A B C D E F G H I K L M N O P R S T U V W X Y Z

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

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(ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet

changeColumnHeader(String, String) - 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(ChangeValue) - Method in class org.biojava.nbio.survival.data.WorkSheet

changeRowHeader(String, String) - 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 - Class in org.biojava.nbio.survival.cox.stats

ChiSq() - Constructor for class org.biojava.nbio.survival.cox.stats.ChiSq

chiSq(double, int) - Static method in 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 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

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

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

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

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

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

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

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

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, boolean, DiscreteQuantizerInterface) - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo

MetaDataInfo(String) - Constructor for class org.biojava.nbio.survival.kaplanmeier.metadata.MetaDataInfo

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

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

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.

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.

process(CoxInfo) - Static method in class org.biojava.nbio.survival.cox.CoxCC

process(String, String, String, String, String, String, ArrayList<String>, boolean, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxHelper

process(WorkSheet, String, String, String, String, String, ArrayList<String>, boolean, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxHelper

process(CoxMethod, ArrayList<SurvivalInfo>, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxMart

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(CoxMethod, ArrayList<SurvivalInfo>, CoxInfo, boolean) - Static method in class org.biojava.nbio.survival.cox.CoxScore

process(CoxInfo, ResidualsCoxph.Type, boolean, ArrayList<String>) - Static method in class org.biojava.nbio.survival.cox.ResidualsCoxph

process(CoxMethod, ArrayList<SurvivalInfo>, CoxInfo, boolean) - Static method in class org.biojava.nbio.survival.cox.stats.AgScore

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(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(LinkedHashMap<String, ArrayList<CensorStatus>>, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM

process(String, String, String, String, String, boolean) - Method in class org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM

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(WorkSheet, String, LinkedHashMap<String, String>, String, Double, ArrayList<MetaDataInfo>) - Static method in class org.biojava.nbio.survival.kaplanmeier.metadata.ClinicalMetaDataOutcome

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

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(String, char) - Static method in class org.biojava.nbio.survival.data.WorkSheet

Read a CSV/Tab delimitted file where you pass in the delimiter

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

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 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

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>, 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.

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

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 in org.biojava.nbio.survival.kaplanmeier.figure

SurvFitKM.ConfType - Enum in org.biojava.nbio.survival.kaplanmeier.figure

SurvFitKM.Error - Enum in org.biojava.nbio.survival.kaplanmeier.figure

SurvFitKM.Method - Enum 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, LinkedHashMap<String, Double>) - Constructor for class org.biojava.nbio.survival.cox.SurvivalInfo

SurvivalInfo(double, int, 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(String, String, String) - 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

transpose(double[][]) - Static method in class org.biojava.nbio.survival.cox.matrix.Matrix

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

V

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

valueOf(String) - Static method in enum org.biojava.nbio.survival.cox.CoxMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.survival.cox.ResidualsCoxph.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.biojava.nbio.survival.cox.CoxMethod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.survival.cox.ResidualsCoxph.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfLower

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.ConfType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Error

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM.Method

Returns an array containing the constants of this enum type, 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(Collection<String>, Collection<String>) - Constructor for class org.biojava.nbio.survival.data.WorkSheet

WorkSheet(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

A B C D E F G H I K L M N O P R S T U V W X Y Z