Class SearchGUI.SGstate

java.lang.Object
  SearchGUI.SGstate

Enclosing class:

SearchGUI

 class SearchGUI.SGstate
extends java.lang.Object

Class SGstate contains the SearchGUI state as well as functions to maintain the state. List of functions ================= copyStateFromCvt() - copy the partial state from cvt Globals readSGstate() - read the state from a saved state file .ssg writeSGstate() - write the state to a saved state file .ssg copyGlobalsToSGstate() - save Globals instance in SGstate variables.

Field Summary

java.lang.String	classAsamples Currently specified EG samples assigned to class A.
java.lang.String	classBsamples Currently specified EG samples assigned to class B.
CvtTabDelim2HTML	cvt
int	dataPrecisionHTMLtable
boolean[]	egSelNamesFlag Number of EG samples selection Choice List.
boolean	evalSearchANDbooleanFlag Eval the search terms as an AND (if true) else OR (if false).
java.lang.String	filterRowStr Optional EG group filter if not null.
java.lang.String[]	flipColumnFile
java.lang.String[]	flipColumnName
java.lang.String[][]	flipColumnValues
java.lang.String[]	flipOrderHdrColList
java.lang.String[]	flipRowGSPIDfilters
boolean	flipTableUseExactMatchFlag
float	foldChangeThr Fold-change threshold value used from the Menu checkbox item foldChangeThrMCB for "Only keep genes/probes with |fold-change| >= threshold" that pops up a dialog to enter the threshold value between 0.0 and some large number.
boolean	foldChangeThrFlag
int	nEGSelNames Number of EG samples selection Choice List.
int	nEntries # of hash table entries after call readNameValuesHashTableFromFile()
int	nFlipColumns
int	nFlipOrderHdrColList
int	nRowGSPIDfilters
int	nStateEntries # of .sgs hash table entries
java.lang.String	outputSearchDir
boolean	reportFoldChangeFlag Flag for "Report Fold Change of 2 sample subsets" set by
java.lang.String[]	sampleRowFilter
boolean	sampleRowFilterALLflag
java.lang.String	searchResultsBaseFile Default Search-Results base file name if not null or "".
java.lang.String	searchTermFilterStr
java.lang.String	searchTermsDemoData The demo argument to load into the searchTermTextArea GUI Set by "-searchTermsDemoData:{list of search terms}"
java.lang.String	searchUserTermListColName The user column name to use when reading data from a user term list file Table to load into the the searchTermTextArea GUI.
java.lang.String	searchUserTermListFile The file name to use when reading data from a user term list file Table to load into the the searchTermTextArea GUI.
java.lang.String	searchUserTermListStr The user search terms list string to use when reading data from a user term list file Table to load into the the searchTermTextArea GUI.
java.lang.String	searchUserTermListTitle The user title string to use when reading data from a user term list file Table to load into the the searchTermTextArea GUI.
java.util.Hashtable	sgStateHT Hash table of .sgs values read
SearchGUI	sGui
boolean	showDataHeatmapFlipTableFlag
java.lang.String	sortFlipTableByColumnName

Constructor Summary

SearchGUI.SGstate(SearchGUI sGui)
SGstate() - Constructor

Method Summary

boolean	copyGlobalsToSGstate(Globals glb) copyGlobalsToSGstate() - copy Globals instance in SGstate variables.
boolean	copySGstateInstance(SearchGUI.SGstate sg) copySGstateInstance() - copy from SGstate instance values to this.
boolean	copyStateFromCvt(CvtTabDelim2HTML cvt) copyStateFromCvt() - copy the partial state from cvt Globals
java.lang.String	cvtSGstateToStr() cvtSGstateToStr() - convert SGstate vars.
java.lang.String	getStateStr() getStateStr() - generate tab-delim SGstate string for writing .sgs state.
boolean	getStateValue(java.lang.String key, boolean def) getStateValue() - get boolean PARAM and use default if not found.
float	getStateValue(java.lang.String key, float def) getStateValue() - get float PARAM and use default if not found.
int	getStateValue(java.lang.String key, int def) getStateValue() - get int PARAM and use default if not found.
long	getStateValue(java.lang.String key, long def) getStateValue() - get float PARAM and use default if not found.
java.lang.String	getStateValue(java.lang.String key, java.lang.String def) getStateValue() - get PARAM and use default if not found.
boolean	parseHTtoSGstate() parseHTtoSGstate() - parse .sgs state hashtable to SGstate variables.
java.util.Hashtable	readNameValuesHashTableFromFile(java.lang.String fileName, int hashTableSize) readNameValuesHashTableFromFile() - read hashtable tab-delim name-value pairs from a file.
boolean	readSGstateFile(java.lang.String stateFile) readSGstateFile() - read the SearchGUI State file stateFile with a .sgs file extension.
void	setStateHashtableForGetValue(java.util.Hashtable ht) setStateHashtableForGetValue() - set working H.T.
void	setStateHashtableForGetValue(java.util.Hashtable ht, int nEntriesVal) setStateHashtableForGetValue() - set working H.T.
boolean	writeSGstate(java.lang.String fileStr) writeSGstate() - write SearchGUI state to .sgs SGstate file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

