Index (biojava-survival 7.2.2 API)

A B C D E F G H I K L M N O P R S T U V W X Y Z
All Classes and Interfaces|All Packages|Serialized Form

A

abs(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
abs(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
add(double[][], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
addCell(String, String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet: Add data to a cell
addColumn(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
addColumns(ArrayList<String>, String) - Method in class org.biojava.nbio.survival.data.WorkSheet: Add columns to worksheet and set default value
addContinuousVariable(String, Double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
addInteraction(String, String, ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper: To test for interactions use two variables and create a third variable where the two are multiplied together.
addRow(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
addRows(ArrayList<String>, String) - Method in class org.biojava.nbio.survival.data.WorkSheet: Add rows to the worksheet and fill in default value
addStrataInfoHashMap(LinkedHashMap<String, StrataInfo>, String) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
addUnknownDataTypeVariable(String, String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
AgScore - Class in org.biojava.nbio.survival.cox.stats
AgScore() - Constructor for class org.biojava.nbio.survival.cox.stats.AgScore
appendWorkSheetColumns(WorkSheet) - Method in class org.biojava.nbio.survival.data.WorkSheet: Add columns from a second worksheet to be joined by common row.
appendWorkSheetRows(WorkSheet) - Method in class org.biojava.nbio.survival.data.WorkSheet: Add rows from a second worksheet to be joined by common column.
applyColumnFilter(String, ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet: Apply filter to a column to change values from say numberic to nominal based on some range
axisStroke - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

B

bottom - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
Breslow - Enum constant in enum class org.biojava.nbio.survival.cox.CoxMethod

C

calculateWaldTestInfo(CoxInfo) - Static method in class org.biojava.nbio.survival.cox.CoxR
categorizeData(ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper: Take a collection of categorical data and convert it to numeric to be used in cox calculations
censored - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
CensorStatus - Class in org.biojava.nbio.survival.kaplanmeier.figure
CensorStatus() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
CensorStatus(String, Double, String) - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
CensorStatusSelect - Interface in org.biojava.nbio.survival.kaplanmeier.figure
change(String) - Method in interface org.biojava.nbio.survival.data.ChangeValue
changeColumnHeader(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
changeColumnHeader(ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet
changeColumnsHeaders(LinkedHashMap<String, String>) - Method in class org.biojava.nbio.survival.data.WorkSheet: Change the columns in the HashMap Key to the name of the value
changeRowHeader(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
changeRowHeader(ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet
ChangeValue - Interface in org.biojava.nbio.survival.data
charAt(int) - Method in class org.biojava.nbio.survival.data.CompactCharSequence
chiSq(double, int) - Static method in class org.biojava.nbio.survival.cox.stats.ChiSq
ChiSq - Class in org.biojava.nbio.survival.cox.stats
ChiSq() - Constructor for class org.biojava.nbio.survival.cox.stats.ChiSq
Cholesky2 - Class in org.biojava.nbio.survival.cox.stats
Cholesky2() - Constructor for class org.biojava.nbio.survival.cox.stats.Cholesky2
Chsolve2 - Class in org.biojava.nbio.survival.cox.stats
Chsolve2() - Constructor for class org.biojava.nbio.survival.cox.stats.Chsolve2
clear() - Method in class org.biojava.nbio.survival.data.WorkSheet: See if we can free up memory
ClinicalMetaDataOutcome - Class in org.biojava.nbio.survival.kaplanmeier.metadata
ClinicalMetaDataOutcome() - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome
column - Variable in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
CompactCharSequence - Class in org.biojava.nbio.survival.data: http://www.javamex.com/tutorials/memory/ascii_charsequence.shtml
CompactCharSequence(String) - Constructor for class org.biojava.nbio.survival.data.CompactCharSequence
compare(CoxVariables, CoxVariables) - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesOverallModelFitComparator
compare(CoxVariables, CoxVariables) - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
compare(CoxVariables, CoxVariables) - Method in class org.biojava.nbio.survival.cox.comparators.MeanModelComparator
compare(SurvivalInfo, SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.comparators.SurvivalInfoComparator
compare(SurvivalInfo, SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.comparators.SurvivalInfoValueComparator
compareTo(SurvivalInfo) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
compareTo(SurvivalInfoIndex) - Method in class org.biojava.nbio.survival.cox.SurvivalInfoIndex
compareTo(CensorStatus) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
CoxCC - Class in org.biojava.nbio.survival.cox
CoxCC() - Constructor for class org.biojava.nbio.survival.cox.CoxCC
CoxCoefficient - Class in org.biojava.nbio.survival.cox
CoxCoefficient() - Constructor for class org.biojava.nbio.survival.cox.CoxCoefficient
CoxComparatorInterface - Interface in org.biojava.nbio.survival.cox.comparators
CoxHelper - Class in org.biojava.nbio.survival.cox: The CoxHelper class is provided to start with a tab delimited file in a similar process in R and return the results as a CoxInfo class.
CoxHelper() - Constructor for class org.biojava.nbio.survival.cox.CoxHelper
CoxInfo - Class in org.biojava.nbio.survival.cox: Holds the results of a cox analysis where calling dump(), toString() will give an output similar to R
CoxInfo() - Constructor for class org.biojava.nbio.survival.cox.CoxInfo
CoxMart - Class in org.biojava.nbio.survival.cox
CoxMart() - Constructor for class org.biojava.nbio.survival.cox.CoxMart
CoxMethod - Enum Class in org.biojava.nbio.survival.cox
coxphfitSCleanup(CoxInfo, boolean, boolean, ArrayList<String>) - Method in class org.biojava.nbio.survival.cox.CoxR
CoxR - Class in org.biojava.nbio.survival.cox: This is a port of the R survival code used for doing Cox Regression.
CoxR() - Constructor for class org.biojava.nbio.survival.cox.CoxR
coxsafe(double) - Method in class org.biojava.nbio.survival.cox.CoxR
CoxScore - Class in org.biojava.nbio.survival.cox
CoxScore() - Constructor for class org.biojava.nbio.survival.cox.CoxScore
CoxVariables - Class in org.biojava.nbio.survival.cox
CoxVariables(String, String, String) - Constructor for class org.biojava.nbio.survival.cox.CoxVariables
CoxVariablesOverallModelFitComparator - Class in org.biojava.nbio.survival.cox.comparators
CoxVariablesOverallModelFitComparator(String) - Constructor for class org.biojava.nbio.survival.cox.comparators.CoxVariablesOverallModelFitComparator: Variables are stored as a string representation of an ArrayList [META_GENE] or [trtg, META_GENE] add variables used in cox regression to an array and then do toString.
CoxVariablesVariableComparator - Class in org.biojava.nbio.survival.cox.comparators
CoxVariablesVariableComparator(String, String) - Constructor for class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator

D

dfbeta - Enum constant in enum class org.biojava.nbio.survival.cox.ResidualsCoxph.Type
dfbetas - Enum constant in enum class org.biojava.nbio.survival.cox.ResidualsCoxph.Type
diag(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
diag(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
discreteQuantizer - Variable in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
DiscreteQuantizerInterface - Interface in org.biojava.nbio.survival.kaplanmeier.metadata
dot(double[], double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
dump() - Method in class org.biojava.nbio.survival.cox.CoxInfo
dump(ArrayList<SurvivalInfo>, PrintStream, String) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper: For each analysis this allows outputing of the data used in the calculations to a printstream/file.

E

ef - Variable in class org.biojava.nbio.survival.cox.CoxInfo
Efron - Enum constant in enum class org.biojava.nbio.survival.cox.CoxMethod
encodeFileURL(String) - Method in class org.biojava.nbio.survival.cox.CoxVariables
ExpressionFigure - Class in org.biojava.nbio.survival.kaplanmeier.figure
ExpressionFigure() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure

F

f(Double) - Method in class org.biojava.nbio.survival.cox.StrataInfo
fh2 - Enum constant in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method
figureLineInfoLowerPercentX - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
figureLineInfoLowerPercentY - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
flemingHarrington - Enum constant in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method
fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.cox.CoxCoefficient
fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.cox.CoxInfo
fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.cox.CoxVariables
fmt(Double, int, int) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
fmtpl(String, int) - Method in class org.biojava.nbio.survival.cox.CoxInfo: Pad left a string with spaces
fmtpr(String, int) - Method in class org.biojava.nbio.survival.cox.CoxInfo

