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java.lang.Objectuserinterface.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)
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 |
evaluateFasta()
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.util.List<java.lang.String> |
getMethods()
Returns the list of filtering methods |
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 |
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 |
hasLinReg()
|
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 |
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 |
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 |
setLR(LinearRegression lr)
Sets the linear regression object needed for evaluation |
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 |
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 |
setPreOut(java.util.List<java.lang.String> lab)
Sets the column labels for pre-existing RNA that will be written into the output |
void |
setTotOut(java.util.List<java.lang.String> lab)
Sets the column labels for total RNA that will be written into the output |
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()
public void saveData()
public boolean hasData()
public boolean hasLinReg()
public boolean hasGenes()
public boolean hasGeneNames()
public void addAttr(java.io.File file)
file
- The file containing the attributepublic 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 setFile(java.io.File file)
file
- The file containing the expression datapublic 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 setLR(LinearRegression lr)
lr
- The linear regression object needed for evaluationpublic void setPQSName(java.lang.String pqs)
pqs
- The name of the file holding the quality scorespublic Data getData()
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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