PK qb8 META-INF/PK pb8QMETA-INF/MANIFEST.MFManifest-Version: 1.0 Ant-Version: Apache Ant 1.7.0 Created-By: 1.6.0_03-b05 (Sun Microsystems Inc.) Main-Class: Abc.Abc Class-Path: X-COMMENT: Main-Class will be added automatically by build PK qb8Abc/PK qb8Abc/dependentCalculators/PK qb8Abc/dependentFilters/PK qb8Abc/independentCalculators/PK qb8Abc/transformers/PK qb8ascertainAllPops/PK qb8 ascertainBp/PK qb8ascertainDiffDensity/PK qb8 ascertainMaf/PK qb8ascertainOnePop/PK qb8ascertainSampleGene/PK qb8ascertainSampleSnp/PK qb8 cositoms/PK qb8fstcalculator/PK qb8mafCalculator/PK qb8 selsimtoms/PK qb8sscosi/PK pb8ZOAbc/Abc$1.class1(     !this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$1; focusGained(Ljava/awt/event/FocusEvent;)VevtLjava/awt/event/FocusEvent; focusLost SourceFileAbc.javaEnclosingMethod" #$  $ %& '& Abc/Abc$1java/awt/event/FocusAdapterAbc/AbcinitComponents()V access$000'(LAbc/Abc;Ljava/awt/event/FocusEvent;)V access$1000  4 *+*    A *+     A *+     PK pb8?Abc/Abc$10.class1(     !this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$10; focusGained(Ljava/awt/event/FocusEvent;)VevtLjava/awt/event/FocusEvent; focusLost SourceFileAbc.javaEnclosingMethod" #$  $ %& '& Abc/Abc$10java/awt/event/FocusAdapterAbc/AbcinitComponents()V access$000'(LAbc/Abc;Ljava/awt/event/FocusEvent;)V access$1000  4 *+* e   A *+ gh    A *+ jk    PK qb8p."Abc/Abc$11.class18 ' ()*+,-./01 234strings[Ljava/lang/String;this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$11;getSize()I getElementAt(I)Ljava/lang/Object;iI SourceFileAbc.javaEnclosingMethod5 67  7java/lang/StringnoneDiscovery sample per geneDiscovery sample per SNP&SNPs polymorphic in a given population#SNPs polymorphic in all populations MAF>thresholdOne SNP every x bp#Diferent SNP density along the gene  Abc/Abc$11javax/swing/AbstractListModelAbc/AbcinitComponents()V0 k=*+**YSYSYSYSYSY SY SY S  o p =0* q ;* 2r !"#$%&  PK qb8!Abc/Abc$12.class1&    this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$12; valueChanged)(Ljavax/swing/event/ListSelectionEvent;)Vevt&Ljavax/swing/event/ListSelectionEvent; SourceFileAbc.javaEnclosingMethod! "#  # $% Abc/Abc$12java/lang/Object'javax/swing/event/ListSelectionListenerAbc/AbcinitComponents()V access$6002(LAbc/Abc;Ljavax/swing/event/ListSelectionEvent;)V0  4 *+* u   A *+ wx    PK qb8"Abc/Abc$13.class1(     !this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$13; focusGained(Ljava/awt/event/FocusEvent;)VevtLjava/awt/event/FocusEvent; focusLost SourceFileAbc.javaEnclosingMethod" #$  $ %& '& Abc/Abc$13java/awt/event/FocusAdapterAbc/AbcinitComponents()V access$000'(LAbc/Abc;Ljava/awt/event/FocusEvent;)V access$1000  4 *+*    A *+     A *+     PK qb8sPFAbc/Abc$14.class1(     !this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$14; focusGained(Ljava/awt/event/FocusEvent;)VevtLjava/awt/event/FocusEvent; focusLost SourceFileAbc.javaEnclosingMethod" #$  $ %& '& Abc/Abc$14java/awt/event/FocusAdapterAbc/AbcinitComponents()V access$000'(LAbc/Abc;Ljava/awt/event/FocusEvent;)V access$1000  4 *+*    A *+     A *+     PK qb8u&m'Abc/Abc$15.class1&    this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$15;actionPerformed(Ljava/awt/event/ActionEvent;)VevtLjava/awt/event/ActionEvent; SourceFileAbc.javaEnclosingMethod! "#  # $% Abc/Abc$15java/lang/Objectjava/awt/event/ActionListenerAbc/AbcinitComponents()V access$700((LAbc/Abc;Ljava/awt/event/ActionEvent;)V0  4 *+*    A *+     PK qb8I[\Abc/Abc$16.class1&    this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$16;actionPerformed(Ljava/awt/event/ActionEvent;)VevtLjava/awt/event/ActionEvent; SourceFileAbc.javaEnclosingMethod! "#  # $% Abc/Abc$16java/lang/Objectjava/awt/event/ActionListenerAbc/AbcinitComponents()V access$800((LAbc/Abc;Ljava/awt/event/ActionEvent;)V0  4 *+*    A *+     PK qb8ERAbc/Abc$17.class1(     !this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$17; focusGained(Ljava/awt/event/FocusEvent;)VevtLjava/awt/event/FocusEvent; focusLost SourceFileAbc.javaEnclosingMethod" #$  $ %& '& Abc/Abc$17java/awt/event/FocusAdapterAbc/AbcinitComponents()V access$000'(LAbc/Abc;Ljava/awt/event/FocusEvent;)V access$1000  4 *+*    A *+     A *+     PK qb8QѼAbc/Abc$18.class1(     !this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$18; focusGained(Ljava/awt/event/FocusEvent;)VevtLjava/awt/event/FocusEvent; focusLost SourceFileAbc.javaEnclosingMethod" #$  $ %& '& Abc/Abc$18java/awt/event/FocusAdapterAbc/AbcinitComponents()V access$000'(LAbc/Abc;Ljava/awt/event/FocusEvent;)V access$1000  4 *+*    A *+     A *+      PK qb8zx$-Abc/Abc$19.class1&    this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$19;actionPerformed(Ljava/awt/event/ActionEvent;)VevtLjava/awt/event/ActionEvent; SourceFileAbc.javaEnclosingMethod! "#  # $% Abc/Abc$19java/lang/Objectjava/awt/event/ActionListenerAbc/AbcinitComponents()V access$900((LAbc/Abc;Ljava/awt/event/ActionEvent;)V0  4 *+*    A *+     PK pb8sUAbc/Abc$2.class1&    this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$2;actionPerformed(Ljava/awt/event/ActionEvent;)VevtLjava/awt/event/ActionEvent; SourceFileAbc.javaEnclosingMethod! "#  # $% Abc/Abc$2java/lang/Objectjava/awt/event/ActionListenerAbc/AbcinitComponents()V access$200((LAbc/Abc;Ljava/awt/event/ActionEvent;)V0  4 *+*    A *+     PK qb8 LAbc/Abc$20.class1&    this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$20;actionPerformed(Ljava/awt/event/ActionEvent;)VevtLjava/awt/event/ActionEvent; SourceFileAbc.javaEnclosingMethod! "#  # $% Abc/Abc$20java/lang/Objectjava/awt/event/ActionListenerAbc/AbcinitComponents()V access$1000((LAbc/Abc;Ljava/awt/event/ActionEvent;)V0  4 *+* !   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"#  # $% Abc/Abc$22java/lang/Objectjava/awt/event/ActionListenerAbc/AbcinitComponents()V access$1200((LAbc/Abc;Ljava/awt/event/ActionEvent;)V0  4 *+* O   A *+ QR    PK qb8xAbc/Abc$23.class1&    this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$23;actionPerformed(Ljava/awt/event/ActionEvent;)VevtLjava/awt/event/ActionEvent; SourceFileAbc.javaEnclosingMethod! "#  # $% Abc/Abc$23java/lang/Objectjava/awt/event/ActionListenerAbc/AbcinitComponents()V access$1300((LAbc/Abc;Ljava/awt/event/ActionEvent;)V0  4 *+* V   A *+ XY    PK qb8rEAbc/Abc$24.class1&    this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$24;actionPerformed(Ljava/awt/event/ActionEvent;)VevtLjava/awt/event/ActionEvent; SourceFileAbc.javaEnclosingMethod! "#  # $% Abc/Abc$24java/lang/Objectjava/awt/event/ActionListenerAbc/AbcinitComponents()V access$1400((LAbc/Abc;Ljava/awt/event/ActionEvent;)V0  4 *+* ]   A *+ _`    PK qb8,kAbc/Abc$25.class1   ()VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$25;run SourceFileAbc.javaEnclosingMethod   Abc/Abc  Abc/Abc$25java/lang/Objectjava/lang/Runnablemain([Ljava/lang/String;)V setVisible(Z)V0  /* _    : Y b c   PK pb8GAbc/Abc$3.class1&    this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$3;actionPerformed(Ljava/awt/event/ActionEvent;)VevtLjava/awt/event/ActionEvent; SourceFileAbc.javaEnclosingMethod! "#  # $% Abc/Abc$3java/lang/Objectjava/awt/event/ActionListenerAbc/AbcinitComponents()V access$300((LAbc/Abc;Ljava/awt/event/ActionEvent;)V0  4 *+*    A *+     PK pb8Abc/Abc$4.class1(     !this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$4; focusGained(Ljava/awt/event/FocusEvent;)VevtLjava/awt/event/FocusEvent; focusLost SourceFileAbc.javaEnclosingMethod" #$  $ %& '& Abc/Abc$4java/awt/event/FocusAdapterAbc/AbcinitComponents()V access$000'(LAbc/Abc;Ljava/awt/event/FocusEvent;)V access$1000  4 *+*    A *+     A *+     PK pb8e+Abc/Abc$5.class1(     !this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$5; focusGained(Ljava/awt/event/FocusEvent;)VevtLjava/awt/event/FocusEvent; focusLost SourceFileAbc.javaEnclosingMethod" #$  $ %& '& Abc/Abc$5java/awt/event/FocusAdapterAbc/AbcinitComponents()V access$000'(LAbc/Abc;Ljava/awt/event/FocusEvent;)V access$1000  4 *+*    A *+     A *+     PK pb8o\Abc/Abc$6.class1. " #$%&' ()*strings[Ljava/lang/String;this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$6;getSize()I getElementAt(I)Ljava/lang/Object;iI SourceFileAbc.javaEnclosingMethod+ ,- -java/lang/StringFstMaf/DafNeutrality Statistics  Abc/Abc$6javax/swing/AbstractListModelAbc/AbcinitComponents()V0   O!