G

getAllColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet: Get the list of column names including those that may be hidden
getAllRows() - Method in class org.biojava.nbio.survival.data.WorkSheet: Get all rows including those that may be hidden
getBottom() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getCell(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet: Get cell value
getCellDouble(String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet
getChiSquare() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getClusterValue() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getCoeff() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getCoefficient(String) - Method in class org.biojava.nbio.survival.cox.CoxInfo
getCoefficientsList() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getCoefficientText(boolean, String, String, String, String) - Method in class org.biojava.nbio.survival.cox.CoxInfo
getCohortName() - Method in class org.biojava.nbio.survival.cox.CoxVariables
getColor(int) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
getColumnIndex(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
getColumnLookup() - Method in class org.biojava.nbio.survival.data.WorkSheet
getColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet: Get the list of column names.
getContinuousVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getCopy() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
getCopyWorkSheet(WorkSheet) - Static method in class org.biojava.nbio.survival.data.WorkSheet: Create a copy of a worksheet.
getCopyWorkSheetSelectedRows(WorkSheet, ArrayList<String>) - Static method in class org.biojava.nbio.survival.data.WorkSheet: Create a copy of a worksheet.
getCoxInfo(String) - Method in class org.biojava.nbio.survival.cox.CoxVariables
getCoxInfoHashMap() - Method in class org.biojava.nbio.survival.cox.CoxVariables
getDataColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
getDataRows() - Method in class org.biojava.nbio.survival.data.WorkSheet: Get the list of row names
getDataVariables() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getDegreeFreedom() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getDescription() - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
getDescription() - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
getDf() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
getDiscreteColumnValues(String) - Method in class org.biojava.nbio.survival.data.WorkSheet: Get back a list of unique values in the column
getDiscreteRowValues(String) - Method in class org.biojava.nbio.survival.data.WorkSheet: Get back a list of unique values in the row
getDiscreteValues() - Method in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
getFileName() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
getFileName() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getGenes() - Method in class org.biojava.nbio.survival.cox.CoxVariables
getGeneSet() - Method in class org.biojava.nbio.survival.cox.CoxVariables
getGroupCategories(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getGroupCategories(String, ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper
getGroups() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure: Get the name of the groups that are being plotted in the figure
getHazardRatio() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getHazardRatioHiCI() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getHazardRatioLoCI() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getHRText() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getId() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getImat() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getIndex() - Method in class org.biojava.nbio.survival.data.HeaderInfo
getIndexColumnName() - Method in class org.biojava.nbio.survival.data.WorkSheet
getKMFigureInfo() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getLeft() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getLinearPredictor() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getLogScale(double) - Method in class org.biojava.nbio.survival.data.WorkSheet: Get the log scale of this worksheet where a zero value will be set to .1 as Log(0) is undefined
getLogScale(double, double) - Method in class org.biojava.nbio.survival.data.WorkSheet: Get the log scale of this worksheet
getLower() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getMean() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getMetaDataColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
getMetaDataColumnsHashMap() - Method in class org.biojava.nbio.survival.data.WorkSheet
getMetaDataFilter() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getMetaDataRows() - Method in class org.biojava.nbio.survival.data.WorkSheet
getMetaDataRowsHashMap() - Method in class org.biojava.nbio.survival.data.WorkSheet
getModelVariables() - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
getModelVariables() - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
getNaive_imat() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getNaiveVariance() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getName() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getNcens() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getNdead() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getNearestAtRisk(double) - Method in class org.biojava.nbio.survival.cox.StrataInfo: Selection of number of risk will depend on the precision and rounding of time in the survival table.
getNearestTime(double) - Method in class org.biojava.nbio.survival.cox.StrataInfo: Need to find the actual time for the nearest time represented as a percentage Would be used to then look up the number at risk at that particular time
getNevent() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getNrisk() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getNumberCoefficients() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getNumberDiscreteValues() - Method in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
getNumberVariables() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getOffset() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getOrder() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getOriginalMetaData(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getOverallModelFitPvalue() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getPercentage() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
getPvalue() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getPvalue() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
getRandomDataColumns(int) - Method in class org.biojava.nbio.survival.data.WorkSheet
getRandomDataColumns(int, ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
getResidual() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getResidualVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getRight() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getRobustStdError() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getRowHeader() - Method in class org.biojava.nbio.survival.data.WorkSheet
getRowIndex(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
getRowLookup() - Method in class org.biojava.nbio.survival.data.WorkSheet
getRows() - Method in class org.biojava.nbio.survival.data.WorkSheet: Get the list of row names.
getRscore() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getRscoreLogrankTestpvalue() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getScore() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getScoreLogrankTest() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getScoreLogrankTestpvalue() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getSortVariable() - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
getSortVariable() - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
getStandardDeviation() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getStatus() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getStatus() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getStderr() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getStdError() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
getStdlow() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getStrata() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getStrataInfoHashMap() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
getSurv() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getSurvivalFitInfo() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getSurvivalInfoList() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getSurvivalInfoList() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure: The data used to draw the graph
getSurvivalTimePercentile(String, double) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure: To get the median percentile for a particular group pass the value of .50.
getTest() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
getTime() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getTime() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getTimeAxisIncrementPercentage() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure: Get the percentage increment for the time axis
getTop() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getUniqueID() - Method in class org.biojava.nbio.survival.cox.CoxVariables: Need a unique id from String
getUnknownDataTypeVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getUnweightedStrataInfoHashMap() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
getUpper() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getVarhaz() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getVariable(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getVariableResiduals() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getVariance() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getWaldTestInfo() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getWeight() - Method in class org.biojava.nbio.survival.cox.StrataInfo
getWeight() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
getWeighted() - Method in class org.biojava.nbio.survival.cox.CoxInfo
getxAxisTimeCoordinates() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getxAxisTimeValues() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
getZ() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
greenwood - Enum constant in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error
group - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
group1 - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
group1WorseOutcome - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
group2 - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
groupByRange(double[], String, String, ArrayList<SurvivalInfo>) - Static method in class org.biojava.nbio.survival.cox.SurvivalInfoHelper: Need to allow a range of values similar to cut in R and a continuous c
GroupResults - Class in org.biojava.nbio.survival.kaplanmeier.figure
GroupResults() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults

H

HeaderInfo - Class in org.biojava.nbio.survival.data
HeaderInfo(Integer) - Constructor for class org.biojava.nbio.survival.data.HeaderInfo
height - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
hideColumn(String, boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
hideEmptyColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet
hideEmptyRows() - Method in class org.biojava.nbio.survival.data.WorkSheet
hideMetaDataColumns(boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
hideMetaDataRows(boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
hideRow(String, boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet

I

identity(int) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
init(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
isHide() - Method in class org.biojava.nbio.survival.data.HeaderInfo
isMetaDataColumn(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
isMetaDataRow(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
isValidColumn(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
isValidRow(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
isWeighted() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo

K

kaplanMeier - Enum constant in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method
KaplanMeierFigure - Class in org.biojava.nbio.survival.kaplanmeier.figure
KaplanMeierFigure() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
kmf - Variable in class org.biojava.nbio.survival.cox.CoxInfo
KMFigureInfo - Class in org.biojava.nbio.survival.kaplanmeier.figure
KMFigureInfo() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
kmStroke - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

L

left - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
legendColor - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
legendUpperPercentX - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
legendUpperPercentY - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
length() - Method in class org.biojava.nbio.survival.data.CompactCharSequence
log - Enum constant in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType
log_log - Enum constant in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType

M

main(String[]) - Static method in class org.biojava.nbio.survival.cox.CoxCC
main(String[]) - Static method in class org.biojava.nbio.survival.cox.CoxHelper
main(String[]) - Static method in class org.biojava.nbio.survival.cox.CoxMart
main(String[]) - Static method in class org.biojava.nbio.survival.cox.CoxR
main(String[]) - Static method in class org.biojava.nbio.survival.cox.CoxScore
main(String[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
main(String[]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO: Test client.
main(String[]) - Static method in class org.biojava.nbio.survival.cox.ResidualsCoxph
main(String[]) - Static method in class org.biojava.nbio.survival.cox.stats.AgScore
main(String[]) - Static method in class org.biojava.nbio.survival.cox.stats.ChiSq
main(String[]) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
main(String[]) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
main(String[]) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel
main(String[]) - Static method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
main(String[]) - Static method in class org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome
markMetaDataColumn(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
markMetaDataColumns(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet: marks columns as containing meta data
markMetaDataRow(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
Matrix - Class in org.biojava.nbio.survival.cox.matrix: *********************************************************************** Compilation: javac Matrix.java Execution: java Matrix A bare-bones collection of static methods for manipulating matrices.
Matrix() - Constructor for class org.biojava.nbio.survival.cox.matrix.Matrix
MeanModelComparator - Class in org.biojava.nbio.survival.cox.comparators
MeanModelComparator(String) - Constructor for class org.biojava.nbio.survival.cox.comparators.MeanModelComparator
MeanQuantizer - Class in org.biojava.nbio.survival.kaplanmeier.metadata
MeanQuantizer() - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.MeanQuantizer
MetaDataInfo - Class in org.biojava.nbio.survival.kaplanmeier.metadata
MetaDataInfo(String) - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
MetaDataInfo(String, boolean, DiscreteQuantizerInterface) - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
modified - Enum constant in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower
multiply(double[][], double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
multiply(double[][], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
multiply(double[], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix

N

ncens - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
nevents - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
none - Enum constant in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType
norm(double) - Static method in class org.biojava.nbio.survival.cox.stats.ChiSq
nrisk - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
NumbersAtRiskPanel - Class in org.biojava.nbio.survival.kaplanmeier.figure
NumbersAtRiskPanel() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel
numeric - Variable in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo

O

oneDivide(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
oneDivide(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
org.biojava.nbio.survival.cox - package org.biojava.nbio.survival.cox
org.biojava.nbio.survival.cox.comparators - package org.biojava.nbio.survival.cox.comparators
org.biojava.nbio.survival.cox.matrix - package org.biojava.nbio.survival.cox.matrix
org.biojava.nbio.survival.cox.stats - package org.biojava.nbio.survival.cox.stats
org.biojava.nbio.survival.data - package org.biojava.nbio.survival.data
org.biojava.nbio.survival.kaplanmeier.figure - package org.biojava.nbio.survival.kaplanmeier.figure
org.biojava.nbio.survival.kaplanmeier.metadata - package org.biojava.nbio.survival.kaplanmeier.metadata

P

padding - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
paintComponent(Graphics) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
paintComponent(Graphics) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
paintComponent(Graphics) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel
peto - Enum constant in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower
plain - Enum constant in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType
print(boolean[]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO: Print an array of booleans to standard output.
print(boolean[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO: Print the M-by-N array of booleans to standard output.
print(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO: Print an array of doubles to standard output.
print(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO: Print the M-by-N array of doubles to standard output.
print(int[]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO: Print an array of ints to standard output.
print(int[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.StdArrayIO: Print the M-by-N array of ints to standard output.
process(double[][], double[][], double) - Static method in class org.biojava.nbio.survival.cox.WaldTest
process(double[][], double[], double) - Static method in class org.biojava.nbio.survival.cox.WaldTest
process(double[][], int, double) - Static method in class org.biojava.nbio.survival.cox.stats.Cholesky2
process(double[][], int, double[][], int) - Static method in class org.biojava.nbio.survival.cox.stats.Chsolve2
process(String, String, String, String, String, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
process(String, String, String, String, String, String, ArrayList<String>, boolean, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxHelper
process(String, ArrayList<SurvivalInfo>, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
process(String, ArrayList<SurvivalInfo>, SurvFitKM.Method, SurvFitKM.Error, boolean, double, SurvFitKM.ConfType, SurvFitKM.ConfLower, Double, Double, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
process(ArrayList<String>, ArrayList<SurvivalInfo>, boolean, boolean, boolean, boolean) - Method in class org.biojava.nbio.survival.cox.CoxR
process(ArrayList<String>, ArrayList<SurvivalInfo>, int, CoxMethod, double, double, double[], int, boolean, boolean, boolean, boolean) - Method in class org.biojava.nbio.survival.cox.CoxR
process(LinkedHashMap<String, ArrayList<CensorStatus>>, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
process(CoxInfo) - Static method in class org.biojava.nbio.survival.cox.CoxCC
process(CoxInfo, ResidualsCoxph.Type, boolean, ArrayList<String>) - Static method in class org.biojava.nbio.survival.cox.ResidualsCoxph
process(CoxMethod, ArrayList<SurvivalInfo>, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxMart
process(CoxMethod, ArrayList<SurvivalInfo>, CoxInfo, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxScore
process(CoxMethod, ArrayList<SurvivalInfo>, CoxInfo, boolean) - Static method in class org.biojava.nbio.survival.cox.stats.AgScore
process(WorkSheet, String) - Method in interface org.biojava.nbio.survival.kaplanmeier.metadata.DiscreteQuantizerInterface
process(WorkSheet, String) - Method in class org.biojava.nbio.survival.kaplanmeier.metadata.MeanQuantizer
process(WorkSheet, String, String, String, String, String, ArrayList<String>, boolean, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxHelper
process(WorkSheet, String, LinkedHashMap<String, String>, String, Double, ArrayList<MetaDataInfo>) - Static method in class org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome
processStrataInfo(String, ArrayList<SurvivalInfo>, SurvFitKM.Method, SurvFitKM.Error, boolean, double, SurvFitKM.ConfType, SurvFitKM.ConfLower, Double, Double, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
putCoxInfo(String, CoxInfo) - Method in class org.biojava.nbio.survival.cox.CoxVariables