sGui

public SearchGUI sGui

cvt

public CvtTabDelim2HTML cvt

sgStateHT

public java.util.Hashtable sgStateHT

Hash table of .sgs values read

nStateEntries

public int nStateEntries

# of .sgs hash table entries

nEntries

public int nEntries

# of hash table entries after call readNameValuesHashTableFromFile()

flipOrderHdrColList

public java.lang.String[] flipOrderHdrColList

nFlipOrderHdrColList

public int nFlipOrderHdrColList

nFlipColumns

public int nFlipColumns

flipColumnFile

public java.lang.String[] flipColumnFile

flipColumnName

public java.lang.String[] flipColumnName

flipColumnValues

public java.lang.String[][] flipColumnValues

sampleRowFilterALLflag

public boolean sampleRowFilterALLflag

sampleRowFilter

public java.lang.String[] sampleRowFilter

reportFoldChangeFlag

public boolean reportFoldChangeFlag

Flag for "Report Fold Change of 2 sample subsets" set by

foldChangeThrFlag

public boolean foldChangeThrFlag

foldChangeThr

public float foldChangeThr

Fold-change threshold value used from the Menu checkbox item foldChangeThrMCB for "Only keep genes/probes with |fold-change| >= threshold" that pops up a dialog to enter the threshold value between 0.0 and some large number.

dataPrecisionHTMLtable

public int dataPrecisionHTMLtable

sortFlipTableByColumnName

public java.lang.String sortFlipTableByColumnName

showDataHeatmapFlipTableFlag

public boolean showDataHeatmapFlipTableFlag

flipTableUseExactMatchFlag

public boolean flipTableUseExactMatchFlag

outputSearchDir

public java.lang.String outputSearchDir

searchResultsBaseFile

public java.lang.String searchResultsBaseFile

Default Search-Results base file name if not null or "". It is used for "-flipSaveOutputFile:{flipSaveOutputFile}" in the generated param map file.

searchTermsDemoData

public java.lang.String searchTermsDemoData

The demo argument to load into the searchTermTextArea GUI Set by "-searchTermsDemoData:{list of search terms}"

searchTermFilterStr

public java.lang.String searchTermFilterStr

searchUserTermListFile

public java.lang.String searchUserTermListFile

The file name to use when reading data from a user term list file Table to load into the the searchTermTextArea GUI. Set by "-searchUserTermList:{userListTable,colName,title string}"

searchUserTermListColName

public java.lang.String searchUserTermListColName

The user column name to use when reading data from a user term list file Table to load into the the searchTermTextArea GUI. Set by "-searchUserTermList:{userListTable,colName,title string}"

searchUserTermListTitle

public java.lang.String searchUserTermListTitle

The user title string to use when reading data from a user term list file Table to load into the the searchTermTextArea GUI. Set by "-searchUserTermList:{userListTable,colName,title string}"

searchUserTermListStr

public java.lang.String searchUserTermListStr

The user search terms list string to use when reading data from a user term list file Table to load into the the searchTermTextArea GUI. Set by "-searchUserTermList:{userListTable,colName,title string}"

evalSearchANDbooleanFlag

public boolean evalSearchANDbooleanFlag

Eval the search terms as an AND (if true) else OR (if false). Set by the andEGnamesRB and orEGnamesRB radio buttons and action commands.

filterRowStr

public java.lang.String filterRowStr

Optional EG group filter if not null. This is set by the GUI JTextField filterRowTextField.

nEGSelNames

public int nEGSelNames

Number of EG samples selection Choice List. Used with boolean egSelNames[] data.

egSelNamesFlag

public boolean[] egSelNamesFlag

Number of EG samples selection Choice List. Used with boolean egSelNames[] data.

flipRowGSPIDfilters

public java.lang.String[] flipRowGSPIDfilters

nRowGSPIDfilters

public int nRowGSPIDfilters

classAsamples

public java.lang.String classAsamples

Currently specified EG samples assigned to class A. -flipAclass:"{classAsamples}" [if reportFoldChangeFlag]

classBsamples

public java.lang.String classBsamples

Currently specified EG samples assigned to class B. -flipBclass:"{classBsamples}" [if reportFoldChangeFlag].

