Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X A abort() (WorkerThread method) addAllele() (AnthonyNolanFilter method) (Filter method) (PassThroughFilter method) AlleleCountAnthonyNolanFilter (class in PyPop.Filter) AlleleCounts (class in PyPop.DataTypes) allPairwise() (Emhaplofreq method) (Haplostats method) AnthonyNolanFilter (class in PyPop.Filter) appendTo2dList() (in module PyPop.Utils) ArlequinBatch (class in PyPop.Arlequin) ArlequinExactHWTest (class in PyPop.Arlequin) ArlequinWrapper (class in PyPop.Arlequin) B BinningFilter (class in PyPop.Filter) C canGenerateExpectedStats() (Homozygosity method) checkAlleleName() (AnthonyNolanFilter method) (Filter method) (PassThroughFilter method) checkIfSequenceData() (in module PyPop.DataTypes) checkXSLFile() (in module PyPop.Utils) chi2 (in module PyPop.HardyWeinberg) citation_output_formats (in module PyPop.citation) CitationAction (class in PyPop.CommandLineInterface) cleanup() (AnthonyNolanFilter method) (ArlequinWrapper method) (Filter method) (PassThroughFilter method) clear() (OrderedDict method) close() (TextOutputStream method) closetag() (XMLOutputStream method) convert_citation_formats() (in module PyPop.citation) convertLineEndings() (in module PyPop.Utils) convertToInts() (StringMatrix method) copy() (OrderedDict method) (StringMatrix method) copyCustomPlatform() (in module PyPop.Utils) copyfileCustomPlatform() (in module PyPop.Utils) copyright_message (in module PyPop) count() (OrderedDict method) countPairs() (StringMatrix method) D DIR (in module PyPop.popmeta) (in module PyPop.pypop) doCalcs() (HomozygosityEWSlatkinExact method) doCustomBinning() (BinningFilter method) doDigitBinning() (BinningFilter method) doFiltering() (AnthonyNolanFilter method) (Filter method) (PassThroughFilter method) dump() (StringMatrix method) dumpTable() (HardyWeinbergGuoThompson method) E Emhaplofreq (class in PyPop.Haplo) emptytag() (XMLOutputStream method) endFiltering() (AnthonyNolanFilter method) (Filter method) (PassThroughFilter method) endFirstPass() (AlleleCountAnthonyNolanFilter method) (AnthonyNolanFilter method) (Filter method) (PassThroughFilter method) estHaplotypes() (Emhaplofreq method) (Haplostats method) estLinkageDisequilibrium() (Emhaplofreq method) EVT_RESULT() (in module PyPop.GUIApp) EVT_RESULT_ID (in module PyPop.GUIApp) exponent_len() (in module PyPop.xslt) F Filter (class in PyPop.Filter) filterAllele() (AnthonyNolanFilter method) (Filter method) (PassThroughFilter method) filterOut() (StringMatrix method) fixForPlatform() (in module PyPop.Utils) flattenCols() (StringMatrix method) flush() (TextOutputStream method) format_number_fixed_width() (in module PyPop.xslt) G generateFlattenedMatrix() (HardyWeinbergGuoThompson method) genHaplotypes() (HaploArlequin method) GENOTYPE_SEPARATOR (in module PyPop.Utils) GENOTYPE_TERMINATOR (in module PyPop.Utils) Genotypes (class in PyPop.DataTypes) genSampleOutput() (ParseFile method) genValidKey() (ParseAlleleCountFile method) (ParseGenotypeFile method) get() (OrderedDict method) get_parent_cli() (in module PyPop.CommandLineInterface) get_popmeta_cli() (in module PyPop.CommandLineInterface) get_pypop_cli() (in module PyPop.CommandLineInterface) get_sequence_directory() (in module PyPop.Main) getAlleleCount() (AlleleCounts method) (Genotypes method) getAlleleCountAt() (Genotypes method) getAlleleTable() (ParseAlleleCountFile method) getConfigInstance() (in module PyPop.Main) getCount() (Homozygosity method) getExpectedHomozygosity() (Homozygosity method) getFileData() (ParseFile method) getHomozygosity() (HomozygosityEWSlatkinExact method) getHWExactTest() (ArlequinExactHWTest method) getIndividualsData() (Genotypes method) getLocusData() (Genotypes method) getLocusDataAt() (Genotypes method) getLocusList() (Genotypes method) getLocusName() (AlleleCounts method) (ParseAlleleCountFile method) getLocusPairs() (in module PyPop.DataTypes) getLumpedDataLevels() (in module PyPop.DataTypes) getMatrix() (ParseAlleleCountFile method) (ParseGenotypeFile method) getMetaLocus() (in module PyPop.DataTypes) getNewStringMatrix() (StringMatrix method) getNormDevHomozygosity() (Homozygosity method) getObservedHomozygosity() (Homozygosity method) getObservedHomozygosityFromAlleleData() (in module PyPop.Homozygosity) getPopData() (ParseFile method) getPValueRange() (Homozygosity method) getSampleMap() (ParseFile method) getStreamType() (in module PyPop.Utils) getSuperType() (StringMatrix method) getTxtOutPath() (Main method) getUniqueAlleles() (StringMatrix method) getUserFilenameInput() (in module PyPop.Utils) getVarExpectedHomozygosity() (Homozygosity method) getXmlOutPath() (Main method) glob_with_pathlib() (in module PyPop.Utils) Group (class in PyPop.Utils) H Haplo (class in PyPop.Haplo) HaploArlequin (class in PyPop.Haplo) Haplostats (class in PyPop.Haplo) HardyWeinberg (class in PyPop.HardyWeinberg) HardyWeinbergEnumeration (class in PyPop.HardyWeinberg) HardyWeinbergGuoThompson (class in PyPop.HardyWeinberg) HardyWeinbergGuoThompsonArlequin (class in PyPop.HardyWeinberg) has_key() (OrderedDict method) Homozygosity (class in PyPop.Homozygosity) HomozygosityEWSlatkinExact (class in PyPop.Homozygosity) HomozygosityEWSlatkinExactPairwise (class in PyPop.Homozygosity) I ID_ABOUT (in module PyPop.GUIApp) ID_EXIT (in module PyPop.GUIApp) ID_OPEN_CONFIG (in module PyPop.GUIApp) ID_OPEN_POP (in module PyPop.GUIApp) Index (class in PyPop.Utils) index() (OrderedDict method) insert() (OrderedDict method) items() (OrderedDict method) K keys() (OrderedDict method) L lookupCustomBinning() (BinningFilter method) M Main (class in PyPop.Main) main() (in module PyPop.popmeta) (in module PyPop.pypop) main_interactive() (in module PyPop.pypop) MainWindow (class in PyPop.GUIApp) makeSeqDictionaries() (AnthonyNolanFilter method) Meta (class in PyPop.Meta) module PyPop PyPop.Arlequin PyPop.citation PyPop.CommandLineInterface PyPop.DataTypes PyPop.Filter PyPop.GUIApp PyPop.Haplo PyPop.HardyWeinberg PyPop.Homozygosity PyPop.Main PyPop.Meta PyPop.ParseFile PyPop.popmeta PyPop.pypop PyPop.RandomBinning PyPop.Utils PyPop.xslt N natural_sort_key() (in module PyPop.Utils) ns (in module PyPop.xslt) num_zeros() (in module PyPop.xslt) O OnAbout() (MainWindow method) OnConfig() (MainWindow method) OnExit() (MainWindow method) OnPop() (MainWindow method) OnResult() (MainWindow method) OnRun() (MainWindow method) OnStop() (MainWindow method) opentag() (XMLOutputStream method) OrderedDict (class in PyPop.Utils) outputArlequin() (ArlequinBatch method) (HaploArlequin method) outputArpFile() (ArlequinWrapper method) outputArsFile() (ArlequinWrapper method) outputRunFiles() (ArlequinBatch method) (ArlequinWrapper method) P ParseAlleleCountFile (class in PyPop.ParseFile) ParseFile (class in PyPop.ParseFile) ParseGenotypeFile (class in PyPop.ParseFile) PassThroughFilter (class in PyPop.Filter) platform_info (in module PyPop) pval() (in module PyPop.HardyWeinberg) PyPop module PyPop.Arlequin module PyPop.citation module PyPop.CommandLineInterface module PyPop.DataTypes module PyPop.Filter module PyPop.GUIApp module PyPop.Haplo module PyPop.HardyWeinberg module PyPop.Homozygosity module PyPop.Main module PyPop.Meta module PyPop.ParseFile module PyPop.popmeta module PyPop.pypop module PyPop.RandomBinning module PyPop.Utils module PyPop.xslt module PyPopFormatter (class in PyPop.CommandLineInterface) R RandomBinsForHomozygosity (class in PyPop.RandomBinning) randomMethod() (RandomBinsForHomozygosity method) remove() (OrderedDict method) ResultEvent (class in PyPop.GUIApp) returnBulkHomozygosityStats() (HomozygosityEWSlatkinExact method) reverse() (OrderedDict method) root (in module PyPop.xslt) run() (WorkerThread method) runArlequin() (ArlequinBatch method) (ArlequinWrapper method) (HaploArlequin method) S sequenceMethod() (RandomBinsForHomozygosity method) serializeAlleleCountDataAt() (AlleleCounts method) (Genotypes method) serializeAlleleCountDataTo() (Genotypes method) serializeEnd() (Emhaplofreq method) (Haplostats method) serializeHomozygosityTo() (Homozygosity method) (HomozygosityEWSlatkinExact method) serializeMetadataTo() (ParseFile method) serializeStart() (Emhaplofreq method) (Haplostats method) serializeSubclassMetadataTo() (AlleleCounts method) (Genotypes method) (ParseAlleleCountFile method) (ParseGenotypeFile method) serializeTo() (HardyWeinberg method) (HardyWeinbergEnumeration method) (HardyWeinbergGuoThompsonArlequin method) (HomozygosityEWSlatkinExactPairwise method) serializeXMLTableTo() (HardyWeinberg method) setup_logging() (in module PyPop) sort() (OrderedDict method) splitIntoNGroups() (in module PyPop.Utils) startFiltering() (AnthonyNolanFilter method) (Filter method) (PassThroughFilter method) startFirstPass() (AnthonyNolanFilter method) (Filter method) (PassThroughFilter method) StringMatrix (class in PyPop.Utils) SubclassError T tagContents() (XMLOutputStream method) TextOutputStream (class in PyPop.Utils) translate_file_to_file() (in module PyPop.Meta) translate_file_to_stdout() (in module PyPop.Meta) translate_string_to_file() (in module PyPop.Meta) translate_string_to_stdout() (in module PyPop.Meta) translateMatrix() (AnthonyNolanFilter method) U unique_elements() (in module PyPop.Utils) update() (OrderedDict method) usage_message (in module PyPop.Arlequin) use_scipy (in module PyPop.HardyWeinberg) V values() (OrderedDict method) W WorkerThread (class in PyPop.GUIApp) write() (TextOutputStream method) writeln() (TextOutputStream method) writeToLog() (AnthonyNolanFilter method) (Filter method) (PassThroughFilter method) X XMLOutputStream (class in PyPop.Utils)