R

random(int, int) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
randomlyDivideSave(double, String, String) - Method in class org.biojava.nbio.survival.data.WorkSheet: Split a worksheet randomly.
readCSV(File, char) - Static method in class org.biojava.nbio.survival.data.WorkSheet
readCSV(InputStream, char) - Static method in class org.biojava.nbio.survival.data.WorkSheet: Read a CSV/Tab delimited file where you pass in the delimiter
readCSV(String, char) - Static method in class org.biojava.nbio.survival.data.WorkSheet: Read a CSV/Tab delimitted file where you pass in the delimiter
replaceColumnValues(String, HashMap<String, String>) - Method in class org.biojava.nbio.survival.data.WorkSheet: Change values in a column where 0 = something and 1 = something different
ResidualsCoxph - Class in org.biojava.nbio.survival.cox
ResidualsCoxph() - Constructor for class org.biojava.nbio.survival.cox.ResidualsCoxph
ResidualsCoxph.Type - Enum Class in org.biojava.nbio.survival.cox
right - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
RiskInfo - Class in org.biojava.nbio.survival.cox
RiskInfo() - Constructor for class org.biojava.nbio.survival.cox.RiskInfo
row - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus

S

save(OutputStream, char, boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
saveCSV(String) - Method in class org.biojava.nbio.survival.data.WorkSheet: Save the worksheet as a csv file
savePNG(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
savePNG(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
savePNGKMNumRisk(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure: Combine the KM and Num risk into one image
saveSurvivalData(String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure: Save data from survival curve to text file
saveTXT(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
scale(double[][], double) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
scale(double[][], double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
score - Enum constant in enum class org.biojava.nbio.survival.cox.ResidualsCoxph.Type
select(WorkSheet, String) - Method in interface org.biojava.nbio.survival.kaplanmeier.figure.CensorStatusSelect
setCacheDoubleValues(boolean) - Method in class org.biojava.nbio.survival.data.WorkSheet
setClusterValue(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
setCoeff(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
setCoefficient(String, CoxCoefficient) - Method in class org.biojava.nbio.survival.cox.CoxInfo
setCoxInfo(ArrayList<String>, CoxInfo, String, LinkedHashMap<String, String>, Boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
setDegreeFreedom(double) - Method in class org.biojava.nbio.survival.cox.CoxInfo
setDescription(String) - Method in interface org.biojava.nbio.survival.cox.comparators.CoxComparatorInterface
setDescription(String) - Method in class org.biojava.nbio.survival.cox.comparators.CoxVariablesVariableComparator
setDf(int) - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
setDiscreteValues(WorkSheet) - Method in class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo
setFigureLineInfo(ArrayList<String>) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
setFigureLineInfo(ArrayList<String>) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
setHazardRatio(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
setHazardRatioHiCI(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
setHazardRatioLoCI(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
setHide(boolean) - Method in class org.biojava.nbio.survival.data.HeaderInfo
setId(String) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
setIndex(Integer) - Method in class org.biojava.nbio.survival.data.HeaderInfo
setIndexColumnName(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
setKaplanMeierFigure(KaplanMeierFigure) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.NumbersAtRiskPanel: Pick up needed info and details from the KM Figure
setKMFigureInfo(KMFigureInfo) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
setKMFigureInfo(KMFigureInfo) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
setLinearPredictor(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
setMean(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
setMetaDataColumns(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet: Clears existing meta data columns and sets new ones
setMetaDataColumnsAfterColumn() - Method in class org.biojava.nbio.survival.data.WorkSheet
setMetaDataColumnsAfterColumn(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
setMetaDataFilter(LinkedHashMap<String, String>) - Method in class org.biojava.nbio.survival.cox.CoxInfo
setMetaDataRows(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet
setMetaDataRowsAfterRow() - Method in class org.biojava.nbio.survival.data.WorkSheet
setMetaDataRowsAfterRow(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
setNaiveVariance(double[][]) - Method in class org.biojava.nbio.survival.cox.CoxInfo
setName(String) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
setOffset(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
setOrder(int) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
setPercentage(Double) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
setPvalue(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
setResidual(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
setResidualVariable(String, Double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo: Set the residual value for the variable for this sample.
setRobustStdError(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
setRowHeader(String) - Method in class org.biojava.nbio.survival.data.WorkSheet
setRscore(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo
setRscoreLogrankTestpvalue(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo
setScore(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
setScoreLogrankTest(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo
setScoreLogrankTestpvalue(Double) - Method in class org.biojava.nbio.survival.cox.CoxInfo
setStandardDeviation(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
setStatus(int) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
setStdError(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
setStdlow(ArrayList<Double>) - Method in class org.biojava.nbio.survival.cox.StrataInfo
setStrata(int) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
setStrataInfoHashMap(LinkedHashMap<String, StrataInfo>) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
setSurvivalData(ArrayList<String>, LinkedHashMap<String, ArrayList<CensorStatus>>, Boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure: The data will set the max time which will result in off time points for tick marks
setSurvivalData(ArrayList<String>, LinkedHashMap<String, ArrayList<CensorStatus>>, Double, Boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure
setSurvivalData(ArrayList<String>, SurvFitInfo, Double) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.KaplanMeierFigure: Allow setting of points in the figure where weighted correction has been done and percentage has already been calculated.
setSurvivalInfo(ArrayList<String>, ArrayList<SurvivalInfo>, String) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
setSurvivalInfoList(ArrayList<SurvivalInfo>) - Method in class org.biojava.nbio.survival.cox.CoxInfo
setTime(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
setUnweightedStrataInfoHashMap(LinkedHashMap<String, StrataInfo>) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
setVariableResiduals(double[][]) - Method in class org.biojava.nbio.survival.cox.CoxInfo
setVariance(double[][]) - Method in class org.biojava.nbio.survival.cox.CoxInfo
setWaldTestInfo(WaldTestInfo) - Method in class org.biojava.nbio.survival.cox.CoxInfo
setWeight(double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
setWeighted(boolean) - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
setZ(double) - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
shuffleColumnsAndThenRows(ArrayList<String>, ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet: Randomly shuffle the columns and rows.
shuffleColumnValues(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet: Need to shuffle column values to allow for randomized testing.
shuffleRowValues(ArrayList<String>) - Method in class org.biojava.nbio.survival.data.WorkSheet: Need to shuffle rows values to allow for randomized testing.
signatureName - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.GroupResults
sqrt(double[]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
sqrt(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
StdArrayIO - Class in org.biojava.nbio.survival.cox.matrix: Standard array IO.
StdArrayIO() - Constructor for class org.biojava.nbio.survival.cox.matrix.StdArrayIO
StrataInfo - Class in org.biojava.nbio.survival.cox: Information needed to represent a survival curve
StrataInfo() - Constructor for class org.biojava.nbio.survival.cox.StrataInfo
subSequence(int, int) - Method in class org.biojava.nbio.survival.data.CompactCharSequence
subtract(double[][], double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
SurvFitInfo - Class in org.biojava.nbio.survival.cox: Contains info for graphing km figures
SurvFitInfo() - Constructor for class org.biojava.nbio.survival.cox.SurvFitInfo
SurvFitKM - Class in org.biojava.nbio.survival.kaplanmeier.figure: Ported from survfitKM.S When combining multiple entries with same time not sure how the weighting adds up
SurvFitKM() - Constructor for class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM
SurvFitKM.ConfLower - Enum Class in org.biojava.nbio.survival.kaplanmeier.figure
SurvFitKM.ConfType - Enum Class in org.biojava.nbio.survival.kaplanmeier.figure
SurvFitKM.Error - Enum Class in org.biojava.nbio.survival.kaplanmeier.figure
SurvFitKM.Method - Enum Class in org.biojava.nbio.survival.kaplanmeier.figure
SurvivalInfo - Class in org.biojava.nbio.survival.cox: Data class to represent a single sample where time and event/censor status is required Additionally each variable and data associated with that variable.
SurvivalInfo(double, int) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfo
SurvivalInfo(double, int, String, double) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfo
SurvivalInfo(double, int, LinkedHashMap<String, Double>) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfo
SurvivalInfoComparator - Class in org.biojava.nbio.survival.cox.comparators
SurvivalInfoComparator() - Constructor for class org.biojava.nbio.survival.cox.comparators.SurvivalInfoComparator
SurvivalInfoHelper - Class in org.biojava.nbio.survival.cox: Used to work with SurvivalInfo
SurvivalInfoHelper() - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoHelper
SurvivalInfoIndex - Class in org.biojava.nbio.survival.cox: Not used and probably should be deleted
SurvivalInfoIndex(double, int, int) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoIndex
SurvivalInfoIndex(double, int, int, double) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoIndex
SurvivalInfoIndex(double, int, int, double[]) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfoIndex
SurvivalInfoValueComparator - Class in org.biojava.nbio.survival.cox.comparators
SurvivalInfoValueComparator(String) - Constructor for class org.biojava.nbio.survival.cox.comparators.SurvivalInfoValueComparator
swapRowAndColumns() - Method in class org.biojava.nbio.survival.data.WorkSheet: Swap the row and columns returning a new worksheet

