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java.lang.Objecthalo.userinterface.gui.session.Session
public class Session
Contains all information of a current session, as well as methods for saving and loading
Field Summary | |
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static java.lang.String |
ALPHACELLDIV
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static java.lang.String |
ALPHACONSTANT
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Constructor Summary | |
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Session()
Constructs a new session with a default file name |
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Session(java.io.File file)
Constructs a new session |
Method Summary | |
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java.io.File |
downloadFile(java.io.File output,
java.lang.String address)
Downloads a file from a given address |
java.lang.String |
getAlpha()
Returns the name of the used alpha function |
java.lang.String[] |
getAttrDescr()
Returns the names of the attributes for the data |
java.util.List<java.lang.String> |
getAttributeFiles()
Returns the list of attribute file names |
java.util.ArrayList<java.util.ArrayList<java.lang.String>> |
getAttributeLabels()
Returns the list of attribute label names |
java.util.ArrayList<java.lang.String> |
getAttributes()
Returns the list of all attributes |
double |
getCcl()
Returns the value of the parameter ccl |
java.util.List<java.lang.String> |
getColumnsNew()
Returns the list of column labels for newly transcribed RNA, only the extracted ones |
java.util.List<java.lang.String> |
getColumnsPre()
Returns the list of column labels for pre-existing RNA, only the extracted ones |
java.util.List<java.lang.String> |
getColumnsTotal()
Returns the list of column labels for total RNA, only the extracted ones |
Data |
getData()
Returns the data object |
java.io.File |
getDataFile()
Returns the file from which the data was extracted |
java.util.List<java.lang.String> |
getDataMethods()
Returns the list of filtering methods |
java.lang.StringBuffer |
getDisplay()
Returns the description of half-life calculation methods and time points |
java.lang.String |
getGeneLabel()
Returns the saved gene label |
GuiFilterData |
getGuiData()
Returns the interface connecting GUI and filtering of the data |
GuiHalfLife |
getGuiHL()
Returns the interface connecting GUI and half-life calculation |
GuiNormal |
getGuiNorm()
Returns the interface connecting GUI and linear regression |
java.util.List<java.lang.String> |
getHlMethods()
Returns the list of methods used for half-life calculation |
double |
getLabelingTime()
Returns the labeling time |
java.util.ArrayList<java.lang.String> |
getLabels()
Returns all the labels available in the data file |
java.lang.String |
getNormMethod()
Returns the name of the normalization method |
java.util.List<java.lang.String> |
getOriginalLabelsCalls()
Returns the list of attributes from the original file (present calls) |
java.util.List<java.lang.String> |
getOriginalLabelsOther()
Returns the list of attributes from the original file (no present calls) |
java.lang.String |
getPathR()
Returns the path to R |
int |
getPosX()
Returns x position of the window |
int |
getPosY()
Returns y position of the window |
int |
getRatioMethod()
Returns the ratio calculation method |
int |
getReplicate()
Returns the constant replicate |
java.util.List<java.lang.Integer> |
getReplicates()
Returns the replicate number used for calculation |
java.util.List<java.lang.Double> |
getTimes()
Returns the list of time points used for half-life calculation |
boolean |
isCalls()
Returns status of attributes from original file: present calls? |
boolean |
isCheckAbs()
Returns information on the checked status of the checkbox for the filtering method 'absence' |
boolean |
isCheckFilt()
Returns information on the checked status of the checkbox for filtering |
boolean |
isCheckHL()
Returns information on the checked status of the checkbox for half-life calculation |
boolean |
isCheckNorm()
Returns information on the checked status of the checkbox for normalization |
boolean |
isCheckPQS()
Returns information on the checked status of the checkbox for the filtering method 'pqs' |
boolean |
isCheckPQSMin()
Returns information on the checked status of the checkbox for the filtering method 'pqs min' |
boolean |
isCheckThresh()
Returns information on the checked status of the checkbox for the filtering method 'threshold' |
boolean |
isMaxim()
Returns maximized status |
boolean |
isPlotQuality()
Returns status of quality plotting |
boolean |
load(java.io.File sessFile)
Loads a session from a given file |
void |
setAlpha(java.lang.String alpha)
Sets the name of the used alpha function |
void |
setAttrDescr(java.lang.String[] attrDescr)
Sets the descriptor for the attributes |
void |
setAttributeFiles(java.util.List<java.lang.String> attributeFiles)
Sets the list of attribute files |
void |
setAttributeLabels(java.util.ArrayList<java.util.ArrayList<java.lang.String>> attributeLabels)
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void |
setAttributes(java.util.ArrayList<java.lang.String> attributes)
Sets the list of attribute labels |
void |
setCalls(boolean calls)
Sets status of attributes from original file |
void |
setCcl(double ccl)
