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java.lang.Objecthalo.userinterface.gui.GuiFilterData
public class GuiFilterData
'Interface' which connects GUI and loading/filtering methods for data
Field Summary | |
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static java.lang.String |
PQS
|
static java.lang.String |
PQSMIN
|
static java.lang.String |
PRESENT
|
static java.lang.String |
THRESHOLD
|
Constructor Summary | |
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GuiFilterData()
Constructor creating an object of GuiFilterData |
Method Summary | |
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void |
addAttr(java.io.File file,
java.util.ArrayList<java.lang.String> labels)
Extracts a new attribute from a given file and adds it to the data |
void |
addAttributesList(java.util.ArrayList<Mapping<java.lang.String,java.lang.String>> list,
java.lang.String[] attrDescr)
Adds a list of attributes to the data, as well as the corresponding descriptors |
void |
addFasta(java.io.File file,
int column)
Adds the necessary information for the multiple fasta file; its location and the column containing the gene name |
void |
addMethod(java.lang.String method,
java.lang.String filterValue)
Adds a filtering method and a corresponding value, e.g. a threshold |
void |
addOriginalAttr(java.util.ArrayList<java.lang.String> labels,
boolean calls)
|
void |
evaluateFasta(java.lang.String uraMeth,
java.lang.String printName,
java.util.HashMap<java.lang.String,java.lang.Double> corr,
boolean plot)
Starts the evaluation using the multiple fasta file |
java.lang.String[] |
getAttrDescr()
Returns the descriptors for the attribute list |
java.util.ArrayList<Mapping<java.lang.String,java.lang.String>> |
getAttributesList()
Returns the list of attributes for the data |
double |
getAvgL()
Returns the average log(e'/n') |
double |
getAvgU()
Returns the average number of uracils |
int |
getColumn()
Returns the column of the fasta header that keeps the gene name |
Data |
getData()
Returns the complete Data object |
java.io.File |
getFasta()
Returns the file containing the sequences for the data |
java.lang.String |
getGenename()
Returns the name of the column with gene names |
java.util.List<java.lang.String> |
getMethods()
Returns the list of filtering methods |
java.util.List<java.lang.String> |
getOriginalAtts()
Returns the attributes from the datafile |
java.lang.String |
getOriginalGene()
Returns the original name of the gene attribute |
java.lang.String |
getPlotName()
Returns the name of the file containing the plotting information for evaluation |
int |
getSize()
Returns the size of the data after the performed filtering steps |
java.lang.String |
getSpotid()
Returns the name of the column with spotIDs |
boolean |
hasData()
Checks whether Data has been set |
boolean |
hasGeneNames()
Checks whether the attribute containing gene names for each spot has been set |
boolean |
hasGenes()
Checks whether the multiple fasta file containing the sequences has been set and whether the attribute describing the gene names for each spot exists |
boolean |
hasNormalization()
Checks whether normalization has been performed |
boolean |
isCalls()
Returns status of attributes in original file: present calls? |
boolean |
isLog()
Returns scale of data (log or linear) |
void |
loadData()
Creates a Data object from previously set variables |
void |
prepareData()
Filters a previously loaded Data object according to the set methods |
void |
saveData()
Saves the Data object into a file |
void |
setAttributes(java.util.List<java.lang.String> attributes)
Sets the list of attributes corresponding to the data |
void |
setAttributesInFile(boolean attributesInFile)
Sets a variable that remembers if attributes were loaded from original file |
void |
setAttributesOut(java.util.List<java.lang.String> attributesOut)
Sets the list of attributes for output |
void |
setCombined(boolean combined)
Defines whether single or combined filtering should be performed |
void |
setFasta(java.lang.String fasta,
int column)
Sets the file containing the sequences for the data, as well as the column defining where the gene name is found in the header of each sequence |
void |
setFile(java.io.File file)
Sets the file containing the initial data |
void |
setFirst(boolean first)
Sets status if data is loaded for the first time |
void |
setGenename(java.lang.String genename)
Sets the name of the gene name attribute |
void |
setLabelsNew(java.util.List<java.lang.String> lab)
Sets the column labels for newly transcribed RNA that will be read in |
void |
setLabelsPre(java.util.List<java.lang.String> lab)
Sets the column labels for pre-existing RNA that will be read in |
void |
setLabelsTot(java.util.List<java.lang.String> lab)
Sets the column labels for total RNA that will be read in |
void |
setLog(boolean log)
Sets the scale; true for log scale, false for linear |
void |
setMethods(java.util.List<java.lang.String> methods)
Sets the list of filtering methods |
void |
setNewOut(java.util.List<java.lang.String> lab)
Sets the column labels for newly transcribed RNA that will be written into the output |
void |
setNorm(Normalization norm)
Sets the normalization object needed for evaluation |
void |
setOriginalAtts(java.util.List<java.lang.String> originalAtts)
Sets the attributes from the data file |
void |
setOutput(java.io.File outputFile)
Sets the file in which the filtered data will be written |
