public class AnalysisData
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
java.util.SortedMap<IndexedString,java.lang.String> |
conditions |
java.io.File |
conditionsFile |
protected int |
countReadsThreshold |
java.io.File |
expressionFile |
protected java.io.File |
finalConditionsFile |
protected java.io.File |
finalCountReadsFile |
protected boolean |
hasReplicates |
Spreadsheet.Info |
info |
protected boolean |
moreThanTwoConditions |
protected Global.RoundingMode |
roundMode |
Constructor and Description |
---|
AnalysisData(java.io.File expressionFile,
java.io.File conditionsFile,
Spreadsheet.Info info,
java.lang.String roundMode,
int countReadsThreshold) |
AnalysisData(java.io.File expressionFile,
java.util.SortedMap<IndexedString,java.lang.String> conditions,
Spreadsheet.Info info,
java.lang.String roundMode,
int countReadsThreshold) |
Modifier and Type | Method and Description |
---|---|
static java.util.SortedMap<IndexedString,java.lang.String> |
applyConditionsToExprFileSamples(java.io.File exprFile,
Spreadsheet.Info info,
java.util.SortedMap<IndexedString,java.lang.String> cond) |
static void |
createConditionsFile(java.io.File file,
java.util.SortedMap<IndexedString,java.lang.String> conditions,
boolean makeHeader,
boolean writeNotUses) |
private void |
defaultBuilderOperations(java.io.File expressionFile,
java.io.File conditionsFile,
Spreadsheet.Info info,
java.lang.String roundMode,
int countReadsThreshold) |
protected boolean |
filterValues(int[] values) |
java.lang.String |
getConditionOf(java.lang.String name) |
static java.util.SortedMap<IndexedString,java.lang.String> |
getConditionsFromExpressionFile(java.io.File file,
Spreadsheet.Info info) |
java.util.Set<java.util.Map.Entry<IndexedString,java.lang.String>> |
getNamesAndConditions() |
int |
getNumberOfConditions() |
int |
getNumberOfGenes() |
int |
getNumberOfSamples() |
boolean |
hasMoreThanTwoConditions() |
boolean |
hasReplicatesInSamples() |
static java.util.SortedMap<IndexedString,java.lang.String> |
loadConditionsFromFile(java.io.File file) |
int |
numberOfColunns() |
protected int[] |
roundValuesAndEraseNotUse(java.lang.String[] values,
java.lang.String[] names) |
void |
setConditionOf(java.lang.String name,
java.lang.String condition) |
void |
setConditions(java.util.SortedMap<IndexedString,java.lang.String> newCond) |
void |
setConditionsFile(java.io.File file) |
void |
setCountReadsFile(java.io.File file) |
private void |
writeCountReadsWithoutConditions() |
void |
writeExpression() |
protected void |
writeFinalConditions() |
public Spreadsheet.Info info
public java.io.File conditionsFile
public java.io.File expressionFile
public java.util.SortedMap<IndexedString,java.lang.String> conditions
protected int countReadsThreshold
protected Global.RoundingMode roundMode
protected boolean hasReplicates
protected boolean moreThanTwoConditions
protected java.io.File finalCountReadsFile
protected java.io.File finalConditionsFile
public AnalysisData(java.io.File expressionFile, java.io.File conditionsFile, Spreadsheet.Info info, java.lang.String roundMode, int countReadsThreshold) throws java.io.IOException
java.io.IOException
public AnalysisData(java.io.File expressionFile, java.util.SortedMap<IndexedString,java.lang.String> conditions, Spreadsheet.Info info, java.lang.String roundMode, int countReadsThreshold) throws java.io.IOException
java.io.IOException
public static java.util.SortedMap<IndexedString,java.lang.String> applyConditionsToExprFileSamples(java.io.File exprFile, Spreadsheet.Info info, java.util.SortedMap<IndexedString,java.lang.String> cond)
private void defaultBuilderOperations(java.io.File expressionFile, java.io.File conditionsFile, Spreadsheet.Info info, java.lang.String roundMode, int countReadsThreshold) throws java.io.IOException
java.io.IOException
public void setCountReadsFile(java.io.File file)
public void setConditionsFile(java.io.File file)
public void setConditions(java.util.SortedMap<IndexedString,java.lang.String> newCond)
public boolean hasReplicatesInSamples()
public boolean hasMoreThanTwoConditions()
public java.util.Set<java.util.Map.Entry<IndexedString,java.lang.String>> getNamesAndConditions()
public int numberOfColunns()
public int getNumberOfSamples()
public void setConditionOf(java.lang.String name, java.lang.String condition)
public java.lang.String getConditionOf(java.lang.String name)
public int getNumberOfGenes()
public int getNumberOfConditions()
public static java.util.SortedMap<IndexedString,java.lang.String> loadConditionsFromFile(java.io.File file)
public static java.util.SortedMap<IndexedString,java.lang.String> getConditionsFromExpressionFile(java.io.File file, Spreadsheet.Info info)
protected void writeFinalConditions()
public static void createConditionsFile(java.io.File file, java.util.SortedMap<IndexedString,java.lang.String> conditions, boolean makeHeader, boolean writeNotUses)
public void writeExpression()
private void writeCountReadsWithoutConditions() throws java.io.IOException
java.io.IOException
protected int[] roundValuesAndEraseNotUse(java.lang.String[] values, java.lang.String[] names)
protected boolean filterValues(int[] values)