Class MJAproperty

java.lang.Object
  |
  +--MJAbase
        |
        +--MJAproperty

public class MJAproperty

extends MJAbase

MAExplorer Open Java API class to access MJAproperty methods and data structures. Access get and put individual properties

List of methods available to Plugin-writers

 -------------------- GET STATE VARIABLES --------------------
 getUserName() - get current user login name if exists
 getPassword() - get current user password name if exists
 getProject() - get current project associated with database
 getRatioString() - get "F1/F2", "Cy3/Cy5" or "Cy5/Cy3", etc. string    
 getMaeCurProjectPath() - get path of current project MAExplorer
 getMaeBrowserTitle() - get current browser MAExplorer title.
 getMaeDatabaseTitle() - get current MAExplorer database title.
 getMaeDbSubsetTitle() - get current MAExplorer DB subset title.
 getFlourescentLabel1Name() - get current fluorescent label 1 name.
 getFlourescentLabel2Name() - get current fluorescent label 2 name.
 getReportFontSize() - get current Report font size
 getReportFontFamily() - get current Report font family
 getGEOplatformID() - get current GEO platform ID for this database
 getListOfGEOplatformsURL() - get URL for list of current GEO platforms 
 getFullGEOplatformDataTableURL() - get URL for current full GEO platform data table
 -------------------- SET STATE VARIABLES --------------------
 setGEOplatformID() - set current GEO platform ID for this database
 setListOfGEOplatformsURL() - set URL for list of current GEO platforms 
 setFullGEOplatformDataTableURL() - set URL for current full GEO platform data table
 -------------------- GET MODES ------------------------------
 getPosQuantTestMode() - get positive Quant data test mode
 getSpotIntensTestMode() - get spot intensity test mode
 getCVtestMode() - get Coefficient of Variation (CV) test mode
 getGoodSpotTestMode() - get Good Spot (QualCheck) test mode
 getReportTestMode() - get Report type mode
 getTblFmtMode() - get Report table format mode
 getSpotIntensRangeMode() - get Spot intensity range mode for filter
 getSpotIntensCompareMode() - get Spot Intensity compare  mode for filter
 getSampleIntensRangeMode() - get Sample intensity range restriction 
 getRatioRangeMode() - get Ratio range  for threshold mode
 getRatioCy3Cy5RangeMode() - get Cy3/Cy5 range mode for threshold filter
 getPlotModeImage() - get pseudoarray image plot mode
 getEditMode() - get EGL mode for 'edited gene list'
 getHierClustMode() - get hierarchical clustering linkage mode
 lookupRangeModeName() - lookup the inside/outside range Mode Name
 lookupompareModeName() - lookup the compare-criteria Mode Name
 lookupFilterSampleSubsetModeName() - lookup the sample-subset Mode Name 

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.

Version:

$Date: 2003/06/04 21:50:10 $ $Revision: 1.11 $

Author:

P. Lemkin (NCI), J. Evans (CIT), C. Santos (CIT), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD

See Also:

