMergeFeature - class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature.
abstract class which contains basic implementation of genemodels, blast and cDNA features.
GFMergeFeature(StrandedFeature) - Constructor for class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
constructor which contains basic implementation for GeneModel and SimFeature objects
GFMergeFeatureAble - interface uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeatureAble.
interface for GFMergeFeature objects
GFMergeInput - class uk.ac.sanger.psu.gfmerge.util.io.GFMergeInput.
class which reads EMBL files into objects using SeqIOTools.readEmbl().
GFMergeInput() - Constructor for class uk.ac.sanger.psu.gfmerge.util.io.GFMergeInput
 
GFMergeOutput - class uk.ac.sanger.psu.gfmerge.util.io.GFMergeOutput.
class which writes EMBL files using BioJava SeqIOTools.writeEmbl().
GFMergeOutput() - Constructor for class uk.ac.sanger.psu.gfmerge.util.io.GFMergeOutput
 
GFMergeRegion - class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeRegion.
class which represents a cluster of overlapping features on a sequence.
GFMergeRegion(Location, ArrayList) - Constructor for class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeRegion
constructor of GFMergeRegion objects
gfmFeature - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.FeatureComponent
reference to genemodel
gmBoundary - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.RecordGmCDna
splice site of a genemodel exon (either start or end position)

H

HighScoringPath - class uk.ac.sanger.psu.gfmerge.analysis.tools.HighScoringPath.
 
HighScoringPath() - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.tools.HighScoringPath
 

I

Intron - class uk.ac.sanger.psu.gfmerge.datacomp.Intron.
class Intron is representing an biological intron which is the Location inbetween two sublocation of a feature.
Intron(GFMergeFeature, Location) - Constructor for class uk.ac.sanger.psu.gfmerge.datacomp.Intron
constructor for Intron objects
IntronAble - interface uk.ac.sanger.psu.gfmerge.datacomp.IntronAble.
interface introns.
introns - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
ArrayList of introns within a genemodel
isFeatureOverlappingGm(boolean, GeneModel, SimFeature) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.BasicFeatureAnalysisTools
method wich finds out if given feature is overlapping genemodel
isNonOverlappingDownstreamObjFurtherUpstream(ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.tools.HighScoringPath
 
isNonOverlappingObjUpstream(ArrayList, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.tools.HighScoringPath
 

L

locatable - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeRegion
ArrayList of features objects (implementing LocateAble interface)
LocateAble - interface uk.ac.sanger.psu.gfmerge.datacomp.LocateAble.
interface for objects which contain a Location.
location - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeRegion
cluster location
location - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.FeatureComponent
Location of genemodel component

M

main(String[]) - Static method in class uk.ac.sanger.psu.gfmerge.GFMerge
Main method of GFMerge which creates the GFMerge_Analysis object
markCoding(ArrayList, StringBuffer) - Static method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
method which marks coding exons as 'C' on a sequence.
maxObjectFound - Variable in class uk.ac.sanger.psu.gfmerge.util.algotools.MyTreeMap
stores maximum length [long] seen during processing.
mergedFeatureTableArr - Variable in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
return value of getMergedFeatureTable, contains regions of picked genemodels
MyTreeMap - class uk.ac.sanger.psu.gfmerge.util.algotools.MyTreeMap.
class MyTreeMap adds some more functionality to TreeMap
MyTreeMap() - Constructor for class uk.ac.sanger.psu.gfmerge.util.algotools.MyTreeMap
constructor of MyTreeMap objects

N

name - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.GenePredicter
name of geneprediction program
name - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.ExonType
 
nextKey(Object) - Method in class uk.ac.sanger.psu.gfmerge.util.algotools.MyTreeMap
method which returns the successor of a key.

O

optarg - Variable in class uk.ac.sanger.psu.gfmerge.util.getopt.GetOpt
The option argument, if there is one.
optarg() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.GetOpt
Retrieve the current option argument
optind - Variable in class uk.ac.sanger.psu.gfmerge.util.getopt.GetOpt
Where we are in the options

P

pattern - Variable in class uk.ac.sanger.psu.gfmerge.util.getopt.GetOpt
The set of characters to look for
PredAccuracy - class uk.ac.sanger.psu.gfmerge.util.PredAccuracy.
class PredAccuracy wraps the calculation of the average conditional probability for a genepredicter program.
PredAccuracy(Sequence, Sequence) - Constructor for class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
constructor which creates PredAccuracy object.
predictedTrainSet - Variable in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
predictions of training set (for acp calculation).
prediction - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.GeneModel
reference to prediction object.
Prediction - class uk.ac.sanger.psu.gfmerge.datacomp.Prediction.
class Prediction is wrapping a BioJava sequence object.
Prediction(Sequence, String, ArrayList) - Constructor for class uk.ac.sanger.psu.gfmerge.datacomp.Prediction
constructor of Prediction objects
PredictionAble - interface uk.ac.sanger.psu.gfmerge.datacomp.PredictionAble.
interface for prediction objects
predictions - Variable in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
predictions which will be collapsed into one (EMBL format).
predictions - Variable in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
ArrayList of prediction objects
previousKey(Object) - Method in class uk.ac.sanger.psu.gfmerge.util.algotools.MyTreeMap
method which returns the predecessor of a key.
putFeatPosInGmTree(MyTreeMap, int, boolean, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.CDnaSpliceSiteAnalysisTools
method which adds SimFeature boundaries to gm boundary tree.
putFeatureInProteinHash(String, SimFeature, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.FeatureOverlapAnalysisTools
method which stores feature in protein hash.
putGmInPosTree(boolean, int, ArrayList, ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.CDnaSpliceSiteAnalysisTools
method which returns a tree of featureComponent positions (Intron, Exon).
putGmsInHash(ArrayList) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.tools.SavScoreInBioFeat
 

