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java.lang.Objectuserinterface.gui.Session
public class Session
Contains all information of a current session, as well as methods for saving and loading
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.lang.String[] |
getAttrDescr()
Returns the names of the attributes for the data |
java.util.ArrayList<Mapping<java.lang.String,java.lang.String>> |
getAttributes()
Returns the list of all attributes |
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> |
getColumnsNewAll()
Returns the list of column labels for newly transcribed RNA, all that are in the data file |
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> |
getColumnsPreAll()
Returns the list of column labels for pre-existing RNA, all that are in the data file |
java.util.List<java.lang.String> |
getColumnsTotal()
Returns the list of column labels for total RNA, only the extracted ones |
java.util.List<java.lang.String> |
getColumnsTotalAll()
Returns the list of column labels for total RNA, all that are in the data file |
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 |
GuiFilterData |
getGuiData()
Returns the interface connecting GUI and filtering of the data |
GuiHalfLife |
getGuiHL()
Returns the interface connecting GUI and half life calculation |
GuiLinReg |
getGuiLR()
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 |
java.util.ArrayList<java.lang.String> |
getLabels()
Returns all the labels available in the data file |
java.lang.String |
getLrMethod()
Returns the name of the linear regression method |
int |
getPosX()
Returns x position of the window |
int |
getPosY()
Returns y position of the window |
int |
getRatioMethod()
Returns the ratio calculation method |
java.util.List<java.lang.Integer> |
getReplicate()
Returns the replicate number used for calculation |
java.util.List<java.lang.Integer> |
getTimes()
Returns the list of time points used for half life calculation |
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 |
isCheckLR()
Returns information on the checked status of the checkbox for linear regression |
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 |
void |
load(java.io.File sessFile)
Loads a session from a given file |
void |
setAttrDescr(java.lang.String[] attrDescr)
Sets the descriptor for the attributes |
void |
setAttributes(java.util.ArrayList<Mapping<java.lang.String,java.lang.String>> attributes)
Sets the list containing all the attributes of the data, each mapped to the spots |
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 |
setCheckLR(boolean checkLR)
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 |
setColumnsNewAll(java.util.List<java.lang.String> columnsNewAll)
Sets the list of column labels for newly transcribed RNA, all those labels that are available in the data file |
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 |
setColumnsPreAll(java.util.List<java.lang.String> columnsPreAll)
Sets the list of column labels for pre-existing RNA, all those labels that are available in the data file |
void |
setColumnsTotal(java.util.List<java.lang.String> columnsTotal)
Sets the list of column labels for total RNA, only those that are extracted |
void |
setColumnsTotalAll(java.util.List<java.lang.String> columnsTotalAll)
Sets the list of column labels for total RNA, all those labels that are available in the data file |
void |
setData(Data data)
Sets the data object needed for linear regression |
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 |
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 |
setGuiLR(GuiLinReg guiLR)
Sets the interface between GUI and linear regression |
void |
setHlMethods(java.util.List<java.lang.String> hlMethods)
Sets the list of descriptions of half life calculation methods |
void |
setLabels(java.util.ArrayList<java.lang.String> labels)
Sets the list of all labels from the data file |
void |
setLrMethod(java.lang.String lrMethod)
Sets the list of methods for linear regression |
void |
setMaxim(int m)
Sets the attribute containing information if the window is maximized or not |
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(java.util.List<java.lang.Integer> replicate)
Sets the (column) number of the used replicate |
void |
setTimes(java.util.List<java.lang.Integer> 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 |
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 void load(java.io.File sessFile)
sessFile
- File containing session informationpublic void setAttrDescr(java.lang.String[] attrDescr)
attrDescr
- The list of names of the attributes
of the datapublic void setReplicate(java.util.List<java.lang.Integer> replicate)
replicate
- Number of the replicate used for calculationpublic void setAttributes(java.util.ArrayList<Mapping<java.lang.String,java.lang.String>> attributes)
attributes
- The list of attributespublic 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 setCheckLR(boolean checkLR)
checkLR
- True, if linear regression is checkedpublic 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 setColumnsNewAll(java.util.List<java.lang.String> columnsNewAll)
columnsNewAll
- The list of all 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 setColumnsPreAll(java.util.List<java.lang.String> columnsPreAll)
columnsPreAll
- The list of all 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 setColumnsTotalAll(java.util.List<java.lang.String> columnsTotalAll)
columnsTotalAll
- The list of all column labels for total RNApublic void setLrMethod(java.lang.String lrMethod)
lrMethod
- The list of methods for linear regressionpublic void setData(Data data)
data
- The data object needed for regressionpublic 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 setGuiLR(GuiLinReg guiLR)
guiLR
- The GuiLinReg object connecting GUI
and linear regressionpublic 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.Integer> 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 setFasta(java.io.File file)
file
- The multiple fasta file for the datapublic void setColumn(int column)
column
- The column which holds the gene namepublic void setDataMethods(java.util.List<java.lang.String> dataMethods)
dataMethods
- The list of filtering methodspublic java.util.List<java.lang.Integer> getReplicate()
public java.util.List<java.lang.String> getColumnsNew()
public java.util.List<java.lang.String> getColumnsNewAll()
public java.util.List<java.lang.String> getColumnsPre()
public java.util.List<java.lang.String> getColumnsPreAll()
public java.util.List<java.lang.String> getColumnsTotal()
public java.util.List<java.lang.String> getColumnsTotalAll()
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 GuiLinReg getGuiLR()
public java.util.List<java.lang.String> getHlMethods()
public java.util.ArrayList<java.lang.String> getLabels()
public java.lang.String getLrMethod()
public int getRatioMethod()
public java.util.List<java.lang.Integer> getTimes()
public java.lang.String[] getAttrDescr()
public java.util.ArrayList<Mapping<java.lang.String,java.lang.String>> getAttributes()
public boolean isCheckAbs()
public boolean isCheckHL()
public boolean isCheckFilt()
public boolean isCheckLR()
public boolean isCheckPQS()
public boolean isCheckPQSMin()
public boolean isCheckThresh()
public int getPosX()
public int getPosY()
public boolean isMaxim()
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