*+**YSYSYS $ % !0*& ;*2' ! PK pb8H1 Abc/Abc$7.class1&    this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$7; valueChanged)(Ljavax/swing/event/ListSelectionEvent;)Vevt&Ljavax/swing/event/ListSelectionEvent; SourceFileAbc.javaEnclosingMethod! "#  # $% Abc/Abc$7java/lang/Object'javax/swing/event/ListSelectionListenerAbc/AbcinitComponents()V access$4002(LAbc/Abc;Ljavax/swing/event/ListSelectionEvent;)V0  4 *+* *   A *+ ,-    PK pb8q\Abc/Abc$8.class1&    this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$8;actionPerformed(Ljava/awt/event/ActionEvent;)VevtLjava/awt/event/ActionEvent; SourceFileAbc.javaEnclosingMethod! "#  # $% Abc/Abc$8java/lang/Objectjava/awt/event/ActionListenerAbc/AbcinitComponents()V access$500((LAbc/Abc;Ljava/awt/event/ActionEvent;)V0  4 *+* D   A *+ FG    PK pb8 iAbc/Abc$9.class1(     !this$0 LAbc/Abc; (LAbc/Abc;)VCodeLineNumberTableLocalVariableTablethis InnerClasses LAbc/Abc$9; focusGained(Ljava/awt/event/FocusEvent;)VevtLjava/awt/event/FocusEvent; focusLost SourceFileAbc.javaEnclosingMethod" #$  $ %& '& Abc/Abc$9java/awt/event/FocusAdapterAbc/AbcinitComponents()V access$000'(LAbc/Abc;Ljava/awt/event/FocusEvent;)V access$1000  4 *+* Y   A *+ [\    A *+ ^_    PK qb8k4mY6j6j Abc/Abc.class1~ X Y Z [ \ ] ^ _ ` a b c d e f $g h i jk gl m 2n op q r s tu g v w xy z{ &g |} )g ~       2g  5g  8g       @g  Cg  Fg                       ^ $ $ & &j & & & g ) k ) ) s &  s s       s   s $       & 2 2  2 5  5  5 8  8         C  C C  C @  F F F  F  F     F 2         2  s  ! s" #$%&' ()* +,  -./ 01 23 45   67 g89:  ; < = > ? @ A jBC g D E F G H I J K L M NO P Q RS T UO CV F $WXYZ[ \ ] ^_ 3g 3`a 3b 5cd 9g 9ef 9g 9h 9i 9j 9k 9l Fm 9n o 9pq Ggr st su Ivw Mxy Ov z{ R|} T~ V~ X Z|  \ _~  b jo i n q  G G G G G   5  g   filesArray[Ljava/io/File; INFILES_TEXTLjava/lang/String; SEQ_LENGHT ITERATIONS MAF_THRESHOLDBP_SNPSDIF_DENSASC_POP OUTFILE_TEXTRANGEDSSIZE aboutButtonLjavax/swing/JButton; aboutFrameLjavax/swing/JFrame;ascBiasLjavax/swing/JList; ascBiasLabelLjavax/swing/JLabel; ascPopulationLjavax/swing/JTextField; bpBetweenSnps browseButton browseDensity clearButton densityInfiledsSize exitButtonfstBothLjavax/swing/JRadioButton; fstCorrectionLjavax/swing/ButtonGroup;fstCorrectionNofstCorrectionYesfstGenefstSnp fstSnpGene infileFormatLjavax/swing/JComboBox;infileFormatLabel infilePanelLjavax/swing/JPanel;infiles infilesLabeljLabel1jLabel2jLabel3jLabel4jPanel1 jScrollPane1Ljavax/swing/JScrollPane; jScrollPane2 msSeqLenght outfileFormatoutfileFormatLabeloutfileFormatSampleoutfileFormatTab outfileNameoutfileNameLabel outfilePanelparametersPanel runButtonstatisticsLabelstatisticsList thresholdMAFuserIterations directoryLjava/io/File;()VCodeLineNumberTableLocalVariableTablethis LAbc/Abc;getDensityFileInfo()Ljava/util/ArrayList; densitiesLjava/util/ArrayList;dFileLjava/io/FileReader;brLjava/io/BufferedReader;line ExceptionsinitComponents jPanel1LayoutLjavax/swing/GroupLayout;aboutFrameLayoutinfilePanelLayoutparametersPanelLayoutoutfilePanelLayoutlayoutbrowseDensityActionPerformed(Ljava/awt/event/ActionEvent;)VfileevtLjava/awt/event/ActionEvent;chooserLjavax/swing/JFileChooser;filter11Ljavax/swing/filechooser/FileNameExtensionFilter;resultIinfilesFocusLost(Ljava/awt/event/FocusEvent;)VLjava/awt/event/FocusEvent;tableLjava/util/Hashtable;label textInFieldinfilesFocusGaineddeleteTextOnFocustextselectedPopForAscertainment([Ljava/lang/String;)Ione infilesArray[Ljava/lang/String;ascPopstatisticsListValueChanged)(Ljavax/swing/event/ListSelectionEvent;)Vi&Ljavax/swing/event/ListSelectionEvent;listStatisticsindex[IaboutButtonActionPerformedbrowseButtonActionPerformedfilter2filter3infileFormatActionPerformedascBiasValueChangedlistoutfileValueChangedrunButtonActionPerformedjamode correctedZctmpexLjava/lang/Exception;paramLAbc/ParameterInput; transformersfiltersindependentCalculatorsdependentCalculatorsappLAbc/Application;paramspreviousErrors infileStringinfileFormatOptionuserIt seqLenghtascBiastoCalculate ascParamsstatisticsToCalculateoutfilePattern outfileKind"outfileFormatSampleActionPerformedoutfileFormatTabActionPerformedclearButtonActionPerformedexitButtonActionPerformedfstGeneActionPerformeddsSizeActionPerformedmain([Ljava/lang/String;)Vargs access$000'(LAbc/Abc;Ljava/awt/event/FocusEvent;)Vx0x1 access$100 access$200((LAbc/Abc;Ljava/awt/event/ActionEvent;)V access$300 access$4002(LAbc/Abc;Ljavax/swing/event/ListSelectionEvent;)V access$500 access$600 access$700 access$800 access$900 access$1000 access$1100 access$1200 access$1300 access$1400 SourceFileAbc.java   : ; 9 8 =   <          java/util/ArrayListjava/io/FileReader   java/io/BufferedReader    javax/swing/ButtonGroup   javax/swing/JFrame javax/swing/JPanel javax/swing/JLabel       javax/swing/JTextField javax/swing/JComboBox javax/swing/JButton      javax/swing/JScrollPane javax/swing/JList javax/swing/JRadioButton                      java/awt/Dimension        java/awt/FontTahoma  java/awt/Color  FABSIM +Anna Ramírez-Soriano and Francesc Calafell version 1.0 June 2008javax/swing/GroupLayout                   Infile informationVerdana  Infile(s) name:Infile(s) format:  Abc/Abc$1 InnerClasses   javax/swing/DefaultComboBoxModeljava/lang/Stringms (Hudson RR, 2002) cosi (Schaffner SF et al., 2005)#SelSim (Spencer C and Coop G, 2004)   Abc/Abc$2 Browse Abc/Abc$3 Abc/Abc$4  Abc/Abc$5         CalculationsAscertainment bias: Statistics: Abc/Abc$6   Abc/Abc$7    Not corrected by n java/awt/Insets  Corrected by nper gene Abc/Abc$8per SNPboth Abc/Abc$9 Abc/Abc$10 Abc/Abc$11 Abc/Abc$12 Abc/Abc$13 Abc/Abc$14 Abc/Abc$15 Abc/Abc$16 Abc/Abc$17  java/awt/Component   !Outfile parametersOutfile Fst name:< Abc/Abc$18Outfile format:Information per sample Abc/Abc$19Tabulated statistics Abc/Abc$20 " Exit Abc/Abc$21Clear Abc/Abc$22Run Abc/Abc$23About Abc/Abc$24 #javax/swing/JFileChooser/javax/swing/filechooser/FileNameExtensionFilterTXT filetxt $ %& '( )* +, -. /. 0java/util/Hashtable  12        3 45 67 8 < 9:; <= >OUT fileout1 file1 ? @A java/lang/StringBuilder BC D EFAbc/ParameterInput GH0 IJ KH LH MN OP QH RS TU VW XYAbc/Application Abc/transformers/MsTransformerMsZ [\ ]F ^"Abc/transformers/MsTransformerCosi _$Abc/transformers/MsTransformerSelsim %Abc/dependentFilters/SampleFilterNone ,Abc/dependentFilters/SampleFilterDSampleGene `+Abc/dependentFilters/SampleFilterDSampleSnp'Abc/dependentFilters/SampleFilterOnePop a(Abc/dependentFilters/SampleFilterAllPops$Abc/dependentFilters/SampleFilterMafb [c d#Abc/dependentFilters/SampleFilterBp +Abc/dependentFilters/SampleFilterDifDensity e.smp.tab.hstaveragexsnp&Abc/dependentCalculators/CalculatorFst java/io/File_fst f+Abc/independentCalculators/CalculatorSStats_sstat g+Abc/independentCalculators/CalculatorMafDaf_mafAbc/transformers/MsTransformer hi![LAbc/transformers/MsTransformer; jkAbc/ParentFilters[LAbc/ParentFilters; lm0Abc/independentCalculators/IndependentCalculator3[LAbc/independentCalculators/IndependentCalculator; no,Abc/dependentCalculators/DependentCalculator/[LAbc/dependentCalculators/DependentCalculator; 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" # $% $&'(headerLAbc/MsHeader;sampleLAbc/MsSample; ascParams[Ljava/lang/String;2(LAbc/MsHeader;LAbc/MsSample;[Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisLAbc/AscertainmentBias;pHeaderpSample pAscParams positionBias()VbpIbiasInPopulation SourceFileAscertainmentBias.java   ) *+ ,-Abc/AscertainmentBiasjava/lang/Objectjava/lang/IntegervalueOf'(Ljava/lang/String;)Ljava/lang/Integer;intValue()I! l**,*-*+ *  F*2<   +3 PK qb8&)--Abc/Histogram.class1   rangeLjava/math/BigDecimal;(Ljava/math/BigDecimal;)VCodeLineNumberTableLocalVariableTablethisLAbc/Histogram;pRangecreateHistogram statistic categoriesLjava/util/ArrayList; SourceFileHistogram.java  java/util/ArrayList Abc/Histogramjava/lang/Object()V!  F **+       K YM "   PK qb8&Abc/Infiles.class1 0vw v /x /y /z /{ /| /} /~ /      v     v  / / $   '    bufferArrayLjava/util/ArrayList; headerArray sampleArray kindOutputIstatisticsToCalculate[IascBiasToApply ascParams[Ljava/lang/String;rangeLjava/math/BigDecimal;1(I[ILjava/math/BigDecimal;[I[Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethis LAbc/Infiles;pKindpStatisticsToCalculatepRangepAscBiasToApply pAscParams infilesOpener(Ljava/lang/String;)VfileLjava/lang/String;infileLjava/io/FileReader;brLjava/io/BufferedReader;i infileStringstLjava/util/StringTokenizer; infilesArray Exceptions readFiles%(LAbc/Outfiles;ILjava/lang/String;I)VheaderLAbc/MsHeader;sampleLAbc/MsSample; ascertainmentLAbc/AscertainmentBias;ffcjoutfilesLAbc/Outfiles;formatuserItlenght iterationsseqtakeCosiSample(ILAbc/MsSample;I)IcalculatedSamplecsSampleLcositoms/CosiSample;takeSelSimSample(ILAbc/MsSample;I)VssSampleLselsimtoms/SelSimSample; SourceFile Infiles.java >java/util/ArrayList 12 32 42 56 78 98 :; <=java/util/StringTokenizer >K java/io/FileReader java/lang/Stringjava/io/BufferedReader > Abc/MsHeader   Abc/MsSample kl pqAbc/AscertainmentBias > cositoms/CosiSamplecositoms/CosiPosition   Abc/Infilesjava/lang/Objectjava/io/IOException()V hasMoreTokens()Z nextToken()Ljava/lang/String;add(Ljava/lang/Object;)Zsize()Iget(I)Ljava/lang/Object;(Ljava/io/Reader;)V readHeader(Ljava/io/BufferedReader;)V getIterationsgetSeqjava/lang/IntegervalueOf'(Ljava/lang/String;)Ljava/lang/Integer;intValue readSample(Ljava/io/BufferedReader;II)V2(LAbc/MsHeader;LAbc/MsSample;[Ljava/lang/String;)Vcositoms/CosiToMsmainG(Ljava/io/BufferedReader;Ljava/io/BufferedReader;)Ljava/util/ArrayList; cosiSample/(Lcositoms/CosiSample;Lcositoms/CosiPosition;)VgetSeqs fillHeader(II)Vselsimtoms/SelSimToMS3(Ljava/io/BufferedReader;)Lselsimtoms/SelSimSample; selsimSample(Lselsimtoms/SelSimSample;)Vselsimtoms/SelSimSample!/0123242567898:;<=>?@A**Y*Y*Y**,* * *- A* *%+*,/-5.;/@0B>ACDAE6AF8AG=AH8AI;JK@b Y+ MYN,,:-W6-0Y-:Y:*WͱA2 3 4567%8(:4;F<Q=[:a?BRLMFNOQ PQ+6R6bCDbSM YTUQV2WXYZ@  666*L8Y:*W*66 -6666  **wY : * W * !&* "6 *  #$Y*  * %: taAbBCDEF#G-H>IEJLKXD^NhOkPzQRSVWX[PNfB#)[\ UR6e]^ _` na6 kb6ac6CDdef6gMh6i6j6WXkl@iY:**`&:,'()Y:*W':*+`A"i j&k<lEmOnZoeqBHiCDib6i]^ii6 `m2E$[\ZnoWXpq@5*,:,-Y:*W.