R

RecordGmCDna - class uk.ac.sanger.psu.gfmerge.datacomp.RecordGmCDna.
class which represents a data record.
RecordGmCDna() - Constructor for class uk.ac.sanger.psu.gfmerge.datacomp.RecordGmCDna
constructor of RecordGmCDna objects.
removeLowScoreGmsFromRegArr(ArrayList, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.tools.HighScoringPath
 
removeNonCdsFeatures(Sequence) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
method which removes non-CDS features from sequence
retrieveName(Sequence, String) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GenePredicter
method which retrieves name of genepredicter program from gene prediction file.
rewind() - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.GetOpt
 

S

saveFeat2File(String, ArrayList, Prediction) - Static method in class uk.ac.sanger.psu.gfmerge.util.io.GFMergeOutput
method which saves picked features to a file.
saveRemovedFeat2File(String, ArrayList, ArrayList, Prediction) - Static method in class uk.ac.sanger.psu.gfmerge.util.io.GFMergeOutput
method which saves removed features to a file.
savScore(ArrayList, String, HashMap) - Static method in class uk.ac.sanger.psu.gfmerge.analysis.tools.SavScoreInBioFeat
 
SavScoreInBioFeat - class uk.ac.sanger.psu.gfmerge.analysis.tools.SavScoreInBioFeat.
 
SavScoreInBioFeat() - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.tools.SavScoreInBioFeat
 
search(MyTreeMap) - Static method in class uk.ac.sanger.psu.gfmerge.util.biotools.BioTools
Search method calculates regions of overlapping features.
seqs2Seq(SequenceIterator) - Static method in class uk.ac.sanger.psu.gfmerge.util.biotools.BioTools
Seq2Seq method returns a sequence object when sequence iterator is given.
sequence - Variable in class uk.ac.sanger.psu.gfmerge.datacomp.Prediction
BioJava sequence object
setAcp(double) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GenePredicter
accessor method which sets average conditional probability of genepredicter program.
setACP(double) - Method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
accessor method which sets average conditional probability value.
setAllArguments(SimpleArg) - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which sets SimpleArg object containing all command line parameters
setAllArguments(SimpleArg) - Method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
accessor method which sets object of command line arguments
setAnalysisObjArr(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which sets ArrayList of analysis objects generated in calcAnalysisObjArr (CDnaSpliceSiteAnalysis, CDnaOverlapAnalysis, BlastOverlapAnalysis, TotalExonLengthAnalysis, GeneModelLengthAnalysis, AvgCondProbAnalysis)
setArguments(String[]) - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
method which retrieves command line arguments and saves them.
setArrListOfBlastRegions(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which sets ArrayList of Blast regions
setArrListOfCDnaRegions(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which sets ArrayList of cDNA regions
setArrListOfFeatRegions(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis
accessor method which sets ArrayList of SimFeature regions (cDNA, Blast)
setArrListOfGMRegions_org(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which sets ArrayList of original genemodel regions
setArrListOfGMRegions(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which sets ArrayList of genemodel regions
setArrListOfGMRegions(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
accessor method which sets ArrayList of genemodel regions
setAttributes(HashMap) - Method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
method which saves HashMap containing the tp, tn, fp, fn values to their appropriate attributes.
setExons(Feature) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
accessor method which calculates exons of feature.
setExonType() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.Exon
accessor method which sets exon type.
setFeature(StrandedFeature) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
accessor method which sets BioJava feature
setFN(int) - Method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
accessor method which sets number of false negative bases.
setFP(int) - Method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
accessor method which sets number of false positive bases.
setGeneModels(Sequence) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.Prediction
accessor method which sets ArrayList of genemodels on sequence
setGenePredicter(String, ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.Prediction
accessor method which sets reference to genepredicter object
setGenePredicterName(Sequence, String) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.Prediction
accessor method which sets genepredicter name
setGenePredicters(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which sets ArrayList of genepredicter objects
setGfmFeature(GFMergeFeature) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.FeatureComponent
accessor method which sets reference to genemodel genemodel component belongs to
setIntrons(Feature) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
accessor method which calculates introns of feature.
setLocateable(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeRegion
accessor method which sets ArrayList of overlapping features in cluster
setLocation(Location) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GFMergeRegion
accessor method which sets location of the cluster
setLocation(Location) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.FeatureComponent
accessor method which sets Location of genemodel component
setMaxObjectFound(long) - Method in class uk.ac.sanger.psu.gfmerge.util.algotools.MyTreeMap
accessor method which sets max length seen.
setMergedFeatureTableArr(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which sets mergedFeatureTableArr with ArrayList of regions which contain high scoring genemodels
setName(String) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GenePredicter
accessor method which sets name of genepredicter.
setPrediction(Prediction) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.GeneModel
accessor method which sets reference to prediction.
setPredictions(ArrayList) - Method in class uk.ac.sanger.psu.gfmerge.analysis.GFMerge_Analysis
accessor method which sets ArrayList of prediction objects
setSequence(Sequence) - Method in class uk.ac.sanger.psu.gfmerge.datacomp.Prediction
accessor method which sets reference to BioJava sequence object
setTN(int) - Method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
accessor method which sets number of true negative bases.
setTP(int) - Method in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
accessor method which setsnumber of true positive bases.
SimFeature - class uk.ac.sanger.psu.gfmerge.datacomp.SimFeature.
class is representing a similarity feature used as evidence for correct predictions.
SimFeature(StrandedFeature) - Constructor for class uk.ac.sanger.psu.gfmerge.datacomp.SimFeature
constructor for SimFeature objects
SimpleArg - class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg.
class for objects containing the command line arguments.
SimpleArg(String[]) - Constructor for class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
constructor of SimpleArg objects.
StrandAble - interface uk.ac.sanger.psu.gfmerge.datacomp.StrandAble.
interface for objects containing strand information (genemodel, Blast, cDNA).
strArrToArrList(String[]) - Method in class uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg
method which converts String[] into an ArrayList