Sets the value of the parameter ccl |
void |
setCheckAbs(boolean checkAbs)
Sets the value holding information on the checked status of the filtering method 'absence' |
void |
setCheckFilt(boolean checkFilt)
Sets the value holding information on the checked status of the checkbox that expands the filtering menu |
void |
setCheckHL(boolean checkHL)
Sets the value holding information on the checked status of the checkbox that expands the half-life calculation |
void |
setCheckNorm(boolean checkNorm)
Sets the value holding information on the checked status of the checkbox that expands the linear regression |
void |
setCheckPQS(boolean checkPQS)
Sets the value holding information on the checked status of the filtering method 'pqs' |
void |
setCheckPQSMin(boolean checkPQSMin)
Sets the value holding information on the checked status of the filtering method 'pqs min' |
void |
setCheckThresh(boolean checkThresh)
Sets the value holding information on the checked status of the filtering method 'threshold' |
void |
setColumn(int column)
Sets the column of the multiple fasta file header which holds the gene name |
void |
setColumnsNew(java.util.List<java.lang.String> columnsNew)
Sets the list of column labels for newly transcribed RNA, only those that are extracted |
void |
setColumnsPre(java.util.List<java.lang.String> columnsPre)
Sets the list of column labels for pre-existing RNA, only those that are extracted |
void |
setColumnsTotal(java.util.List<java.lang.String> columnsTotal)
Sets the list of column labels for total RNA, only those that are extracted |
void |
setData(Data data)
Sets the data object needed for normalization |
void |
setDataFile(java.io.File dataFile)
Sets the file containing the data |
void |
setDataMethods(java.util.List<java.lang.String> dataMethods)
Sets the list of filtering methods |
void |
setDisplay(java.lang.StringBuffer display)
Sets the description of all used half-life calculation methods |
void |
setFasta(java.io.File file)
Sets the file which contains the sequences for the data |
void |
setFile(java.io.File file)
Sets the file into which the session will be saved |
void |
setGeneLabel(java.lang.String geneLabel)
Sets the gene name label |
void |
setGuiData(GuiFilterData guiData)
Sets the interface between GUI and data handling |
void |
setGuiHL(GuiHalfLife guiHL)
Sets the interface between GUI and half-life calculation |
void |
setGuiNorm(GuiNormal guiNorm)
Sets the interface between GUI and normalization |
void |
setHlMethods(java.util.List<java.lang.String> hlMethods)
Sets the list of descriptions of half-life calculation methods |
void |
setLabelingTime(double labelingTime)
Sets the constant labeling time |
void |
setLabels(java.util.ArrayList<java.lang.String> labels)
Sets the list of all labels from the data file |
void |
setLog(boolean log)
Sets scale of data (log or linear) |
void |
setMaxim(int m)
Sets the attribute containing information if the window is maximized or not |
void |
setNormMethod(java.lang.String normMethod)
Sets the list of methods for normalization |
void |
setOriginalLabelsCalls(java.util.List<java.lang.String> originalLabels)
Sets the list of attributes from the original file (present calls) |
void |
setOriginalLabelsOther(java.util.List<java.lang.String> originalLabels)
Sets the list of attributes from the original file (no present calls) |
void |
setPathR(java.lang.String pathR)
Sets the constant path to R |
void |
setPlotQuality(boolean plotQuality)
Sets status of quality plotting |
void |
setPosX(int x)
Sets the x position of the window |
void |
setPosY(int y)
Sets the y position of the window |
void |
setRatioMethod(int ratioMethod)
Sets the ratio calculation method |
void |
setReplicate(int replicate)
Sets a constant replicate |
void |
setReplicates(java.util.List<java.lang.Integer> replicate)
Sets the (column) number of the used replicate |
void |
setTimes(java.util.List<java.lang.Double> times)
Sets the list of time points for half-life calculation |
void |
store()
Stores the session in the previously defined file |
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 ALPHACONSTANT
public static final java.lang.String ALPHACELLDIV
Constructor Detail |
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public Session(java.io.File file)
file
- The file into which the session will be savedpublic Session()
Method Detail |
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public void store()
public boolean load(java.io.File sessFile)
sessFile
- File containing session information
public java.io.File downloadFile(java.io.File output, java.lang.String address)
output
- The output fileaddress
- The URL address
public void setAlpha(java.lang.String alpha)
alpha
- The name of the used alpha functionpublic void setCcl(double ccl)
ccl
- The parameter cclpublic void setAttrDescr(java.lang.String[] attrDescr)
attrDescr
- The list of names of the attributes
of the datapublic void setReplicates(java.util.List<java.lang.Integer> replicate)
replicate
- Number of the replicate used for calculationpublic void setAttributes(java.util.ArrayList<java.lang.String> attributes)
attributes
- The list of attributespublic void setOriginalLabelsCalls(java.util.List<java.lang.String> originalLabels)
originalLabels
- List of attributes from original filepublic void setOriginalLabelsOther(java.util.List<java.lang.String> originalLabels)