+Auvwx)y4zB>5CD5a65]^5i6%rs[\WXtuPK qb8Abc/MsHeader.class1K . / 0 123 4 5 6789: ;<=>seqI iterations()VCodeLineNumberTableLocalVariableTablethisLAbc/MsHeader;getSeq()I getIterations readHeader(Ljava/io/BufferedReader;)VlineLjava/lang/String;stLjava/util/StringTokenizer; exceptionLjava/lang/Exception;brLjava/io/BufferedReader; Exceptions? fillHeader(II)V pIterationspSeq SourceFile MsHeader.java   @ ABjava/util/StringTokenizer C DBE FGjava/lang/Exception!Incorrect infile or infile formatErrorH IJ Abc/MsHeaderjava/lang/Objectjava/io/IOExceptionjava/io/BufferedReaderreadLine()Ljava/lang/String;(Ljava/lang/String;)V nextTokenjava/lang/IntegerparseInt(Ljava/lang/String;)Ijavax/swing/JOptionPaneshowMessageDialog<(Ljava/awt/Component;Ljava/lang/Object;Ljava/lang/String;I)V! E***  /*# /*( CM+MY,N-W*-*-+W+W M   58 2 -./01 2+304578596B843% !9 "#CC$%&'()Q **;< =   * +,-PK qb8EAbc/MsSample.class1 )e (f (g hij k l m (n (o pq k r s (t u vw (xyz{ |} ~ ~ ~  v   ( (segsitesI positions[I sampleLines[Ljava/lang/String; sampleNumber()VCodeLineNumberTableLocalVariableTablethisLAbc/MsSample; getSegsites()IgetSampleLines()[Ljava/lang/String;(I)Ljava/lang/String;possetSampleLines([Ljava/lang/String;)V readSample(Ljava/io/BufferedReader;II)VLjava/math/BigDecimal;ilineLjava/lang/String;stLjava/util/StringTokenizer;p exceptionLjava/lang/Exception;brLjava/io/BufferedReader;seqlenght Exceptions cosiSample/(Lcositoms/CosiSample;Lcositoms/CosiPosition;)VcSampleLcositoms/CosiSample; cPositionLcositoms/CosiPosition; selsimSample(Lselsimtoms/SelSimSample;)VssSampleLselsimtoms/SelSimSample; setSegsites(I)V setPositions([I)V getPositions()[IgetSampleNumbersetSampleNumber SourceFile MsSample.java 12 *+ ./ java/util/StringTokenizer 1 [\ ]^ java/math/BigDecimal 1\ _` 9java/lang/String >?java/lang/Exception!Incorrect infile or infile formatError  9 : 89 java/lang/Integer  9 _; ,- 0+ Abc/MsSamplejava/lang/Objectjava/io/IOExceptionjava/io/BufferedReaderreadLine()Ljava/lang/String;(Ljava/lang/String;)V nextTokenparseInt(Ljava/lang/String;)I hasMoreTokens()Zmultiply.(Ljava/math/BigDecimal;)Ljava/math/BigDecimal;setScale(II)Ljava/math/BigDecimal;intValuejavax/swing/JOptionPaneshowMessageDialog<(Ljava/awt/Component;Ljava/lang/Object;Ljava/lang/String;I)Vcositoms/CosiSamplegetSeqs()Ljava/util/ArrayList;java/util/ArrayListget(I)Ljava/lang/Object;cositoms/CosiPositiongetPositionsArrayvalueOf(I)Ljava/lang/Integer;selsimtoms/SelSimSamplegetSeq'(Ljava/lang/String;)Ljava/lang/Integer;!()*+,-./0+ 123< **4  !5  67893/*4%5 67:;3/*4)5 67:<3;*24-567=+>?3>*+4 12567./@A3:+W+:Y:W* ** 6*|+:Y:W 7 Y : Y:*O*6+:*S+W:4r68:;<=+?5@8A?BECPDVG^HlI{JKLORSTRX[YZ\5f l#=BC+DEFG8H+ IJ67KLM+N+OPQR3i*+>+*+S*+ *+ >+#*, O۱4* _ ab&a,e4g>hHibhhk54 C+@(C+i67iSTiUVWX3n*+!=+!*+"S*+# *+# =+#*+$2%O M`c46 o pq&p,t4v>wHxZw`|czd{m}54 C+@ C+d IJn67nYZ[\3>*4 567*+]^3>*+&4 567,-_`3/*&45 67a93/*'45 67b\3>*'4 5670+cdPK qb8EEI Abc/Outfiles.class1z "KL !MN !O !P !Q !RSTUV !WXYZ[ K \ ] ^ _ !` !a bcd e f ghijkl outputArray[Ljava/io/FileWriter;bwArray[Ljava/io/BufferedWriter;kindI statistics[IoutfilePatternLjava/lang/String;(I[ILjava/lang/String;)VCodeLineNumberTableLocalVariableTablethisLAbc/Outfiles;pKindstatisticsToCalculatepOutfilePatternorganizeOutfileOpener()Vik Exceptionsm outfileOpener((Ljava/lang/String;ILjava/lang/String;)V statPatternoutfileLjava/io/FileWriter;bwLjava/io/BufferedWriter;writeHeaderTabs-(Ljava/lang/String;Ljava/io/BufferedWriter;)VstatwriteHeadersHistogramwritingStatsSamples SourceFile Outfiles.java -8java/io/FileWriter #$java/io/BufferedWriter %& '( )* +,.smp.tab.hst_fst =>_stats_maf_dafjava/lang/StringBuilder no pq -r -s DE GEt uviSample sequences segsites pi singl Ts_D FL_D2 FL_F2 FL_D FL_F R2 FW_H Fs EHH_a EHH_m Dh W_B W_Q ZnS Za ZZ wr x8 y8Sample snp maf daf_statClass Frequency Abc/Outfilesjava/lang/Objectjava/io/IOExceptionappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/String;)V(Ljava/io/Writer;)Vjava/lang/Stringequals(Ljava/lang/Object;)ZwritenewLineflush!!"#$%&'()*+,-./$*****,*-0  !"##1*$23$4($5*$6,78/L*  L*  L* L=*m*.* *.+ N*.**.+ 4*.**.+ *.**.+ 0>'()*(-3.</L1V2f4p578-<1 *s9(23:,;<=>/_YY*+-:*SY:*S* *+* *+0@"A*C5D=FOG^H1>_23_?,_9(_:,"=@A5*BC;<DE/E+ +,,,+,,,+0. 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W>* e* :*:686*:2SĄ.2  (5BO\ l!~$/\ \"45l67E?8$5O9:BB;<m=$01>$?:@,-W*** W<* 9* M,**N,-,*±.. '( )* +,,4-C.H/P*V1/*,$A:C 67AB$W01CDEF-~0* L=* +*O+.4 56(5.8/  ">$001 &GHIJ-/*.</ 01K,-I=* >*N- L6-+S*+ W.& A BC!D-E3D9GBAHI/4$B$)L<!'67F>$I01MN->*. 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" # $ % &'( ascertainLascertainBp/AscertainBp;bpI ascPopulation(IIZ)VCodeLineNumberTableLocalVariableTablethis%LAbc/dependentFilters/SampleFilterBp;pBp dependentZ applyFilterA(Ljava/util/ArrayList;Ljava/util/ArrayList;)Ljava/util/ArrayList;headerLjava/util/ArrayList;sample SourceFileSampleFilterBp.java )ascertainBp/AscertainBp *  +,#Abc/dependentFilters/SampleFilterBp*Abc/dependentFilters/DependentSampleFilter(Z)V()VmainC(Ljava/util/ArrayList;Ljava/util/ArrayList;II)Ljava/util/ArrayList;!   s**Y***  V*,+**M,  ! PK qb8=402Abc/dependentFilters/SampleFilterDSampleGene.class1- ! " # $ % &'( ascertain)LascertainSampleGene/AscertainSampleGene;dSizeI ascPopulation(IIZ)VCodeLineNumberTableLocalVariableTablethis.LAbc/dependentFilters/SampleFilterDSampleGene;pDSize dependentZ applyFilterA(Ljava/util/ArrayList;Ljava/util/ArrayList;)Ljava/util/ArrayList;headerLjava/util/ArrayList;sample SourceFileSampleFilterDSampleGene.java )'ascertainSampleGene/AscertainSampleGene *  +,,Abc/dependentFilters/SampleFilterDSampleGene*Abc/dependentFilters/DependentSampleFilter(Z)V()VmainC(Ljava/util/ArrayList;Ljava/util/ArrayList;II)Ljava/util/ArrayList;!   s**Y***  W*W,+**M,  ! PK qb8+f1Abc/dependentFilters/SampleFilterDSampleSnp.class1- ! " # $ % &'( ascertain'LascertainSampleSnp/AscertainSampleSnp;dSizeI ascPopulation(IIZ)VCodeLineNumberTableLocalVariableTablethis-LAbc/dependentFilters/SampleFilterDSampleSnp;pDSize dependentZ applyFilterA(Ljava/util/ArrayList;Ljava/util/ArrayList;)Ljava/util/ArrayList;headerLjava/util/ArrayList;sample SourceFileSampleFilterDSampleSnp.java )%ascertainSampleSnp/AscertainSampleSnp *  +,+Abc/dependentFilters/SampleFilterDSampleSnp*Abc/dependentFilters/DependentSampleFilter(Z)V()VmainC(Ljava/util/ArrayList;Ljava/util/ArrayList;II)Ljava/util/ArrayList;!   s**Y***  W*W,+**M,   PK qb8wT1Abc/dependentFilters/SampleFilterDifDensity.class1. !" # $ % & '() ascertain+LascertainDiffDensity/AscertainDiffDensity; densitiesLjava/util/ArrayList; ascPopulationI(Ljava/util/ArrayList;IZ)VCodeLineNumberTableLocalVariableTablethis-LAbc/dependentFilters/SampleFilterDifDensity; pDensitiesascPopulations dependentZ applyFilterA(Ljava/util/ArrayList;Ljava/util/ArrayList;)Ljava/util/ArrayList;headersample SourceFileSampleFilterDifDensity.java *)ascertainDiffDensity/AscertainDiffDensity +  ,-+Abc/dependentFilters/SampleFilterDifDensity*Abc/dependentFilters/DependentSampleFilter(Z)V()VmainW(Ljava/util/ArrayList;Ljava/util/ArrayList;Ljava/util/ArrayList;I)Ljava/util/ArrayList;!  s**Y*+** V*,+**M,      PK qb8*Abc/dependentFilters/SampleFilterMaf.class14 "# $ % & ' () *+, ascertainLascertainMaf/AscertainMaf; mafThresholdLjava/lang/Double; ascPopulationI(Ljava/lang/Double;IZ)VCodeLineNumberTableLocalVariableTablethis&LAbc/dependentFilters/SampleFilterMaf; pMafThreshold dependentZ applyFilterA(Ljava/util/ArrayList;Ljava/util/ArrayList;)Ljava/util/ArrayList;headerLjava/util/ArrayList;sample SourceFileSampleFilterMaf.java -ascertainMaf/AscertainMaf .  / 01 23$Abc/dependentFilters/SampleFilterMaf*Abc/dependentFilters/DependentSampleFilter(Z)V()Vjava/lang/Double doubleValue()DmainC(Ljava/util/ArrayList;Ljava/util/ArrayList;DI)Ljava/util/ArrayList;!  s**Y*+**Y*,+**M,  !  !PK qb8ʼ??+Abc/dependentFilters/SampleFilterNone.class1 (Z)VCodeLineNumberTableLocalVariableTablethis'LAbc/dependentFilters/SampleFilterNone; dependentZ applyFilterA(Ljava/util/ArrayList;Ljava/util/ArrayList;)Ljava/util/ArrayList;headerLjava/util/ArrayList;sample SourceFileSampleFilterNone.java %Abc/dependentFilters/SampleFilterNone*Abc/dependentFilters/DependentSampleFilter!>*    @,  PK qb8[Xtt-Abc/dependentFilters/SampleFilterOnePop.class1)    ! "#$ ascertain!LascertainOnePop/AscertainOnePop; ascPopulationI(IZ)VCodeLineNumberTableLocalVariableTablethis)LAbc/dependentFilters/SampleFilterOnePop; dependentZ applyFilterA(Ljava/util/ArrayList;Ljava/util/ArrayList;)Ljava/util/ArrayList;headerLjava/util/ArrayList;sample SourceFileSampleFilterOnePop.java %ascertainOnePop/AscertainOnePop & '('Abc/dependentFilters/SampleFilterOnePop*Abc/dependentFilters/DependentSampleFilter(Z)V()VmainB(Ljava/util/ArrayList;Ljava/util/ArrayList;I)Ljava/util/ArrayList;!  `**Y*  R*+,*M,  PK qb8@ tpp1Abc/independentCalculators/CalculatorMafDaf.class1= )* + ,-. / 0 1 2 345mafLmafCalculator/MafCalculator;kindIbwLjava/io/BufferedWriter;(Ljava/io/File;II)VCodeLineNumberTableLocalVariableTablethis-LAbc/independentCalculators/CalculatorMafDaf;fileLjava/io/File;pKind fileNumber Exceptions6execute(LAbc/MsHeader;LAbc/MsSample;)VheaderLAbc/MsHeader;sampleLAbc/MsSample; SourceFileCalculatorMafDaf.java 7mafCalculator/MafCalculator 8 java/io/BufferedWriterjava/io/FileWriter 9 :   ;<+Abc/independentCalculators/CalculatorMafDaf0Abc/independentCalculators/IndependentCalculatorjava/lang/Exception(I)V()V(Ljava/io/File;)V(Ljava/io/Writer;)Vmain8(LAbc/MsSample;LAbc/MsHeader;Ljava/io/BufferedWriter;I)V! )**Y*YY+ * "##%('*)))) !"U*W,+* *  *+ #$%& '(PK qb8[[1Abc/independentCalculators/CalculatorSStats.class1= )* + ,-. / 0 1 2 345 samplestatLsscosi/SSCosi;kindIbwLjava/io/BufferedWriter;(Ljava/io/File;II)VCodeLineNumberTableLocalVariableTablethis-LAbc/independentCalculators/CalculatorSStats;fileLjava/io/File;pKind fileNumber Exceptions6execute(LAbc/MsHeader;LAbc/MsSample;)VheaderLAbc/MsHeader;sampleLAbc/MsSample; SourceFileCalculatorSStats.java 7 sscosi/SSCosi 8 java/io/BufferedWriterjava/io/FileWriter 9 :   ;<+Abc/independentCalculators/CalculatorSStats0Abc/independentCalculators/IndependentCalculatorjava/lang/Exception(I)V()V(Ljava/io/File;)V(Ljava/io/Writer;)Vmain8(LAbc/MsSample;LAbc/MsHeader;Ljava/io/BufferedWriter;I)V! )**Y*YY+ * "##%('*)))) !"U*W,+* *  *+ #$%& '(PK qb86Abc/independentCalculators/IndependentCalculator.class1   fileNumberI(I)VCodeLineNumberTableLocalVariableTablethis2LAbc/independentCalculators/IndependentCalculator;execute(LAbc/MsHeader;LAbc/MsSample;)V Exceptions getFileNumber()I setFileNumber SourceFileIndependentCalculator.java  0Abc/independentCalculators/IndependentCalculatorjava/lang/Objectjava/lang/Exception()V! F **     /*    >* "#  PK qb8o$Abc/transformers/MsTransformer.class1&  ! "#$headerLAbc/MsHeader;sampleLAbc/MsSample;()VCodeLineNumberTableLocalVariableTablethis LAbc/transformers/MsTransformer; getMsSample()LAbc/MsSample; Exceptions%calculateMsHeader()LAbc/MsHeader;close getHeader setHeader(LAbc/MsHeader;)V getSample setSample(LAbc/MsSample;)V SourceFileMsTransformer.java   Abc/transformers/MsTransformerjava/lang/Objectjava/lang/Exception!   E***     + #  /* &  >*+ *+ /* .  >*+ 23 PK qb8:f (Abc/transformers/MsTransformerCosi.class1} !I J K LMN O P QRST UV WX Y Z [\ I ] ^_ I `ab I cde fgh sampleFileLjava/io/File; positionsFileuserItIbrSampleLjava/io/BufferedReader; brPosition (Ljava/io/File;Ljava/io/File;I)VCodeLineNumberTableLocalVariableTable exceptionLjava/lang/Exception;this$LAbc/transformers/MsTransformerCosi; pSampleFilepPositionsFilepUserIt Exceptions getMsSample()LAbc/MsSample;tmpLAbc/MsSample;calculateMsHeader()LAbc/MsHeader;csSampleLcositoms/CosiSample;transformCosiSample()Lcositoms/CosiSample;calculatedSampleLjava/util/ArrayList;i setSampleFile(Ljava/io/File;)VsetPositionsFile SourceFileMsTransformerCosi.java *j "# $# %&java/io/BufferedReaderjava/io/FileReader *E *k '(java/lang/ExceptionSample infile not foundErrorl mn )(Positions infile not found o: ?@ pq Abc/MsHeader rs tujava/util/ArrayListv wx Abc/MsSample yzcositoms/CosiSamplecositoms/CosiPosition {|"Abc/transformers/MsTransformerCosiAbc/transformers/MsTransformerjava/io/IOException()V(Ljava/io/Reader;)Vjavax/swing/JOptionPaneshowMessageDialog<(Ljava/awt/Component;Ljava/lang/Object;Ljava/lang/String;I)VsampleheaderLAbc/MsHeader;getSeqs()I fillHeader(II)Vcositoms/CosiToMsmainG(Ljava/io/BufferedReader;Ljava/io/BufferedReader;)Ljava/util/ArrayList;get(I)Ljava/lang/Object; cosiSample/(Lcositoms/CosiSample;Lcositoms/CosiPosition;)V! !"#$#%&'()(*+,\**+*,**YY* :   *YY*:  ), 7MP -6 #$ %'*)-,+.,7/M2P0R1[3.>. /0R /0\12\3#\4#\5&6 78,n"L* *L *W*L*+-67 8:;> @."12 9:6 ;<,o+*"*Y*L**+*-DEFG&J.=>+126 ?@,?YL* *L*Y*+++-NOPQ6S.?127AB6CDE,>*+- WX.12"#FE,>*+- [\.12$#GHPK qb8=5&Abc/transformers/MsTransformerMs.class1X 1 2 345 6 7 89:; <=> 1 ? @ A BC 1 DEF sampleFileLjava/io/File;lenghtIbrSampleLjava/io/BufferedReader;(Ljava/io/File;I)VCodeLineNumberTableLocalVariableTable exceptionLjava/lang/Exception;this"LAbc/transformers/MsTransformerMs; pSampleFilepLenght ExceptionsG getMsSample()LAbc/MsSample;calculateMsHeader()LAbc/MsHeader; SourceFileMsTransformerMs.java H  java/io/BufferedReaderjava/io/FileReader I J java/lang/ExceptionInfile not foundErrorK LM Abc/MsSample NO PQ RS TU Abc/MsHeader VW Abc/transformers/MsTransformerMsAbc/transformers/MsTransformerjava/io/IOException()V(Ljava/io/File;)V(Ljava/io/Reader;)Vjavax/swing/JOptionPaneshowMessageDialog<(Ljava/awt/Component;Ljava/lang/Object;Ljava/lang/String;I)VsampleLAbc/MsSample;headerLAbc/MsHeader;getSeq()I readSample(Ljava/io/BufferedReader;II)V readHeader(Ljava/io/BufferedReader;)V! 2**+**YY* N   $' !" !#$&'$(%1("*( #$2%&2'2()*+, X&* Y*****!+ ,!." &%&)*-. M*Y***!2 35" %&)*/0PK qb8~[[*Abc/transformers/MsTransformerSelsim.class1f 7 8 9:; < = >?@A BC D E FG 7 HI JK 7 LM NOP sampleFileLjava/io/File;userItIbrSampleLjava/io/BufferedReader;(Ljava/io/File;I)VCodeLineNumberTableLocalVariableTable exceptionLjava/lang/Exception;this&LAbc/transformers/MsTransformerSelsim; pSampleFilepUserIt Exceptions getMsSample()LAbc/MsSample;QcalculateMsHeader()LAbc/MsHeader;ssSampleLselsimtoms/SelSimSample;transformSelsimSample()Lselsimtoms/SelSimSample; SourceFileMsTransformerSelsim.java R  java/io/BufferedReaderjava/io/FileReader S T java/lang/ExceptionInfile not foundErrorU VW XY 34 Z[ Abc/MsHeader\ ]^ _` Abc/MsSamplea bc de$Abc/transformers/MsTransformerSelsimAbc/transformers/MsTransformerjava/io/IOException()V(Ljava/io/File;)V(Ljava/io/Reader;)Vjavax/swing/JOptionPaneshowMessageDialog<(Ljava/awt/Component;Ljava/lang/Object;Ljava/lang/String;I)VsampleLAbc/MsSample;headerLAbc/MsHeader;selsimtoms/SelSimSamplegetSeq()I fillHeader(II)Vselsimtoms/SelSimToMSmain3(Ljava/io/BufferedReader;)Lselsimtoms/SelSimSample; selsimSample(Lselsimtoms/SelSimSample;)V! !"2**+**YY* N   $' #" ! "%$('&('1)$*( %&2'(2)2*+ ,-"L* * *W* #,- /2$ '(+./0"o+*"*Y*L**+*#6789&<$12+'(+.34"]*Y *L* ++#@ BCE$'( 12+.56PK qb8!h'ascertainAllPops/AscertainAllPops.class1G ( )*+ ), -./ 012 3 4 56 789()VCodeLineNumberTableLocalVariableTablethis#LascertainAllPops/AscertainAllPops;mainA(Ljava/util/ArrayList;Ljava/util/ArrayList;)Ljava/util/ArrayList;sampleaLAbc/MsSample;iIasc$LascertainAllPops/AscertainmentBias;sample0 exceptionLjava/lang/Exception;headerALLjava/util/ArrayList;sampleAL SourceFileAscertainAllPops.java : ;< Abc/MsSample => ?>Error in 'SNPs polymorphic in all populations' bias. The samples in different files have not the same number of segregating sitesError@ AB"ascertainAllPops/AscertainmentBias C D Ejava/lang/Exception F!ascertainAllPops/AscertainAllPopsjava/lang/Objectjava/util/ArrayListget(I)Ljava/lang/Object;size()I getSegsitesjavax/swing/JOptionPaneshowMessageDialog<(Ljava/awt/Component;Ljava/lang/Object;Ljava/lang/String;I)V-(Ljava/util/ArrayList;Ljava/util/ArrayList;)V ascertain ascertainNoSsprintStackTrace!3*  -o,N6,),:- - Y+, :  Y+, : N-,eh B  ,5;BM R!U"`#e'h%i&m(\  /M` \ i!"oo#$o%$&'PK qb8S (ascertainAllPops/AscertainmentBias.class1R / 0 1 2 3456 7 389 : ; < = >?@-(Ljava/util/ArrayList;Ljava/util/ArrayList;)VCodeLineNumberTableLocalVariableTablethis$LascertainAllPops/AscertainmentBias;pHeaderLjava/util/ArrayList;pSample ascertain()VsampleaLAbc/MsSample; subsampleLascertainAllPops/SubSamples; absAlleleFreqIapolymorphicAllZisample0headerLAbc/MsHeader; ExceptionsA SourceFileAscertainmentBias.java  B C DE FG Abc/MsSample Abc/MsHeader HI JIascertainAllPops/SubSamples K LM NI OP Q"ascertainAllPops/AscertainmentBiasAbc/dependentFilters/CodeFilterjava/lang/ExceptionheaderALsampleALinitializeAscSamplejava/util/ArrayListget(I)Ljava/lang/Object; getSegsites()Isize(LAbc/MsHeader;LAbc/MsSample;)VcalculateAlleleFreqs(I)IgetSeq addSegsite(ILAbc/MsSample;)V replaceSample!Y**+*,  P **L*M>+f66* B*: Y, : 6 , 6 6 *+*N&)8 F!R"Z#h$k%n'qw+},01\ F+R !Z"#,K$#)Z%&k'#~(r)*+,-.PK qb8Ktt!ascertainAllPops/SubSamples.class15  ! " #$ %& '()*headerLAbc/MsHeader;sampleLAbc/MsSample; alleleFreqLjava/math/BigDecimal;(LAbc/MsHeader;LAbc/MsSample;)VCodeLineNumberTableLocalVariableTablethisLascertainAllPops/SubSamples;pHeaderpSamplecalculateAlleleFreqs(I)IsnpI absAlleleFreqi SourceFileSubSamples.java + , -./ 012 34ascertainAllPops/SubSamplesjava/lang/Object()V Abc/MsHeadergetSeq()I Abc/MsSamplegetSampleLines(I)Ljava/lang/String;java/lang/StringcharAt(I)C! Y**+*,     +=>**1$'(#').*++)'PK qb8꠴ascertainBp/AscertainBp.class1I * +,- +. /01 234 5 6 78 9:;()VCodeLineNumberTableLocalVariableTablethisLascertainBp/AscertainBp;mainC(Ljava/util/ArrayList;Ljava/util/ArrayList;II)Ljava/util/ArrayList;sampleaLAbc/MsSample;iIascLascertainBp/AscertainmentBias;sample0 exceptionLjava/lang/Exception;sampleALLjava/util/ArrayList;headerALbpascPop SourceFileAscertainBp.java < => Abc/MsSample ?@ A@pError in 'One SNP every x bp' bias. The samples in different files have not the same number of segregating sitesErrorB CDascertainBp/AscertainmentBias E F Gjava/lang/Exception HascertainBp/AscertainBpjava/lang/Objectjava/util/ArrayListget(I)Ljava/lang/Object;size()I getSegsitesjavax/swing/JOptionPaneshowMessageDialog<(Ljava/awt/Component;Ljava/lang/Object;Ljava/lang/String;I)V/(Ljava/util/ArrayList;Ljava/util/ArrayList;II)V ascertain ascertainNoSsprintStackTrace!3*  Lz+:6+*+:  Y,+ :  Y,+ : :+nq B !.7=ES X!["i#n(q&s'x*p ! 0Si d s!"zz#$z%$z&z'()PK qb8 #ascertainBp/AscertainmentBias.class1~ MN M O P Q R S T UV WX Y Z [ \] \^ _ ` a b c de M f ghisampleLAbc/MsSample;bpI ascSample[Ljava/lang/String;firstPositionsLjava/util/ArrayList;/(Ljava/util/ArrayList;Ljava/util/ArrayList;II)VCodeLineNumberTableLocalVariableTablethisLascertainBp/AscertainmentBias;pHeaderpSamplepBppAscPop ascertain()VabiheaderLAbc/MsHeader;startstartPosnextPosoldi ExceptionsjaddSelectedPosition(I)VfindFirstPositionsfindNextPosition(I)InextfindStartPosition()I getAscSample()[Ljava/lang/String; setAscSample([Ljava/lang/String;)V SourceFileAscertainmentBias.java '3java/util/ArrayList %& k& l& !" m" n3 op Abc/MsSample   Abc/MsHeader A3 EF qrs tu vF ?@ BC w3 xy z{ |Fjava/util/Random }C #$ascertainBp/AscertainmentBiasAbc/dependentFilters/CodeFilterjava/lang/ExceptionheaderALsampleALascPopinitializeAscSampleget(I)Ljava/lang/Object; getPositions()[Ijava/lang/IntegervalueOf(I)Ljava/lang/Integer;intValue replaceSample addSegsite(ILAbc/MsSample;)Vadd(Ljava/lang/Object;)ZsizenextInt! !"#$%&'()%**Y*+*,***$+4%,-%.&%/&%0"%1"23)/ 9* *** * L**=* .>*66*`* * d.*`6*6* ."