void |
setPQSName(java.lang.String pqs)
Sets the name of the file in which the quality scores will be written |
void |
setPqsPlot(boolean pqsPlot)
Sets the pqs-plot variable |
void |
setPreOut(java.util.List<java.lang.String> lab)
Sets the column labels for pre-existing RNA that will be written into the output |
void |
setSpotid(java.lang.String spot)
Sets the name of the column with probe-set-ids |
void |
setTotOut(java.util.List<java.lang.String> lab)
Sets the column labels for total RNA that will be written into the output |
void |
setTurnReverseMapOff(boolean turnReverseMapOff)
Should be set true for present calls |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final java.lang.String THRESHOLD
public static final java.lang.String PRESENT
public static final java.lang.String PQSMIN
public static final java.lang.String PQS
Constructor Detail |
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public GuiFilterData()
Method Detail |
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public void loadData()
public void prepareData()
public void evaluateFasta(java.lang.String uraMeth, java.lang.String printName, java.util.HashMap<java.lang.String,java.lang.Double> corr, boolean plot)
public void saveData()
public boolean hasData()
public boolean hasNormalization()
public boolean hasGenes()
public boolean hasGeneNames()
public void addAttr(java.io.File file, java.util.ArrayList<java.lang.String> labels)
file
- The file containing the attributepublic void addOriginalAttr(java.util.ArrayList<java.lang.String> labels, boolean calls)
public void addAttributesList(java.util.ArrayList<Mapping<java.lang.String,java.lang.String>> list, java.lang.String[] attrDescr)
list
- A list of different attributes, each mapped to spotsattrDescr
- A descriptor which holds the name of each attributepublic void addFasta(java.io.File file, int column)
file
- The multiple fasta file containing sequences of the datacolumn
- The 'column' of the fasta header which contains the
gene name; columns are divided by '|'public void addMethod(java.lang.String method, java.lang.String filterValue)
method
- The name of a filtering methodfilterValue
- The value used in this filtering method, e.g. a thresholdpublic void setAttributesOut(java.util.List<java.lang.String> attributesOut)
attributesOut
- List of attributes for outputpublic void setOriginalAtts(java.util.List<java.lang.String> originalAtts)
originalAtts
- Attributes from the data filepublic void setFile(java.io.File file)
file
- The file containing the expression datapublic void setAttributesInFile(boolean attributesInFile)
attributesInFile
- TRUE if attributes are contained in data filepublic void setPqsPlot(boolean pqsPlot)
pqsPlot
- TRUE if pqs should be plotted, FALSE otherwisepublic void setTurnReverseMapOff(boolean turnReverseMapOff)
turnReverseMapOff
- TRUE for present callspublic void setLog(boolean log)
log
- TRUE for log scale, false for linear scalepublic void setGenename(java.lang.String genename)
genename
- The name of the gene name attribute in the datapublic void setSpotid(java.lang.String spot)
spot
- The name of the column with spot-idspublic void setLabelsNew(java.util.List<java.lang.String> lab)
lab
- The list of column labels for newly transcribed RNApublic void setLabelsPre(java.util.List<java.lang.String> lab)
lab
- The list of column labels for pre-existing RNApublic void setLabelsTot(java.util.List<java.lang.String> lab)
lab
- The list of column labels for total RNApublic void setNewOut(java.util.List<java.lang.String> lab)
lab
- The list of column labels for newly transcribed RNApublic void setPreOut(java.util.List<java.lang.String> lab)
lab
- The list of column labels for pre-existing RNApublic void setTotOut(java.util.List<java.lang.String> lab)
lab
- The list of column labels for total RNApublic void setAttributes(java.util.List<java.lang.String> attributes)
attributes
- The list of attributespublic void setMethods(java.util.List<java.lang.String> methods)
methods
- The list of filtering methodspublic void setFasta(java.lang.String fasta, int column)
fasta
- The name of the multiple fasta file containing
sequences corresponding to the datacolumn
- The 'column' of the fasta header which keeps
the gene name; columns are separated by '|'public void setOutput(java.io.File outputFile)
outputFile
- The file which will hold the filtered datapublic void setFirst(boolean first)
first
- TRUE if data is loaded for the first timepublic void setNorm(Normalization norm)
norm
- The normalization object needed for evaluationpublic void setCombined(boolean combined)
combined
- TRUE if all filtering steps should be performed togetherpublic void setPQSName(java.lang.String pqs)
pqs
- The name of the file holding the quality scorespublic Data getData()
public java.lang.String getSpotid()
public boolean isCalls()
public boolean isLog()
public java.util.List<java.lang.String> getOriginalAtts()
public java.lang.String getGenename()
public java.lang.String getOriginalGene()
public java.io.File getFasta()
public int getColumn()
public int getSize()
public java.util.List<java.lang.String> getMethods()
public java.lang.String[] getAttrDescr()
public java.util.ArrayList<Mapping<java.lang.String,java.lang.String>> getAttributesList()
public double getAvgU()
public double getAvgL()
public java.lang.String getPlotName()
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