public class RNASeq
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
java.util.SortedMap<IndexedString,java.lang.String> |
conditions |
java.io.File |
conditionsFile |
java.io.File |
expressionFile |
Spreadsheet.Info |
info |
Constructor and Description |
---|
RNASeq(java.io.File expressionFile,
java.io.File conditionsFile,
Spreadsheet.Info info) |
RNASeq(java.io.File expressionFile,
java.util.SortedMap<IndexedString,java.lang.String> conditions,
Spreadsheet.Info info) |
Modifier and Type | Method and Description |
---|---|
static void |
createConditionsFile(java.io.File file,
java.util.SortedMap<IndexedString,java.lang.String> conditions,
boolean makeHeader) |
private void |
defaultBuilderOperations(java.io.File expressionFile,
java.io.File conditionsFile,
Spreadsheet.Info info) |
java.lang.String |
getCondition(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() |
static java.util.SortedMap<IndexedString,java.lang.String> |
loadConditionsFromFile(java.io.File file) |
int |
numberOfColunns() |
void |
setCondition(java.lang.String name,
java.lang.String condition) |
void |
writeExpression() |
void |
writeFinalConditions() |
private void |
writeRNASeqWithoutConditions() |
public Spreadsheet.Info info
public java.io.File conditionsFile
public java.io.File expressionFile
public java.util.SortedMap<IndexedString,java.lang.String> conditions
public RNASeq(java.io.File expressionFile, java.io.File conditionsFile, Spreadsheet.Info info) throws java.io.IOException
java.io.IOException
public RNASeq(java.io.File expressionFile, java.util.SortedMap<IndexedString,java.lang.String> conditions, Spreadsheet.Info info) throws java.io.IOException
java.io.IOException
private void defaultBuilderOperations(java.io.File expressionFile, java.io.File conditionsFile, Spreadsheet.Info info) throws java.io.IOException
java.io.IOException
public java.util.Set<java.util.Map.Entry<IndexedString,java.lang.String>> getNamesAndConditions()
public int numberOfColunns()
public int getNumberOfSamples()
public void setCondition(java.lang.String name, java.lang.String condition)
public java.lang.String getCondition(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)
public void writeFinalConditions()
public static void createConditionsFile(java.io.File file, java.util.SortedMap<IndexedString,java.lang.String> conditions, boolean makeHeader)
public void writeExpression()
private void writeRNASeqWithoutConditions() throws java.io.IOException
java.io.IOException