* .6*6* .d6* d.d6Pd(* d.6*dd6>* .6*6* .6*6** !"#"&&'+(;)@,C-F.b/k0s12346789:;<>?@C'D-E1H4M8N+\ 4"p5"s6"9,-"78+9";:"C;"F<"=>?@)I** * QR+,-6"A3)}9<* -* .*** .Wͱ*VWX2V8]+66"9,-BC)a=* . *`abd+ ,-D"6"EF)i%<*<Y*<*ij km#o+%,-#9"GH)/**s+ ,-IJ)>*+* wx+,-#$KLPK qb89ia::/ascertainDiffDensity/AscertainDiffDensity.class1I * +,- +. /01 234 5 6 78 9:;()VCodeLineNumberTableLocalVariableTablethis+LascertainDiffDensity/AscertainDiffDensity;mainW(Ljava/util/ArrayList;Ljava/util/ArrayList;Ljava/util/ArrayList;I)Ljava/util/ArrayList;sampleaLAbc/MsSample;iIasc(LascertainDiffDensity/AscertainmentBias;sample0 exceptionLjava/lang/Exception;sampleALLjava/util/ArrayList;headerAL densitiesascPop SourceFileAscertainDiffDensity.java < => Abc/MsSample ?@ A@Error in 'Diferent SNP density along the gene' bias. The samples in different files have not the same number of segregating sitesErrorB CD&ascertainDiffDensity/AscertainmentBias E F Gjava/lang/Exception H)ascertainDiffDensity/AscertainDiffDensityjava/lang/Objectjava/util/ArrayListget(I)Ljava/lang/Object;size()I getSegsitesjavax/swing/JOptionPaneshowMessageDialog<(Ljava/awt/Component;Ljava/lang/Object;Ljava/lang/String;I)VC(Ljava/util/ArrayList;Ljava/util/ArrayList;Ljava/util/ArrayList;I)V ascertain ascertainNoSsprintStackTrace!3*  Lz+:6+*+:  Y,+- :  Y,+- : :+nq B !.7=ES X!["i#n(q&s'x*p ! 0Si d s!"zz#$z%$z&$z'()PK qb8 ,ascertainDiffDensity/AscertainmentBias.class1 $^_ ^ #` #a #b #c #d #e fg #hi jkl m no np q #r #s #t u nv wx ^ y #z #{ #| #} #~sampleLAbc/MsSample; densitiesLjava/util/ArrayList; ascSample[Ljava/lang/String;firstPositionsC(Ljava/util/ArrayList;Ljava/util/ArrayList;Ljava/util/ArrayList;I)VCodeLineNumberTableLocalVariableTablethis(LascertainDiffDensity/AscertainmentBias;pHeaderpSample pDensitiespAscPopI ascertain()V densityLineendiheaderLAbc/MsHeader;bp endFragment startFragmentstartFragmentValuee ExceptionsaddSelectedPosition(I)VfindFirstPositions(III)VstartPos startValuefindNextPosition(I)InextfindStartPosition()Istart getAscSample()[Ljava/lang/String; setAscSample([Ljava/lang/String;)VselectSnpsInFragment(IIII)VabnextPosoldi SourceFileAscertainmentBias.java ,9java/util/ArrayList +( ( ( '( 7 9  Abc/MsSample %& Abc/MsHeader Pjava/lang/String  P VW 9 9 java/util/Random M )* HI OP FG LM&ascertainDiffDensity/AscertainmentBiasAbc/dependentFilters/CodeFilterjava/lang/ExceptionheaderALsampleALascPopinitializeAscSampleget(I)Ljava/lang/Object;sizesplit'(Ljava/lang/String;)[Ljava/lang/String;java/lang/IntegervalueOf'(Ljava/lang/String;)Ljava/lang/Integer;intValue getPositions()[I replaceSample addSegsite(ILAbc/MsSample;)Vclear(I)Ljava/lang/Integer;add(Ljava/lang/Object;)ZnextInt!#$%&'()*+( ,-.%**Y*+*,*-*/$04%12%3(%4(%5(%6789. * *** * L=>6666** :26 6* 5* . d>* . > 2=*62`6i*/j!"#"%$&&')(,)/*>+Q,]-m.|/0234-789:*@A0f Qu:*]i;7 2<712"=>$?7&@7)A7,B7/C7DEFG.I** / DE012<7HI.C*6* .* .`** .W˱/IJK'L<JBQ04 8<7C12CJ7CK7C?7LM.a=* . /TUVX0 12N7<7OP.i%<*<Y*</\] ^`#b0%12#Q7RS./*/f0 12TU.>*+/ jk012)*VW. ** 6* `.6*`!6`6`* .`6*"6 *  ."*  .6* ! 6*  .d6 *  d.d6   P d(*  d.6* d! d6>*  .6* ! 6*  .6* ! 6$/rpqr"s*v.w4xDyJzR{a|s}y~ 0z X7 pY7 R<7 12?7@7A7B7Q7"J7.Z74[7\]PK qb8^ascertainMaf/AscertainMaf.class1J + ,-. ,/ 012 345 6 7 89 :;<()VCodeLineNumberTableLocalVariableTablethisLascertainMaf/AscertainMaf;mainC(Ljava/util/ArrayList;Ljava/util/ArrayList;DI)Ljava/util/ArrayList;sampleaLAbc/MsSample;iIasc LascertainMaf/AscertainmentBias;sample0 exceptionLjava/lang/Exception;sampleALLjava/util/ArrayList;headerAL mafThresholdDascPop SourceFileAscertainMaf.java = >? Abc/MsSample @A BAkError in 'MAF>threshold' bias. The samples in different files have not the same number of segregating sitesErrorC DEascertainMaf/AscertainmentBias F G Hjava/lang/Exception IascertainMaf/AscertainMafjava/lang/Objectjava/util/ArrayListget(I)Ljava/lang/Object;size()I getSegsitesjavax/swing/JOptionPaneshowMessageDialog<(Ljava/awt/Component;Ljava/lang/Object;Ljava/lang/String;I)V/(Ljava/util/ArrayList;Ljava/util/ArrayList;DI)V ascertain ascertainNoSsprintStackTrace!3*  L z+:6+*+:  Y,+) :  Y,+) : :+nq B !.7=ES X!["i#n(q&s'x*p ! 0Si d s!"zz#$z%$z&'z()*PK qb89dC$ascertainMaf/AscertainmentBias.class1\ 4 5 6 7 8 9 :;<= >? @ AB C D E FGH mafThresholdD/(Ljava/util/ArrayList;Ljava/util/ArrayList;DI)VCodeLineNumberTableLocalVariableTablethis LascertainMaf/AscertainmentBias;pHeaderLjava/util/ArrayList;pSample pMafThresholdpAscPopI ascertain()VsampleaLAbc/MsSample; subsampleLascertainMaf/SubSamples;snpMafLjava/math/BigDecimal;isample0headerLAbc/MsHeader; ExceptionsI SourceFileAscertainmentBias.java % J K  L# M%N OP Abc/MsSample Abc/MsHeader QRascertainMaf/SubSamples S TUjava/math/BigDecimal V WX YZ [%ascertainMaf/AscertainmentBiasAbc/dependentFilters/CodeFilterjava/lang/ExceptionheaderALsampleALascPopinitializeAscSamplejava/util/ArrayListget(I)Ljava/lang/Object; getSegsites()I(LAbc/MsHeader;LAbc/MsSample;)VcalculateAlleleFreqs(I)Ljava/math/BigDecimal;(D)V compareTo(Ljava/math/BigDecimal;)I addSegsite(ILAbc/MsSample;)V replaceSample!**+*,*)* 4 !"#$%o**L* M>+ G**: Y, : :Y* *+*2  "&#6$B%J&^-d"j4n6H6.&'B"()J*+L,#o_-'S./0123PK qb8\ascertainMaf/SubSamples.class1Q * + ,-. / 0 12 34 56 7 89 :; <=>headerLAbc/MsHeader;sampleLAbc/MsSample; alleleFreqLjava/math/BigDecimal;(LAbc/MsHeader;LAbc/MsSample;)VCodeLineNumberTableLocalVariableTablethisLascertainMaf/SubSamples;pHeaderpSamplecalculateAlleleFreqs(I)Ljava/math/BigDecimal;snpI absAlleleFreqi SourceFileSubSamples.java ?  java/math/BigDecimal0 @ A BCD EFG HI J KL0.5 MN1 OPascertainMaf/SubSamplesjava/lang/Object()V(Ljava/lang/String;)V Abc/MsHeadergetSeq()I Abc/MsSamplegetSampleLines(I)Ljava/lang/String;java/lang/StringcharAt(I)C(I)Vdivide0(Ljava/math/BigDecimal;II)Ljava/math/BigDecimal; compareTo(Ljava/math/BigDecimal;)Isubtract.(Ljava/math/BigDecimal;)Ljava/math/BigDecimal;!Y**+*,    !"#*Y=>**  1*Y Y*   *Y *Y**"# $'(0'6+V,~.*$%t&%r'%()PK qb8W%ascertainOnePop/AscertainOnePop.class1H ) *+, *- ./0 123 4 5 67 89:()VCodeLineNumberTableLocalVariableTablethis!LascertainOnePop/AscertainOnePop;mainB(Ljava/util/ArrayList;Ljava/util/ArrayList;I)Ljava/util/ArrayList;sampleaLAbc/MsSample;iIasc#LascertainOnePop/AscertainmentBias;sample0 exceptionLjava/lang/Exception;headerALLjava/util/ArrayList;sampleALascPop SourceFileAscertainOnePop.java ; <= Abc/MsSample >? @?Error in 'SNPs polymorphic in one populations' bias. The samples in different files have not the same number of segregating sitesErrorA BC!ascertainOnePop/AscertainmentBias D E Fjava/lang/Exception GascertainOnePop/AscertainOnePopjava/lang/Objectjava/util/ArrayListget(I)Ljava/lang/Object;size()I getSegsitesjavax/swing/JOptionPaneshowMessageDialog<(Ljava/awt/Component;Ljava/lang/Object;Ljava/lang/String;I)V.(Ljava/util/ArrayList;Ljava/util/ArrayList;I)V ascertain ascertainNoSsprintStackTrace!3*  >v,:6,*,:  Y+, :  Y+, : :,jm B !.7=EQ V!Y"e#j'm%o&t(f ! 0Qe ` o!"vv#$v%$v&'(PK qb8%p>'ascertainOnePop/AscertainmentBias.class1R / 0 1 2 3 4567 89 : ; < = >?@.(Ljava/util/ArrayList;Ljava/util/ArrayList;I)VCodeLineNumberTableLocalVariableTablethis#LascertainOnePop/AscertainmentBias;pHeaderLjava/util/ArrayList;pSamplepAscPopI ascertain()VpolymorphicOneZsampleaLAbc/MsSample; subsampleLascertainOnePop/SubSamples; absAlleleFreqisample0headerLAbc/MsHeader; ExceptionsA SourceFileAscertainmentBias.java  B C D EF GH Abc/MsSample Abc/MsHeader IJascertainOnePop/SubSamples K LM NJ OP Q!ascertainOnePop/AscertainmentBiasAbc/dependentFilters/CodeFilterjava/lang/ExceptionheaderALsampleALascPopinitializeAscSamplejava/util/ArrayListget(I)Ljava/lang/Object; getSegsites()I(LAbc/MsHeader;LAbc/MsSample;)VcalculateAlleleFreqs(I)IgetSeq addSegsite(ILAbc/MsSample;)V replaceSample!l**+*,* *'{**L*M>+ S6**: Y, : 6 , 66 *+*B&) 9!E"M#[$a&d)j*pv.z/R)G !97"#E+$%M#&X'{k(#_)*+,-.PK qb8uqrr ascertainOnePop/SubSamples.class15  ! " #$ %& '()*headerLAbc/MsHeader;sampleLAbc/MsSample; alleleFreqLjava/math/BigDecimal;(LAbc/MsHeader;LAbc/MsSample;)VCodeLineNumberTableLocalVariableTablethisLascertainOnePop/SubSamples;pHeaderpSamplecalculateAlleleFreqs(I)IsnpI absAlleleFreqi SourceFileSubSamples.java + , -./ 012 34ascertainOnePop/SubSamplesjava/lang/Object()V Abc/MsHeadergetSeq()I Abc/MsSamplegetSampleLines(I)Ljava/lang/String;java/lang/StringcharAt(I)C! Y**+*,     +=>**1$'(#').*++)'PK qb8@B..-ascertainSampleGene/AscertainSampleGene.class1f < =>?@ =A BCD EFG H IJ K L M NO PQ PR PS PTU()VCodeLineNumberTableLocalVariableTablethis)LascertainSampleGene/AscertainSampleGene;mainC(Ljava/util/ArrayList;Ljava/util/ArrayList;II)Ljava/util/ArrayList;sampleaLAbc/MsSample;iIasc'LascertainSampleGene/AscertainmentBias;sample0header0LAbc/MsHeader; subsample LascertainSampleGene/SubSamples;ex!Ljava/lang/NumberFormatException;Ljava/io/FileNotFoundException;Ljava/io/IOException;Ljava/lang/Exception;sampleALLjava/util/ArrayList;headerALdSizeascPop SourceFileAscertainSampleGene.java V WX Abc/MsSample Abc/MsHeader YZ [ZwError in 'Discovery sample per gene' bias. The samples in different files have not the same number of segregating sitesError\ ]^ascertainSampleGene/SubSamples _ .