T

tn - Variable in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
attribute records the number of true negative bases (bases which are predicted to be non-coding and are non-coding in the annotation).
toString() - Method in class uk.ac.sanger.psu.gfmerge.datacomp.ExonType
 
TotalExonLengthAnalysis - class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.TotalExonLengthAnalysis.
Analysis class which calculates the high scoring path in a clustered sequence using the accumulated exon length as a scoring system
TotalExonLengthAnalysis(ArrayList, SimpleArg) - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.TotalExonLengthAnalysis
constructor for TotalExonLengthAnalysis objects
TotalExonLengthAnalysisTools - class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.TotalExonLengthAnalysisTools.
class which contains computing tools for TotalExonLengthAnalysis.
TotalExonLengthAnalysisTools() - Constructor for class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.TotalExonLengthAnalysisTools
 
tp - Variable in class uk.ac.sanger.psu.gfmerge.util.PredAccuracy
attribute records the number of true positive bases (bases which are predicted to be coding and are coding in the annotation).
TYPE_3_END - Static variable in class uk.ac.sanger.psu.gfmerge.datacomp.ExonType
 
TYPE_5_END - Static variable in class uk.ac.sanger.psu.gfmerge.datacomp.ExonType
 
TYPE_INTERNAL - Static variable in class uk.ac.sanger.psu.gfmerge.datacomp.ExonType
 
TYPE_SINGLE_EXON_GENE - Static variable in class uk.ac.sanger.psu.gfmerge.datacomp.ExonType
 

U

uk.ac.sanger.psu.gfmerge - package uk.ac.sanger.psu.gfmerge
 
uk.ac.sanger.psu.gfmerge.analysis - package uk.ac.sanger.psu.gfmerge.analysis
 
uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis - package uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis
 
uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools - package uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools
 
uk.ac.sanger.psu.gfmerge.analysis.tools - package uk.ac.sanger.psu.gfmerge.analysis.tools
 
uk.ac.sanger.psu.gfmerge.datacomp - package uk.ac.sanger.psu.gfmerge.datacomp
 
uk.ac.sanger.psu.gfmerge.util - package uk.ac.sanger.psu.gfmerge.util
 
uk.ac.sanger.psu.gfmerge.util.algotools - package uk.ac.sanger.psu.gfmerge.util.algotools
 
uk.ac.sanger.psu.gfmerge.util.biotools - package uk.ac.sanger.psu.gfmerge.util.biotools
 
uk.ac.sanger.psu.gfmerge.util.debug - package uk.ac.sanger.psu.gfmerge.util.debug
 
uk.ac.sanger.psu.gfmerge.util.getopt - package uk.ac.sanger.psu.gfmerge.util.getopt
 
uk.ac.sanger.psu.gfmerge.util.io - package uk.ac.sanger.psu.gfmerge.util.io
 

W

writeSeq2File(String, Sequence) - Static method in class uk.ac.sanger.psu.gfmerge.util.io.GFMergeOutput
method which writes BioJava sequence to a file.

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