originalLabels
- List of attributes from original filepublic void setAttributeFiles(java.util.List<java.lang.String> attributeFiles)
attributeFiles
- The list of attribute filespublic void setAttributeLabels(java.util.ArrayList<java.util.ArrayList<java.lang.String>> attributeLabels)
public void setCheckAbs(boolean checkAbs)
checkAbs
- True, if filtering method 'absence' is checkedpublic void setCheckFilt(boolean checkFilt)
checkFilt
- True, if filtering is checkedpublic void setCheckHL(boolean checkHL)
checkHL
- True, if half-life is checkedpublic void setCheckNorm(boolean checkNorm)
checkNorm
- True, if normalization is checkedpublic void setPlotQuality(boolean plotQuality)
plotQuality
- TRUE if quality plot has been performedpublic void setCheckPQS(boolean checkPQS)
checkPQS
- True, if filtering method 'pqs' is checkedpublic void setCheckPQSMin(boolean checkPQSMin)
checkPQSMin
- True, if filtering method 'pqs min' is checkedpublic void setCheckThresh(boolean checkThresh)
checkThresh
- True, if filtering method 'threshold' is checkedpublic void setPosX(int x)
x
- The x position of the windowpublic void setPosY(int y)
y
- The y position of the windowpublic void setRatioMethod(int ratioMethod)
ratioMethod
- The ratio calculation methodpublic void setMaxim(int m)
m
- True if the window is maximizedpublic void setColumnsNew(java.util.List<java.lang.String> columnsNew)
columnsNew
- The list of column labels for newly transcribed RNApublic void setColumnsPre(java.util.List<java.lang.String> columnsPre)
columnsPre
- The list of column labels for pre-existing RNApublic void setColumnsTotal(java.util.List<java.lang.String> columnsTotal)
columnsTotal
- The list of column labels for total RNApublic void setNormMethod(java.lang.String normMethod)
normMethod
- The list of methods for normalizationpublic void setData(Data data)
data
- The data object needed for normalizationpublic void setDataFile(java.io.File dataFile)
dataFile
- The file containing the datapublic void setDisplay(java.lang.StringBuffer display)
display
- The description of all half-life
calculation methods and time pointspublic void setGuiData(GuiFilterData guiData)
guiData
- The GuiFilterData object connecting GUI
and data handlingpublic void setGuiHL(GuiHalfLife guiHL)
guiHL
- The GuiHalfLife object connecting GUI
and half-life calculationpublic void setGuiNorm(GuiNormal guiNorm)
guiNorm
- The GuiLinReg object connecting GUI
and normalizationpublic void setLabels(java.util.ArrayList<java.lang.String> labels)
labels
- The list of labels from the data filepublic void setHlMethods(java.util.List<java.lang.String> hlMethods)
hlMethods
- The list of description of half-life methodspublic void setTimes(java.util.List<java.lang.Double> times)
times
- The list of time points for half-life calculationpublic void setFile(java.io.File file)
file
- The file into which the session will be savedpublic void setLabelingTime(double labelingTime)
labelingTime
- A constant labeling timepublic void setPathR(java.lang.String pathR)
pathR
- The path to the R bin folderpublic void setReplicate(int replicate)
replicate
- The constant replicatepublic void setFasta(java.io.File file)
file
- The multiple fasta file for the datapublic void setGeneLabel(java.lang.String geneLabel)
geneLabel
- The gene name labelpublic void setColumn(int column)
column
- The column which holds the gene namepublic void setCalls(boolean calls)
calls
- TRUE if attributes from original file are present callspublic void setDataMethods(java.util.List<java.lang.String> dataMethods)
dataMethods
- The list of filtering methodspublic void setLog(boolean log)
log
- TRUE if data is in log scalepublic java.lang.String getAlpha()
public double getCcl()
public java.util.List<java.lang.Integer> getReplicates()
public java.util.List<java.lang.String> getOriginalLabelsCalls()
public java.util.List<java.lang.String> getOriginalLabelsOther()
public double getLabelingTime()
public java.lang.String getPathR()
public int getReplicate()
public java.util.List<java.lang.String> getColumnsNew()
public java.util.List<java.lang.String> getColumnsPre()
public java.util.List<java.lang.String> getColumnsTotal()
public Data getData()
public java.io.File getDataFile()
public java.util.List<java.lang.String> getDataMethods()
public java.lang.StringBuffer getDisplay()
public GuiFilterData getGuiData()
public GuiHalfLife getGuiHL()
public GuiNormal getGuiNorm()
public java.util.List<java.lang.String> getHlMethods()
public java.util.ArrayList<java.lang.String> getLabels()
public java.lang.String getNormMethod()
public int getRatioMethod()
public java.util.List<java.lang.Double> getTimes()
public java.lang.String[] getAttrDescr()
public java.util.ArrayList<java.lang.String> getAttributes()
public java.util.List<java.lang.String> getAttributeFiles()
public java.lang.String getGeneLabel()
public java.util.ArrayList<java.util.ArrayList<java.lang.String>> getAttributeLabels()
public boolean isCalls()
public boolean isCheckAbs()
public boolean isCheckHL()
public boolean isCheckFilt()
public boolean isCheckNorm()
public boolean isCheckPQS()
public boolean isCheckPQSMin()
public boolean isCheckThresh()
public int getPosX()
public int getPosY()
public boolean isMaxim()
public boolean isPlotQuality()
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