%ascertainSampleGene/AscertainmentBias `a bZ c djava/lang/NumberFormatException ejava/io/FileNotFoundExceptionjava/io/IOExceptionjava/lang/Exception'ascertainSampleGene/AscertainSampleGenejava/lang/Objectjava/util/ArrayListget(I)Ljava/lang/Object;size()I getSegsitesjavax/swing/JOptionPaneshowMessageDialog<(Ljava/awt/Component;Ljava/lang/Object;Ljava/lang/String;I)V(LAbc/MsSample;I)VdSample[Ljava/lang/String;getSeqB(Ljava/util/ArrayList;[Ljava/lang/String;Ljava/util/ArrayList;II)V ascertainprintStackTrace!3*  !" #$*:+:6***:  ӻ Y* :# Y+*:(::: :*f# $% &+'8(A%G,Y-a/f4|6JBCJDEJFGJHIL +%&0'(|)* w+&m,-Y(./0102030456768(9(:;PK qb8h +ascertainSampleGene/AscertainmentBias.class1 (ef e 'g 'h 'i 'j 'k 'l mn 'o 'p 'q 'r 'st u v w 'x y z{| }~ e      ' dSample[Ljava/lang/String;dInpolymorphicPositionsDLjava/util/ArrayList;B(Ljava/util/ArrayList;[Ljava/lang/String;Ljava/util/ArrayList;II)VCodeLineNumberTableLocalVariableTablethis'LascertainSampleGene/AscertainmentBias;pHeaderpDSample pSampleALpDpN ascertain()Vsample0LAbc/MsSample; ExceptionsgenerateAscertainedSample(Ljava/util/ArrayList;)VjnSampleAscertainedLjava/lang/String;rpisampleaapolymorphicPositionsheaderLAbc/MsHeader; initialSnpsfindPolymorphicPositions%([Ljava/lang/String;ILAbc/MsSample;)VsamplenumSeqsoriginalSamplec getDSample()[Ljava/lang/String; setDSample([Ljava/lang/String;)VgetD()IsetD(I)VgetNsetNgetPolymorphicPositionsD()Ljava/util/ArrayList;setPolymorphicPositionsD SourceFileAscertainmentBias.java 0=java/util/ArrayList ./ / )* / +, -,  Abc/MsSample VW Z[ PQ `a BC Abc/MsHeader [ [ ] [java/lang/Integer [java/lang/StringBuilder W [ / %ascertainSampleGene/AscertainmentBiasAbc/dependentFilters/CodeFilterjava/lang/ExceptionheaderALsampleALget(I)Ljava/lang/Object; getSegsitessize setSegsitesconvertNewPositions()[I setPositions([I)VgetSeqintValueappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;getSampleLinesjava/lang/StringcharAt(I)C(C)Ljava/lang/StringBuilder;toString()Ljava/lang/String;lengthvalueOf(I)Ljava/lang/Integer;add(Ljava/lang/Object;)Z newPositions getPositions!'()*+,-,./ 012+**Y*+*,*-** 3" "#$$*%4>+56+7/+8*+9/+:,+;,<=2b"* L** * +**3) *+!,4"56 >?@ABC2 * M* N,66** :+**6-r:6 6 6  N+  d2Y2  !: +d   S6-S-3j/ 013-4;5B6N7W8c9g:j;m<w=>?@C<E8HIH3M4 pRD, geEFjbG, m_H, ZxI,I,;J?!K,56L/ >?MNO,PQ2f66+2"W6++21'"*#$W*%-&.#$W632 UVXZ)[,Y2_=`Ja\d_Weg4HD,_I,f56fR*fS,fT?cU,VW2/*3j4 56XY2>*+3 no456)*Z[2/*3x4 56\]2>*3 |}456+,^[2/* 34 56_]2>* 3 456-,`a2/*34 56bC2>*+3 456./cdPK qb8sabb$ascertainSampleGene/SubSamples.class1O 0 1 23 4 5 67 89 : ;< = > ?@ABsampleLAbc/MsSample;dIdSample[Ljava/lang/String; dSequences[I(LAbc/MsSample;I)VCodeLineNumberTableLocalVariableTablethis LascertainSampleGene/SubSamples;pSamplepD subsample()V findDSamplerusedZirNumberLjava/util/Random; checkIfUsed(ILjava/util/Random;I)Zj SourceFileSubSamples.java #  java/lang/String   $#java/util/RandomC DE FG HI JK +,L MNascertainSampleGene/SubSamplesjava/lang/Objectjava/lang/SystemnanoTime()J(J)V Abc/MsSamplegetSampleLines()[Ljava/lang/String;nextInt(I)Ijava/util/Arrayssort([I)V!Y**+*    !"#P**** *# $&( $#XY L=*>6+* >*+ 6*O** 2S*. + -/1%2.344;5J-P8W94%%%2&' C(X M)*+,|6*.< =<?4-()*%./PK qb8.((+ascertainSampleSnp/AscertainSampleSnp.class1U 3 456 47 89: ;<= > ? @A BC BD BE BFG()VCodeLineNumberTableLocalVariableTablethis'LascertainSampleSnp/AscertainSampleSnp;mainC(Ljava/util/ArrayList;Ljava/util/ArrayList;II)Ljava/util/ArrayList;sampleaLAbc/MsSample;iIasc&LascertainSampleSnp/AscertainmentBias;sample0ex!Ljava/lang/NumberFormatException;Ljava/io/FileNotFoundException;Ljava/io/IOException;Ljava/lang/Exception;sampleALLjava/util/ArrayList;headerALdSizeascPop SourceFileAscertainSampleSnp.java H IJ Abc/MsSample KL MLvError in 'Discovery sample per SNP' bias. The samples in different files have not the same number of segregating sitesErrorN OP$ascertainSampleSnp/AscertainmentBias Q R Sjava/lang/NumberFormatException Tjava/io/FileNotFoundExceptionjava/io/IOExceptionjava/lang/Exception%ascertainSampleSnp/AscertainSampleSnpjava/lang/Objectjava/util/ArrayListget(I)Ljava/lang/Object;size()I getSegsitesjavax/swing/JOptionPaneshowMessageDialog<(Ljava/awt/Component;Ljava/lang/Object;Ljava/lang/String;I)V/(Ljava/util/ArrayList;Ljava/util/ArrayList;II)V ascertain ascertainNoSsprintStackTrace!3*   *:6***:  Y+* :  Y+* : (::: :*lo lyllf# $%!&.'7$=+E,R-W/Z0g1l=o5q6v=y7{8=9:=;<? ! ! 0"#R$%g$% b&!q'({')'*'+,-.-/#0#12PK qb84*ascertainSampleSnp/AscertainmentBias.class1l = > ? @ A B CDE FG HI J K L M N O P QR STUsampleLAbc/MsSample;dI ascSample[Ljava/lang/String;/(Ljava/util/ArrayList;Ljava/util/ArrayList;II)VCodeLineNumberTableLocalVariableTablethis&LascertainSampleSnp/AscertainmentBias;pHeaderLjava/util/ArrayList;pSamplepDpAscPop ascertain()V subsampleLascertainSampleSnp/SubSamples;ciheaderLAbc/MsHeader; ExceptionsVsearchPolymorphism#(LascertainSampleSnp/SubSamples;I)Ix getAscSample()[Ljava/lang/String; setAscSample([Ljava/lang/String;)V SourceFileAscertainmentBias.java + W& X&  Y Z+[ \] Abc/MsSample  Abc/MsHeader ^_ascertainSampleSnp/SubSamples ` a+ 45 bc d+ ef ghi jk $ascertainSampleSnp/AscertainmentBiasAbc/dependentFilters/CodeFilterjava/lang/ExceptionheaderALsampleALascPopinitializeAscSamplejava/util/ArrayListget(I)Ljava/lang/Object; getSegsites()I(LAbc/MsHeader;I)V findDSample addSegsite(ILAbc/MsSample;)V replaceSample dSequences[IgetSampleLines(I)Ljava/lang/String;java/lang/StringcharAt(I)C! **+*,**!  !""4#$%&'&()*+ l**** ** L=* 8 Y+* N-*-6***!2 %&'%)2+?,C-K.Q5a)g;k<"4?",-K.'@/l#$%G012345 >>6*#* +.1* !@AB(A.E<F"4)6>#$>,->/<.78 /*!J" #$9: >*+! NO"#$;(LAbc/MsHeader;I)VCodeLineNumberTableLocalVariableTablethisLascertainSampleSnp/SubSamples;pHeaderpD findDSample()VrusedZirNumberLjava/util/Random; checkIfUsed(ILjava/util/Random;I)Zj SourceFileSubSamples.java   java/util/Random: ;< = > ?@ AB %&C DEascertainSampleSnp/SubSamplesjava/lang/Objectjava/lang/SystemnanoTime()J(J)V Abc/MsHeadergetSeq()InextInt(I)Ijava/util/Arrayssort([I)V! Y**+*   RYL** =*.6+* >*+ 6*O* . * ,.0"2.374=5D.J9Q:4."" !3"R G#$%&|6*.= >=@4'"#$()PK qb8Ⲅ**cositoms/CosiPosition.class1[ 34 3 5 678 9:; <= >? @ < A B C DE FGHpositionsArrayLjava/util/ArrayList;()VCodeLineNumberTableLocalVariableTablethisLcositoms/CosiPosition; readPositions(Ljava/io/BufferedReader;)VstLjava/util/StringTokenizer;posLjava/math/BigDecimal;positIbrLjava/io/BufferedReader;lineLjava/lang/String; ExceptionsIgetPositionsArray()Ljava/util/ArrayList;setPositionsArray(Ljava/util/ArrayList;)V SourceFileCosiPosition.java java/util/ArrayList J KLM NOjava/util/StringTokenizer P QRjava/math/BigDecimal QL ST UV -.W XY ZOcositoms/CosiPositionjava/lang/Objectjava/io/IOExceptionjava/io/BufferedReaderreadLine()Ljava/lang/String;java/lang/Stringequals(Ljava/lang/Object;)Z(Ljava/lang/String;)V nextToken&(Ljava/lang/String;)Ljava/lang/String;setScale(II)Ljava/math/BigDecimal;intValue()Ijava/lang/IntegervalueOf(I)Ljava/lang/Integer;add!B**Y  Y+W+M,HY, N- W- W Y- :6*W+M2 " #$%#&*'7(C)P*U+X,>9!"7#$C%&YY'( O)*+,-./*/ /0>*+ 3412PK qb8i;cositoms/CosiSample.class1c <= < > ? @ ABC DEF GH I JK DLMN DO P QRS sampleLinesLjava/util/ArrayList;segsitesIseqs()VCodeLineNumberTableLocalVariableTablethisLcositoms/CosiSample; readSample(Ljava/io/BufferedReader;)VtkLjava/util/StringTokenizer;chromLjava/lang/String;brLjava/io/BufferedReader;iline ExceptionsT getSegsites()IgetSampleLines()Ljava/util/ArrayList;setSampleLines(Ljava/util/ArrayList;)V setSegsites(I)VgetSeqssetSeqs SourceFileCosiSample.java java/util/ArrayList   U VWX YZjava/util/StringTokenizer [ \] \W ^_20 `1 67 abcositoms/CosiSamplejava/lang/Objectjava/io/IOExceptionjava/io/BufferedReaderreadLine()Ljava/lang/String;java/lang/String compareTo(Ljava/lang/String;)I(Ljava/lang/String;)V nextToken&(Ljava/lang/String;)Ljava/lang/String;replaceD(Ljava/lang/CharSequence;Ljava/lang/CharSequence;)Ljava/lang/String;lengthadd(Ljava/lang/Object;)Z!T**Y** ! 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"#97>* QR!"#:;PK qb8S‹cositoms/CosiToMs.class12 #$ # %& # '( # )*+()VCodeLineNumberTableLocalVariableTablethisLcositoms/CosiToMs;mainG(Ljava/io/BufferedReader;Ljava/io/BufferedReader;)Ljava/util/ArrayList;brSamLjava/io/BufferedReader;brPossampleLcositoms/CosiSample;positionLcositoms/CosiPosition;thingsLjava/util/ArrayList; Exceptions, SourceFile CosiToMs.java cositoms/CosiSample -.cositoms/CosiPosition /.java/util/ArrayList 01cositoms/CosiToMsjava/lang/Objectjava/io/IOException readSample(Ljava/io/BufferedReader;)V readPositionsadd(Ljava/lang/Object;)Z!  3*   4YM,*YN-+Y :, W- W"34 679#:*;1H444,# !"PK qb8,.#fstcalculator/FstCalculations.class1 ,def g +h +i +j +k +l +m +no p +q +r 'st uv w x y z { | } '~   + + + +  'd ' + headersArrayLjava/util/ArrayList; samplesArrayaveragePLjava/math/BigDecimal;hwhafstnpqparamsLfstcalculator/FstParameters; popNumberI.(Ljava/util/ArrayList;Ljava/util/ArrayList;I)VCodeLineNumberTableLocalVariableTablethisLfstcalculator/FstCalculations; pHeadersArray pSamplesArray pPopNumber calculateNPQ(II)IsnppopoutLAbc/MsHeader;fixedvalue1value0calculatePAverage(I)Vi calculateHw(I)If calculateHa calculateFstfstNumfstDentempcalculateFstNotCorrected alleleFreqaverageAlleleFreqvariancedenomcalculateVarianceC(Ljava/util/ArrayList;Ljava/math/BigDecimal;)Ljava/math/BigDecimal;freq differencesum SourceFileFstCalculations.java :java/math/BigDecimal0 : 01 21 31 41 51 -. /.fstcalculator/FstParameters : 67 89  Abc/MsHeader 1 Y1 :N 9 9 DE MN PQ SN 1 java/util/ArrayList ]^fstcalculator/FstCalculationsjava/lang/Object()V(Ljava/lang/String;)V-(Ljava/util/ArrayList;Ljava/util/ArrayList;)Vget(I)Ljava/lang/Object;calculateAlleleFreqs(II)Vdivide0(Ljava/math/BigDecimal;II)Ljava/math/BigDecimal;equals(Ljava/lang/Object;)Zsubtract.(Ljava/math/BigDecimal;)Ljava/math/BigDecimal;multiplygetSeq()Isize absAlleleFreqaddnTotalcalculateNTotalcalculateSumNWheighted nWheighted compareTo(Ljava/math/BigDecimal;)I!