MAExplorer Home

Fields inherited from class MJAbase

COMPARE_ALL, COMPARE_ANY, COMPARE_AT_LEAST, COMPARE_AT_MOST, COMPARE_PRODUCT, COMPARE_SUM, DATA_F1TOT, DATA_F2TOT, DATA_MEAN_F1F2TOT, DATA_RATIO_F1F2TOT, DRAW_BIN, DRAW_BOX, DRAW_CIRCLE, DRAW_PLUS, EDIT_ADD, EDIT_NOP, EDIT_RMV, GENE_ATCC_ID, GENE_BAD_DATA, GENE_BAD_LOCAL_SPOT_BKGRD, GENE_BAD_MID, GENE_BAD_SPOT, GENE_BAD_SPOT_GEOMETRY, GENE_DUP_SPOT, GENE_GOOD_MID, GENE_IMAGE_ID, GENE_IS_CUR_GENE, GENE_IS_EGL_GENE, GENE_IS_FILTERED, GENE_IS_KMEANS, GENE_IS_NOT_FILTERED, GENE_LOW_SPOT_REF_SIGNAL, GENE_MARGINAL_SPOT, GENE_USE_GBID_FOR_CLONEID, HIER_CLUST_NEXT_MIN_LNKG, HIER_CLUST_PGMA_LNKG, HIER_CLUST_PGMC_LNKG, MARKER_CIRCLE, MARKER_CURRENT, MARKER_GENES, MARKER_KMEANS_CLUSTER, MARKER_NONE, MARKER_PLUS, MARKER_SQUARE, MASTER_CLONE_ID, MASTER_DBEST3, MASTER_DBEST5, MASTER_GENBANK, MASTER_GENBANK3, MASTER_GENBANK5, MASTER_GENE_NAME, MASTER_GENERIC_ID, MASTER_LOCUSLINK, MASTER_SWISS_PROT, MASTER_UG_ID, MASTER_UG_NAME, MAX_COLORS, PLOT_CLUSTER_GENES, PLOT_CLUSTER_HIER, PLOT_CLUSTER_HYBSAMPLES, PLOT_CLUSTERGRAM, PLOT_EXPR_PROFILE, PLOT_F1_F2_INTENS, PLOT_F1_F2_MVSA, PLOT_HIST_F1F2_RATIO, PLOT_HIST_HP_XY_RATIO, PLOT_HIST_HP_XY_SETS_RATIO, PLOT_HP_XY_INTENS, PLOT_INTENS_HIST, PLOT_KMEANS_CLUSTERGRAM, PLOT_PSEUDO_F1F2_IMG, PLOT_PSEUDO_F1F2_RYG_IMG, PLOT_PSEUDO_HP_XY_IMG, PLOT_PSEUDO_HP_XY_RYG_IMG, PLOT_PSEUDOIMG, PRPROP_CUR_GENE, PRPROP_FILTER, PRPROP_LABEL, PRPROP_SLIDER, PRPROP_TIMEOUT, PRPROP_UNIQUE, QUALTYPE_ALPHA, QUALTYPE_PROP_CODE, QUALTYPE_THR, RANGE_INSIDE, RANGE_OUTSIDE, RPT_FMT_DYN, RPT_FMT_TAB_DELIM, RPT_NONE, RPT_TBL_ALL_GENES_CLUSTER, RPT_TBL_CALIB_DNA_STAT, RPT_TBL_CUR_GENE_CLUSTER, RPT_TBL_EDITED_GENE_LIST, RPT_TBL_EXPR_PROFILE, RPT_TBL_FILTERED_GENES, RPT_TBL_GENE_CLASS, RPT_TBL_HIER_CLUSTER, RPT_TBL_HIGH_F1F2, RPT_TBL_HIGH_RATIO, RPT_TBL_HP_DB_INFO, RPT_TBL_HP_HP_CORR, RPT_TBL_HP_MN_VAR_STAT, RPT_TBL_HP_XY_SET_STAT, RPT_TBL_KMEANS_CLUSTER, RPT_TBL_LOW_F1F2, RPT_TBL_LOW_RATIO, RPT_TBL_MAE_PRJ_DB, RPT_TBL_MN_KMEANS_CLUSTER, RPT_TBL_NAMED_GENES, RPT_TBL_NORMALIZATION_GENE_LIST, RPT_TBL_OCL_STAT, RPT_TBL_SAMPLES_DB_INFO, RPT_TBL_SAMPLES_WEB_LINKS, SS_MODE_ELIST, SS_MODE_MS, SS_MODE_XANDY_SETS, SS_MODE_XORY_SETS, SS_MODE_XSET, SS_MODE_XY, SS_MODE_YSET