Constructor Detail

SearchGUI.SGstate

public SearchGUI.SGstate(SearchGUI sGui)

SGstate() - Constructor

Parameters:

sGui - is an instance of the SearchGUI class

Method Detail

copyStateFromCvt

public boolean copyStateFromCvt(CvtTabDelim2HTML cvt)

copyStateFromCvt() - copy the partial state from cvt Globals

Parameters:

cvt - instance of CvtTabDelim2HTML

Returns:

true if succeed

copySGstateInstance

public boolean copySGstateInstance(SearchGUI.SGstate sg)

copySGstateInstance() - copy from SGstate instance values to this.

Parameters:

sg - - instance to copy FROM

Returns:

SGstate string in .sps file format. if succeed.

cvtSGstateToStr

public java.lang.String cvtSGstateToStr()

cvtSGstateToStr() - convert SGstate vars. to .sgs state string to write to file. It makes lists of variables of the form "param=value\n" called the .sgs file format.

Returns:

SGstate string in .sps file format. if succeed.

copyGlobalsToSGstate

public boolean copyGlobalsToSGstate(Globals glb)

copyGlobalsToSGstate() - copy Globals instance in SGstate variables. The file being imported was a previous paramsSearchFlip.map file created by createParamsMapFile().
This method parses and sets following parameters if the switch exists from the list:

   -flipOrderHdrColNames:"*LIST*,Stat5a,"
   -flipColumnName:"*LIST*,Gene,Stat5a,Stat5b"
   -flipColumnName:"*LIST*,Feature ID,1438470_at,1441476_at,1446085_at"
   -flipRowFilterNames:\"*LIST*,EG003.1,EG003.2"
  
   -flipRowGSPIDfilterSubstring:"AND,.stat,.GH"
   -flipAclass:"{classAsamples}"  [if reportFoldChangeFlag]
   -flipAclass:"{classBsamples}"  [if reportFoldChangeFlag]
   -flipFCthreshold:{foldChangeThr} [if foldChangeThrFlag && foldChangeThr>0.0F]
   -dataPrecisionHTMLtable:{precision of HTML table}
   -sortFlipTableByColumnName:{sort column}
   -showDataHeatmapFlipTable
   -flipUseExactColumnNameMatch:{glb.flipTableUseExactMatchFlag}
   -flipDirectory:"{outputSearchDir}"
   -flipSaveOutputFile:"{searchResultsBaseFile}"
 

Parameters:

glb - Globals instance of parsed data file

Returns:

true if succeed.

readSGstateFile

public boolean readSGstateFile(java.lang.String stateFile)

readSGstateFile() - read the SearchGUI State file stateFile with a .sgs file extension.

Parameters:

stateFile - is the name of the Flicker state file

Returns:

true if setup and parsed the .sgs hashtable correctly

parseHTtoSGstate

public boolean parseHTtoSGstate()

parseHTtoSGstate() - parse .sgs state hashtable to SGstate variables. It checks for each of the variables and then sets the corresponding SGstate variable.

Returns:

set the state variables if succeed and return true.

writeSGstate

public boolean writeSGstate(java.lang.String fileStr)

writeSGstate() - write SearchGUI state to .sgs SGstate file.

Parameters:

fileStr - - name of file to write

Returns:

true if succeed.

readNameValuesHashTableFromFile

public java.util.Hashtable readNameValuesHashTableFromFile(java.lang.String fileName,
                                                           int hashTableSize)

readNameValuesHashTableFromFile() - read hashtable tab-delim name-value pairs from a file. Convert the (name\tvalue\n) data to a hashtable.

Parameters:

fileName - is the name of the file to read

hashTableSize - initial size of hashtable

Returns:

hashtable else null if not found. The global variable nEntries contains the number of entries.

setStateHashtableForGetValue

public void setStateHashtableForGetValue(java.util.Hashtable ht,
                                         int nEntriesVal)

setStateHashtableForGetValue() - set working H.T. for next getStateValue calls

Parameters:

ht - is hashtable to use

nEntriesVal - is the number of elements used in the hash table.

setStateHashtableForGetValue

public void setStateHashtableForGetValue(java.util.Hashtable ht)

setStateHashtableForGetValue() - set working H.T. for next getStateValue calls

Parameters:

ht - is hashtable to use

getStateStr

public java.lang.String getStateStr()

getStateStr() - generate tab-delim SGstate string for writing .sgs state. The format is tab-delimited (name \t value \n) with one entry/line.

Returns:

the state string

getStateValue

public java.lang.String getStateValue(java.lang.String key,
                                      java.lang.String def)

getStateValue() - get PARAM and use default if not found.

getStateValue

public int getStateValue(java.lang.String key,
                         int def)

getStateValue() - get int PARAM and use default if not found.

getStateValue

public long getStateValue(java.lang.String key,
                          long def)

getStateValue() - get float PARAM and use default if not found.

getStateValue

public float getStateValue(java.lang.String key,
                           float def)

getStateValue() - get float PARAM and use default if not found.

getStateValue

public boolean getStateValue(java.lang.String key,
                             boolean def)

getStateValue() - get boolean PARAM and use default if not found.