+, -./.01213141516789:;<h**Y*Y*Y*Y*Y *+ *, * Y* * *=. +8E J!O"b#g$>*h?@hA.hB.hC9DE<d* N Y* * :6Y:Y :Y:Y :6*Y **  *Y-*  =:( )+ ,'.2/E0P1c23678:>R?@F9G9 HI67 J92K1PpL1MN<R=* +***Y***Y* =@ AB/@5EQF> R?@RF9PO9PQ<==>* %*6`=*** *=& ILMNO+L1Q9R;T>4R9=?@=F9;J99O9SN<A* *Y**Y****=YZ1[@\>A?@AF9TQ<**!*"*#=*$YNY:Y:*Y*Y* N*Y* Y:-N*Y*Y* :Y:*Y* Y*%::*-*Y&*Y=R_`abce g*h5i@kglmopqrtvw(z>>*?@*F9J9*U15V1@W1XQ<oͻ'Y(MYN6* +*,*)W-*N-Y* N-Y&-Y&*,-*:-Y-:**Y&*Y=B~!+7CI_>H?@F9Y.Z1O9D[11\1]^<jY:6* .+:,:::Y* YN-=& %-6?Eh>R%_1-`1j?@jY.jZ1h[1 _a1\O9bcPK qb8ܯ!fstcalculator/FstCalculator.class1a b c d e fg h i j 0kl mn o p q rst ku v w x yz{ k| } ~   /   /  outputAverageG(ILfstcalculator/Output;IILjava/util/ArrayList;Ljava/math/BigDecimal;)VCodeLineNumberTableLocalVariableTablekindIoutputLfstcalculator/Output; totalFixediallFstLjava/util/ArrayList; fstAverageLjava/math/BigDecimal; Exceptions outputSnps2(Ljava/math/BigDecimal;Lfstcalculator/Output;III)Vfstfixed()VthisLfstcalculator/FstCalculator;mainn(Ljava/util/ArrayList;Ljava/util/ArrayList;Ljava/io/BufferedWriter;[Ljava/lang/String;ILjava/lang/String;ZII)VtestLfstcalculator/FstCalculations;pSamplepHeaderbwLjava/io/BufferedWriter; infilesArray[Ljava/lang/String; popNumbermodeLjava/lang/String; correctionZ iteration samplesArray headersArraysampleLAbc/MsSample; SourceFileFstCalculator.javajava/math/BigDecimal F 9999 F FGfstcalculator/Output  Abc/MsSample F  java/lang/StringBuilderComputing Fst for sample  java/util/ArrayList0 fstcalculator/FstCalculations F xsnp D? BCbothaverage 12  Gfstcalculator/FstCalculatorjava/lang/Objectjava/io/IOExceptionjava/lang/Exception(I)Vsubtract.(Ljava/math/BigDecimal;)Ljava/math/BigDecimal;divide0(Ljava/math/BigDecimal;II)Ljava/math/BigDecimal; writeAverage.(Ljava/math/BigDecimal;Ljava/util/ArrayList;)VwriteAverageTabs(Ljava/lang/String;)V writeXSnps(Ljava/math/BigDecimal;I)VwriteXSnpsTabsget(I)Ljava/lang/Object;getSampleNumber()I(Ljava/io/BufferedWriter;I)V writeHeader([Ljava/lang/String;I)Vjava/lang/SystemoutLjava/io/PrintStream;append-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/PrintStreamprintlnwriteSampleNumberwriteHeaderTab getSegsites.(Ljava/util/ArrayList;Ljava/util/ArrayList;I)V calculateFst(I)IcalculateFstNotCorrectedjava/lang/Stringequals(Ljava/lang/Object;)Zadd writeAllTabsE(Ljava/math/BigDecimal;ILjava/math/BigDecimal;Ljava/util/ArrayList;)Vjava/io/BufferedWriterflush!/0 1235YY:+ +4!,45>5675895:75;75<=5>?@A BC3@)+Y '+Y  +* +* 4" ! "$,'0(9*?-54@D?@89@;7@67@E7@AFG33* 4 015 HI JK3% Y,* :   -Y* Y: *: +: 6 Y: Y:  : *   66 Y  !:"6 #6 `6 $%& '(%d& ')%(% &*: &+WS)%   ,(%; YY :  d d -,.4&ABC"^E_NgQhTjWkblkmvo{prsvxy{|~4@KxQ\kv5LMN=O=PQRST7UVWX67Y789 NeZ= T_[= W\:7 bQ>? kH<=v=\]E7;7@^_`PK qb8:!fstcalculator/FstParameters.class1m @AB C D E F G H I JKL M N OP Q R ST @ U V WXYZ headersArrayLjava/util/ArrayList; samplesArray alleleFreqLjava/math/BigDecimal; nWheighted absAlleleFreqInTotal-(Ljava/util/ArrayList;Ljava/util/ArrayList;)VCodeLineNumberTableLocalVariableTablethisLfstcalculator/FstParameters; pHeadersArray pSamplesArraycalculateAlleleFreqs(II)Vsnp populationoutLAbc/MsHeader;sampleLAbc/MsSample;icalculateNTotal()VcalculateSumNWheighted nPopSquared popWheighted nPopWheighted sumNWheighted SourceFileFstParameters.java %8java/math/BigDecimal0 %[  ! 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D<.=>?@1k+* *Y ` * 2/0#1*23+45+A.=>BC1i+Y.*Y ` * /*Y ` + * 25627<9a:h<3 i45iDEiF.=>GC1+Y<*Y *` ` * =*Y *` ` + * 2?@@AJC}DF3 45DEF.=>HI1\* +** :+** +* * 2. IJKL$M.N7OAPKQTR[T3\45\JK=>LM1**Y! + Y"NY:6,#0,$:-%N%:*Y& -'  * 26 WY$Z/[;\F]P^S`^ab[hdef3HFNE26<.45OEPQ$pRE/eSE=>TM1#Y"NY:6,#0,$:-%N%:*Y *`( + -  * 22 i jk!l,m6n9pDqHkNtuv3H,NE6<.45OEPQ RE|SE=>UV1  Y":Y:6#3$:%:%:+YT*Y *` ` -   * Z*Y *` ` + -   * 2>y z{#|/}:~>IM{Sd 3\ /NE:<. 45 DE F. OE PQ RESE=>WXPK qb8 2=zz#mafCalculator/MafCalculations.class1U . / 012 3 4 56 78 9: ; < => ?@ ABCsampleLAbc/MsSample;headerLAbc/MsHeader; alleleFreqLjava/math/BigDecimal;(LAbc/MsSample;LAbc/MsHeader;)VCodeLineNumberTableLocalVariableTablethisLmafCalculator/MafCalculations;pSamplepHeadercalculateAlleleFreqs(II)VsnpImd absAlleleFreqi calculateMaf()V SourceFileMafCalculations.java +  java/math/BigDecimal0 D E FGH IJK LM N OP *+0.5 QR1 STmafCalculator/MafCalculationsjava/lang/Object(Ljava/lang/String;)V Abc/MsHeadergetSeq()I Abc/MsSamplegetSampleLines(I)Ljava/lang/String;java/lang/StringcharAt(I)C(I)Vdivide0(Ljava/math/BigDecimal;II)Ljava/math/BigDecimal; compareTo(Ljava/math/BigDecimal;)Isubtract.(Ljava/math/BigDecimal;)Ljava/math/BigDecimal;!Y**+*,   !"#$b*Y>6**  1*Y Y*   * " "#3"9&Y'a(4b b%&b'&S(&P)&*+W)*Y*Y* +(, ) ,-PK qb8?K!mafCalculator/MafCalculator.class1R ,- . /0 1 2 /34 5 6 7 8 9 :;<=()VCodeLineNumberTableLocalVariableTablethisLmafCalculator/MafCalculator;main8(LAbc/MsSample;LAbc/MsHeader;Ljava/io/BufferedWriter;I)VmafLmafCalculator/MafCalculations;dafsampleLAbc/MsSample;headerLAbc/MsHeader;bwLjava/io/BufferedWriter;kindIoutfileLmafCalculator/Outfile;i Exceptions> SourceFileMafCalculator.java mafCalculator/Outfile ?@ AB CD E FBmafCalculator/MafCalculations G HI JK LM NOP QmafCalculator/MafCalculatorjava/lang/Objectjava/io/IOException(Ljava/io/BufferedWriter;)V Abc/MsSamplegetSampleNumber()IwriteSampleRSample(I)VwriteTabsHeader getSegsites(LAbc/MsSample;LAbc/MsHeader;)VcalculateAlleleFreqs(II)V alleleFreqLjava/math/BigDecimal;writeResultsSample0(Ljava/math/BigDecimal;Ljava/math/BigDecimal;I)VwriteResultsTab1(ILjava/math/BigDecimal;Ljava/math/BigDecimal;I)Vjava/io/BufferedWriternewLine!3*   7Y,:* 6*aY*+ :Y*+ :     *   ,6 N OP$R0S;TFUNVVWnXR]^R;MFB !"#$ %&'p'$()*+PK qb8~mafCalculator/Outfile.class1Q 1 23 14 5 6 7 89 8:;< => 8?@ABCDbwLjava/io/BufferedWriter;(Ljava/io/BufferedWriter;)VCodeLineNumberTableLocalVariableTablethisLmafCalculator/Outfile;pBwwriteSampleRSample(I)ViI ExceptionsEwriteResultsSample0(Ljava/math/BigDecimal;Ljava/math/BigDecimal;I)V mafAlleleFreqLjava/math/BigDecimal; dafAlleleFreq snpNumberwriteTabsHeader()VwriteResultsTab1(ILjava/math/BigDecimal;Ljava/math/BigDecimal;I)V SourceFile Outfile.java , java/lang/StringBuilderSAMPLE FG FH IJK LM N,Snp  Maf: FO Daf: P,Sample SNP maf daf mafCalculator/Outfilejava/lang/Objectjava/io/IOExceptionappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/BufferedWriterwrite(Ljava/lang/String;)VnewLine-(Ljava/lang/Object;)Ljava/lang/StringBuilder;flush!F **+    `$*Y` * !"##$$!"#$%&m*Y ` * *Y +  * *Y,  * *"'(#)=*D+^,e.l/*mm'(m)(m*"#$+,C* * 2 34 #$-.Z*Y` *Y`, -  * *89K:R<Y=4ZZ!"Z'(Z)(Z*"#$/0PK qb8.]) ) selsimtoms/SelSimSample.class1| JK J L M N OPQ RS TU VWX YZ [\ ] ^ _ ` abcd ef ghi sampleLinesLjava/util/ArrayList;segsitesI positions[Ljava/lang/String;seq()VCodeLineNumberTableLocalVariableTablethisLselsimtoms/SelSimSample;getSampleLines()Ljava/util/ArrayList; readHeader(Ljava/io/BufferedReader;)VbrLjava/io/BufferedReader;jlineLjava/lang/String; Exceptionsj readSamplepostkLjava/util/StringTokenizer;tk2 exceptionLjava/lang/Exception; getSegsites()I getPositions()[Ljava/lang/String; setPositions([Ljava/lang/String;)VgetSeqsetSeq(I)V SourceFileSelSimSample.java &'java/util/ArrayList  !" %"k lmjava/util/StringTokenizer &n op q rsjava/lang/String CD AB tu vw xu E@ FGjava/lang/Exception!Incorrect infile or infile formatErrory z{ #$selsimtoms/SelSimSamplejava/lang/Objectjava/io/IOExceptionjava/io/BufferedReaderreadLine()Ljava/lang/String;(Ljava/lang/String;)V nextToken&(Ljava/lang/String;)Ljava/lang/String;java/lang/IntegerparseInt(Ljava/lang/String;)Iequals(Ljava/lang/Object;)Z replaceAll8(Ljava/lang/String;Ljava/lang/String;)Ljava/lang/String;addjavax/swing/JOptionPaneshowMessageDialog<(Ljava/awt/Component;Ljava/lang/Object;Ljava/lang/String;I)V! !"#$%" &'(T**Y**) !* +,-.(/*)$* +,/0(mN=+W))+ ,+.**+,123"456780(:>+W+:Y : W* **+:Y :>* :*S+W+:+ :*W**`+:+: M)n46 76;<&=.><AGBMCXEbFkGsEyJ~KLMNOPTXVWY*Rk953"45&:;Xd<; =>+,1267?@(/*)\* +,AB(/*)`* +,CD(>*+) de*+,#$E@(/*)h* +,FG(>*) lm*+,%"HIPK qb8~QI{{selsimtoms/SelSimToMS.class1   ()VCodeLineNumberTableLocalVariableTablethisLselsimtoms/SelSimToMS;main3(Ljava/io/BufferedReader;)Lselsimtoms/SelSimSample;brLjava/io/BufferedReader;sampleLselsimtoms/SelSimSample; Exceptions SourceFileSelSimToMS.java selsimtoms/SelSimSample selsimtoms/SelSimToMSjava/lang/Objectjava/io/IOException readSample(Ljava/io/BufferedReader;)V! 3*    KYL+*+ 78 : PK qb8&:sscosi/ClassIIResults.class1 Du Cv Cw Cx Cy Cz C{ C| C} C~ C u                     headerLAbc/MsHeader; newSampleLsscosi/SegregatingSample;wallLsscosi/WallTests;zTestsLsscosi/ZTests;ehhLsscosi/EHHTests;dhLsscosi/DhTest;fsLsscosi/FuFsTest;tajFuLsscosi/TajFuTests;r2Lsscosi/R2Test;fhLsscosi/FayWuHTest;(LAbc/MsHeader;Lsscosi/SegregatingSample;Lsscosi/WallTests;Lsscosi/ZTests;Lsscosi/EHHTests;Lsscosi/DhTest;Lsscosi/FuFsTest;Lsscosi/TajFuTests;Lsscosi/R2Test;Lsscosi/FayWuHTest;)VCodeLineNumberTableLocalVariableTablethisLsscosi/ClassIIResults;pHeader pNewSamplepWallpZTestspEhhpDhpFspTajFupR2pFhwriteResultsSample(ILjava/io/BufferedWriter;)ViIbwLjava/io/BufferedWriter; ExceptionswriteResultsTab SourceFileClassIIResults.java Y EF GH IJ KL MN OP QR ST UV WXjava/lang/StringBuilderSAMPLE   Sequences:   Seg. sites:   Pi:  Singletons: Class I Statistics Tajima's D:  Fu and Li D*:  Fu and Li F*:  Fu and Li D:  Fu and Li F: R2:  Fay and Wu H:  Class II Statistics Fu's Fs:   EHH average:   EHH maximum: Dh:   Wall's B:   Wall's Q: ZnS:   Za:  ZZ:  sscosi/ClassIIResultsjava/lang/Objectjava/io/IOException()Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;toString()Ljava/lang/String;java/io/BufferedWriterwrite(Ljava/lang/String;)VnewLine Abc/MsHeadergetSeq()Isscosi/SegregatingSamplegetRealSegregatinggetPi()Ljava/math/BigDecimal;-(Ljava/lang/Object;)Ljava/lang/StringBuilder; getSingletonssscosi/TajFuTests getTajimaD()D(D)Ljava/lang/StringBuilder;getFuD2getFuF2getFuDgetFuF sscosi/R2TestgetR2sscosi/FayWuHTestgetHsscosi/FuFsTestgetFssscosi/EHHTests getEhhAverage getEhhMaximum sscosi/DhTestgetDhsscosi/WallTestsgetBgetQ sscosi/ZTestsgetZnSgetZagetZZflush!CD EFGHIJKLMNOPQRSTUVWXYZ[ >**+*,*-***** * * \2 #$ %&'()%*++1,7-=.]p >^_>`F>aH>bJ>cL>dN>eP>fR>gT>hV >iX jk[:, Y `,, Y **, Y **,,,, Y *  ,, Y !