T

time - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
timeScale - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
titleHeight - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
top - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.ExpressionFigure
toString() - Method in class org.biojava.nbio.survival.cox.CoxCoefficient
toString() - Method in class org.biojava.nbio.survival.cox.CoxInfo
toString() - Method in class org.biojava.nbio.survival.cox.CoxVariables
toString() - Method in class org.biojava.nbio.survival.cox.StrataInfo
toString() - Method in class org.biojava.nbio.survival.cox.SurvFitInfo
toString() - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
toString() - Method in class org.biojava.nbio.survival.cox.SurvivalInfoIndex
toString() - Method in class org.biojava.nbio.survival.cox.WaldTestInfo
toString() - Method in class org.biojava.nbio.survival.data.CompactCharSequence
toString() - Method in class org.biojava.nbio.survival.data.HeaderInfo
toString() - Method in class org.biojava.nbio.survival.data.WorkSheet
toString() - Method in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
toString(String, String, String) - Method in class org.biojava.nbio.survival.cox.CoxInfo
transpose(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix
tsiatis - Enum constant in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error

U

unionWorkSheetsRowJoin(String, String, char, boolean) - Static method in class org.biojava.nbio.survival.data.WorkSheet: Combine two work sheets where you join based on rows.
unionWorkSheetsRowJoin(WorkSheet, WorkSheet, boolean) - Static method in class org.biojava.nbio.survival.data.WorkSheet: * Combine two work sheets where you join based on rows.
updateContinousVariable(String, Double) - Method in class org.biojava.nbio.survival.cox.SurvivalInfo
usual - Enum constant in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower

V

value - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
valueOf(String) - Static method in enum class org.biojava.nbio.survival.cox.CoxMethod: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biojava.nbio.survival.cox.ResidualsCoxph.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.biojava.nbio.survival.cox.CoxMethod: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biojava.nbio.survival.cox.ResidualsCoxph.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method: Returns an array containing the constants of this enum class, in the order they are declared.

W

WaldTest - Class in org.biojava.nbio.survival.cox
WaldTest() - Constructor for class org.biojava.nbio.survival.cox.WaldTest
WaldTestInfo - Class in org.biojava.nbio.survival.cox
WaldTestInfo() - Constructor for class org.biojava.nbio.survival.cox.WaldTestInfo
weight - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus
width - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
WorkSheet - Class in org.biojava.nbio.survival.data: Need to handle very large spreadsheets of expression data so keep memory footprint low
WorkSheet() - Constructor for class org.biojava.nbio.survival.data.WorkSheet
WorkSheet(String[][]) - Constructor for class org.biojava.nbio.survival.data.WorkSheet
WorkSheet(Collection<String>, Collection<String>) - Constructor for class org.biojava.nbio.survival.data.WorkSheet
WorkSheet(CompactCharSequence[][]) - Constructor for class org.biojava.nbio.survival.data.WorkSheet

X

xAxisLabels - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
xAxisLegend - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
xaxisPercentIncrement - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

Y

yAxisLegend - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo
yaxisPercentIncrement - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.KMFigureInfo

Z

zscore - Variable in class org.biojava.nbio.survival.kaplanmeier.figure.CensorStatus

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