* " #* $ ,, Y %* & '* ( ,, Y )* * ,, Y +* , ,,-,, Y .*/ ,, Y 0*12*3,, Y 4*5,, Y 6*78*9,, Y :*;<*=>*?,,,@\ 235I6u7y89:;<=>?@!A%BBCFDLEPFmGqHIJKLMN-O1P5R9S] :^_:lm:nopqrk[p, Y A`, Y B*B*, Y B*B*, Y B*  , Y B* " B* $ , Y B* & B* ( , Y B* * , Y B* , , Y B*/ , Y B*1B*3, Y B*5, Y B*7B*9, Y B*;B*=B*?,,@\BWXEYqZ[\]^ _=`iabcegh] ^_lmnopqstPK qb83{=]sscosi/DhTest.class1_ 56 7 8 9 : ; <= >? @A <B CD E F G H IJKdhLjava/math/BigDecimal;differentHaplotypesIheaderLAbc/MsHeader; newSampleLsscosi/SegregatingSample;+(LAbc/MsHeader;Lsscosi/SegregatingSample;)VCodeLineNumberTableLocalVariableTablethisLsscosi/DhTest;pHeader pNewSample calculateDh()VsamplesfirstHaplotypeLjava/lang/String;hicalculateHaplotypeFrequency/(ILjava/math/BigDecimal;)Ljava/math/BigDecimal; frequencygetDh()Ljava/math/BigDecimal;getDifferentHaplotypes()I SourceFile DhTest.java &java/math/BigDecimal L    M NOP QRS T2 NUV WX ,- YZ [Z \Z ]^ sscosi/DhTestjava/lang/Object(I)Vsscosi/SegregatingSamplegetNewSampleLines()[Ljava/lang/String;java/util/Arrayssort([Ljava/lang/Object;)V Abc/MsHeadergetSeq(I)Ljava/lang/String;java/lang/StringequalsIgnoreCase(Ljava/lang/String;)Zadd.(Ljava/math/BigDecimal;)Ljava/math/BigDecimal;subtractmultiplydivide0(Ljava/math/BigDecimal;II)Ljava/math/BigDecimal;!r **Y**+*, !"  !" # $%&T* Y* L>* M6* G* ,  ****+ * M>*Y`***+ *Y***+**+YF& (*.$/30D1J4[5e6g7q/w<>?@B 4!"'$()*'+,-nYN-,N--N-E FGI *!"*' ./0/*M !"12/*U !"34PK qb8jsscosi/EHHTests.class1 $`a b #c #d #e #f #g #h #i jk lm #n #o jp #q #r #s? t u #v #w jx yz {| y} #~ y     ehhAverageLjava/math/BigDecimal; ehhMaximumnumberSeqsCore[InumberI ehhActualfirstSubstringLjava/lang/String; startPositionheaderLAbc/MsHeader; newSampleLsscosi/SegregatingSample;+(LAbc/MsHeader;Lsscosi/SegregatingSample;)VCodeLineNumberTableLocalVariableTablethisLsscosi/EHHTests;pHeader pNewSample calculateEhh()VcMaxflagjuniquei findCorescorepNumberSeqsCorefindFirstString(II)VpcountMajorHapInCore(II)InccalculateEhhActualcopies hapsInCorecalculateEhhAverage(III)VposactualEhhAverage haplotypessamples uniqueHapspositioncalculateEhhMaximum(I)V getEhhAverage()Ljava/math/BigDecimal; getEhhMaximum SourceFile EHHTests.java 4>java/math/BigDecimal 4Z %& '& *+ ,& /+ 01 23  D> () GH JK NH 4 QR YZ   -. sscosi/EHHTestsjava/lang/Objectsscosi/SegregatingSamplegetNewSampleLines()[Ljava/lang/String;java/util/Arrayssort([Ljava/lang/Object;)VgetRealSegregating()I(D)V compareTo(Ljava/math/BigDecimal;)I(I)Ljava/lang/String;java/lang/String substring(II)Ljava/lang/String; Abc/MsHeadergetSeqequalsIgnoreCase(Ljava/lang/String;)Zequals(Ljava/lang/Object;)Zdivide0(Ljava/math/BigDecimal;II)Ljava/math/BigDecimal;multiply.(Ljava/math/BigDecimal;)Ljava/math/BigDecimal;subtractadd!#$ %&'&()*+,&-./+0123 456=**Y*Y**Y**+ *, 7& !!-2"7#<$8 =9:=;1=<3=>6l<* * =**.=**.o6>* `D**6**Y**6 *dh*dh7b(* ,01'0-577A8D9S:Y;a<h=|>?@A9DEF5K8>a3?+Di@+FgA+9:B+C+D>6 * M*  N<* C* ,-*\.`O* M*Y`*Y`** <**-.`O76 RST%UGWUX_Te[o_y`a`c8*9:{C+E.}F)GH6b*!** *Y`=>*Y*.`** **Y`7"gi jk'oCpWqas8*)8I+b9:bC+bA+JK6m66*>**.`dQ* * "** 6667* wxz{:}K~VYdzj8>m9:mC+mA+ bL+jM+g?+NH65YNY*.:*-*** 7 %48459:5C+5?+ ,O&P&QR6 iY:Y*.:Y* :Y:Y:!:: :**"7* )3=FR[h8\ i9:iC+iS+iB+ _T&PU&)@V&36W&=,X&YZ6aYM,**,7 8 9:S+ X&[\6/*78 9:]\6/*78 9:^_PK qb8P(kksscosi/FayWuHTest.class1B * + , -. /0 12È 3 -4@ 567hDheaderLAbc/MsHeader; newSampleLsscosi/SegregatingSample;+(LAbc/MsHeader;Lsscosi/SegregatingSample;)VCodeLineNumberTableLocalVariableTablethisLsscosi/FayWuHTest;pHeader pNewSample calculateFayH()VthiIgetH()DsetH(D)V SourceFileFayWuHTest.java   8 9:; <%= >? &' @A sscosi/FayWuHTestjava/lang/Objectsscosi/SegregatingSamplegetPi()Ljava/math/BigDecimal;java/math/BigDecimal doubleValue Abc/MsHeadergetSeq()IgetSi(I)I!Y**+*,   pH** * >*'* hhcH' **dhokH**'g "$#'F)_+o, pn!%K"#$%/* 5 &'>*'  9:()PK qb8Oʑoosscosi/FuFsTest.class1j G H I J K LM NO P?+%5uÈ QR@È QS<V@ TU VW QXYZfsDheaderLAbc/MsHeader; newSampleLsscosi/SegregatingSample;dhTestLsscosi/DhTest;:(LAbc/MsHeader;Lsscosi/SegregatingSample;Lsscosi/DhTest;)VCodeLineNumberTableLocalVariableTablethisLsscosi/FuFsTest;pHeader pNewSamplepDhTestgetFs()D calculateFs()VpnsumaPrestaPqew[DqIallelecalculateFunEq23Ewens(I[DI)DjjinSampleaccessvalueNvalueD SourceFile FuFsTest.java &3  ! "# $%[ \]^ _] =>` ab cbd efg h1 ibsscosi/FuFsTestjava/lang/Object Abc/MsHeadergetSeq()I sscosi/DhTestgetDifferentHaplotypesjava/lang/Mathlog(D)Dabssscosi/SegregatingSamplegetPi()Ljava/math/BigDecimal;java/math/BigDecimal doubleValueexp! !"#$%&'(u***+*,*-)  !**+,-!.#/%01(/*)$* +,23( HJ**h:6**hR6* '** cH' ]* 6*)** cJ) **))gg)g99 $' **'g'g**)R-.03<7K9]7c<k=>=@ABCDEFIJ*R45 +,6789:;?<;=>( /dh`d699,1o#9   c9 c9 *c99  !* cc9 c9 ,gRJ*k99  !* cc9 c9 ,gRQL,*,d d*cgok*d,d **cgokcR,1)FN OPSTV$WDYVZ[]_`ace*k*f )? Y2? 2? /+,/@;/89/A; $B;!CDEFPK qb8V2sscosi/R2Test.class1r ? @ A B CD EFÈ G H I J CK LM@ NO NP<V Q CR CS CT UV CW XYZr2Dunic[IheaderLAbc/MsHeader; newSampleLsscosi/SegregatingSample;+(LAbc/MsHeader;Lsscosi/SegregatingSample;)VCodeLineNumberTableLocalVariableTablethisLsscosi/R2Test;pHeader pNewSample calculateR2()ViI createUnicjgetR2()DsetR2(D)VgetUnic()[IsetUnic([I)V SourceFile R2Test.java &0  "# $%[ \]^ _] 78 30 56 9: `ab c6d ef gh ;< i] jk lmn op qp ! sscosi/R2Testjava/lang/Objectsscosi/SegregatingSamplegetRealSegregating()I Abc/MsHeadergetSeqgetPi()Ljava/math/BigDecimal;java/math/BigDecimal doubleValuejava/lang/Mathpow(DD)Dsqrt(D)DgetSingletonArraysgetNewSampleLines(I)Ljava/lang/String;getSingletonPosition(I)Ijava/lang/StringcharAt(I)CgetSingletonChar! !"#$%&'(b***+*,) * +,-#.%/0( * * * * <*.** * .* ogc ** *o*o * * )"#%',(Q'W+t-.*+,!d1230(y** <** O=*G<*4**** \.`O DŽ)* 1 4'748A9_:i;l8r7x@* y+,j42)P1256(/*)C* +,78(>*') GH*+,9:(/*)K* +,;<(>*+) OP*+, !=>PK qb8 sscosi/SSCosi.class1 1_ `ab c d ef g hi j k l mn g op g qr st uv s w x y z { | }~ "g " %g % ( ( + ` + +()VCodeLineNumberTableLocalVariableTablethisLsscosi/SSCosi;main8(LAbc/MsSample;LAbc/MsHeader;Ljava/io/BufferedWriter;I)V newSampleLsscosi/SegregatingSample; coeficientsLsscosi/TajFuCoefficients;tajFuLsscosi/TajFuTests;r2Lsscosi/R2Test;fhLsscosi/FayWuHTest; frequenciesLsscosi/ZFrequencies;ztestsLsscosi/ZTests;wallLsscosi/WallTests;ehhLsscosi/EHHTests;dhTLsscosi/DhTest;fsTLsscosi/FuFsTest;outfileLsscosi/ClassIIResults;sampleLAbc/MsSample;headerLAbc/MsHeader;bwLjava/io/BufferedWriter;kindI Exceptions SourceFile SSCosi.java 23 sscosi/SegregatingSample 2 3 3sscosi/TajFuCoefficients 2 3sscosi/TajFuTests 2 3 3 3 sscosi/R2Test 3sscosi/FayWuHTest 3sscosi/ZFrequencies 2 sscosi/ZTests 2sscosi/WallTests 3 3 3 3 3 3sscosi/EHHTests 3 sscosi/DhTest 3sscosi/FuFsTest 2 3sscosi/ClassIIResults 2  sscosi/SSCosijava/lang/Objectjava/io/IOException Abc/MsSample getSegsites()I(LAbc/MsSample;LAbc/MsHeader;)VcreateSegSample calculatePi+(LAbc/MsHeader;Lsscosi/SegregatingSample;)VcalculateCoefficientsE(LAbc/MsHeader;Lsscosi/SegregatingSample;Lsscosi/TajFuCoefficients;)V calculateTajD calculateFuD calculateFuF calculateR2 calculateFayH9(LAbc/MsSample;LAbc/MsHeader;Lsscosi/SegregatingSample;)VN(LAbc/MsSample;LAbc/MsHeader;Lsscosi/SegregatingSample;Lsscosi/ZFrequencies;)VgetRealSegregating calculateZa calculateZnS calculateZZcalculateCongruentPositions calculateB calculateQ calculateEhh calculateDh:(LAbc/MsHeader;Lsscosi/SegregatingSample;Lsscosi/DhTest;)V calculateFs(LAbc/MsHeader;Lsscosi/SegregatingSample;Lsscosi/WallTests;Lsscosi/ZTests;Lsscosi/EHHTests;Lsscosi/DhTest;Lsscosi/FuFsTest;Lsscosi/TajFuTests;Lsscosi/R2Test;Lsscosi/FayWuHTest;)VgetSampleNumberwriteResultsSample(ILjava/io/BufferedWriter;)VwriteResultsTab!012343*5 6 78 9:4{ 7*2Y*+:Y+: Y+ :  Y+:Y+:Y*+: Y*+ : Y*+: !      !"Y+#:  $%Y+&:  '(Y+ ):*+Y+    ,:*-,. *-,/5"45678(9-:;;@<E=J>V?[@gAlByCDEFGHIJKMNOPQRST'U6X6$;<(=>;?@VABgCDyEF GH IJ nKL TMN AOP QR7ST7UV7WX7YZ[\]^PK qb8/IIsscosi/SegregatingSample.class1 "j !kl m !n !o !p !q !r stuv wx wy z {| {} {~    ! ! ! ! ! !   ! ! !newSampleLines[Ljava/lang/String;realSegregatingIpiLjava/math/BigDecimal; singletonssingletonPosition[I singletonChar[CsingletonArrayssisampleLAbc/MsSample;headerLAbc/MsHeader;(LAbc/MsSample;LAbc/MsHeader;)VCodeLineNumberTableLocalVariableTablethisLsscosi/SegregatingSample;pSamplepHeadergetNewSampleLines()[Ljava/lang/String;(I)Ljava/lang/String;posgetRealSegregating()IgetPi()Ljava/math/BigDecimal; getSingletonscreateSegSample()ValleleLjava/lang/Character;flag firstAlleleij calculatePicountp1seqsfactorccalculateAlleleFreq(CI)ICcountSingletons(II)VgetSingletonPosition()[IsetSingletonPosition([I)V(I)IgetSingletonChar()[CsetSingletonChar([C)V(I)CgetSingletonArrayssetSingletonArrays(I)VgetSisetSi SourceFileSegregatingSample.java 4G %&java/math/BigDecimal 4e '( )& 01 23 #$ Bjava/lang/String B ? 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