Method Summary

int	getCVtestMode() getCVtestMode() - get Coefficient of Variation (CV) test mode: SS_MODE_xxxx
int	getEditMode() getEditMode() - get EGL mode for 'edited gene list': EDIT_xxxx
java.lang.String	getFlourescentLabel1Name() getFlourescentLabel1Name() - get current fluorescent label 1 name.
java.lang.String	getFlourescentLabel2Name() getFlourescentLabel2Name() - get current fluorescent label 1 name.
java.lang.String	getFullGEOplatformDataTableURL() getFullGEOplatformDataTableURL() - get URL for current full GEO platform data table
java.lang.String	getGEOplatformID() getGEOplatformID() - get current GEO platform ID for this database
int	getGoodSpotTestMode() getGoodSpotTestMode() - get Good Spot (QualCheck) test mode: SS_MODE_xxxx
int	getHierClustMode() getHierClustMode() - get hierarchical clustering linkage mode: HIER_CLUST_xxxxx
java.lang.String	getListOfGEOplatformsURL() getListOfGEOplatformsURL() - get URL for list of current GEO platforms
java.lang.String	getMaeBrowserTitle() getMaeBrowserTitle() - get current browser MAExplorer title.
java.lang.String	getMaeCurProjectPath() getMaeCurProjectPath() - get path of current project MAExplorer session.
java.lang.String	getMaeDatabaseTitle() getMaeDatabaseTitle() - get current MAExplorer database title.
java.lang.String	getMaeDbSubsetTitle() getMaeDbSubsetTitle() - get current MAExplorer DB subset title.
java.lang.String	getPassword() getPassword() - get current user password name if exists
int	getPlotModeImage() getPlotModeImage() - get pseudoarray image plot mode: PLOT_xxxx_IMAGE
int	getPosQuantTestMode() getPosQuantTestMode() - get positive Quant data test mode: SS_MODE_xxxx
java.lang.String	getProject() getProject() - get current project associated with database
int	getRatioCy3Cy5RangeMode() getRatioCy3Cy5RangeMode() - get Cy3/Cy5 range restriction mode for threshold filter: RANGE_xxxx
int	getRatioRangeMode() getRatioRangeMode() - get Ratio range restriction for threshold mode: RANGE_xxxx
java.lang.String	getRatioString() getRatioString() - get "F1/F2", "Cy3/Cy5" or "Cy5/Cy3", or user-defined channels "channel1/channel2" etc.
java.lang.String	getReportFontFamily() getReportFontFamily() - get current Report font family
java.lang.String	getReportFontSize() getReportFontSize() - get current Report font size
int	getReportTestMode() getReportTestMode() - get Report type mode: 'RPT_xxxx'
int	getSampleIntensRangeMode() getSampleIntensRangeMode() - get Sample intensity range restriction mode for filter: RANGE_xxxx
int	getSpotIntensCompareMode() getSpotIntensCompareMode() - get Spot Intensity compare restriction mode for filter: COMPARE_xxxx
int	getSpotIntensRangeMode() getSpotIntensRangeMode() - get Spot intensity range restriction mode for filter: RANGE_xxxx
int	getSpotIntensTestMode() getSpotIntensTestMode() - get spot intensity test mode: SS_MODE_xxxx
int	getTblFmtMode() getTblFmtMode() - get Report table format mode: RPT_FMT_xxxx
java.lang.String	getUserName() getUserName() - get current user login name if exists
java.lang.String	lookupCompareModeName(int mode) lookupCompareModeName() - lookup the compare-criteria Mode Name for values COMPARE-xxxx.
java.lang.String	lookupFilterSampleSubsetModeName(int mode) lookupFilterSampleSubsetModeName() - lookup the sample-subset Mode Name for values SS_MODE-xxxx.
java.lang.String	lookupRangeModeName(int mode) lookupRangeModeName() - lookup the inside/outside range Mode Name for values RANGE-xxxx.
boolean	setFullGEOplatformDataTableURL(java.lang.String newFullGEOplatformDataTableURL) setFullGEOplatformDataTableURL() - set URL for current full GEO platform data table
boolean	setGEOplatformID(java.lang.String newGeoPlatformID) setGEOplatformID() - set current GEO platform ID for this database.
boolean	setListOfGEOplatformsURL(java.lang.String newListOfGEOplatformsURL) setListOfGEOplatformsURL() - set URL for list of current GEO platforms

Methods inherited from class MJAbase

cvtHashtable2SimpleTable, cvtTable2Hashtable

Methods inherited from class java.lang.Object

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

Method Detail

getUserName

public final java.lang.String getUserName()

getUserName() - get current user login name if exists

Returns:

value else null if not found.

getPassword

public final java.lang.String getPassword()

getPassword() - get current user password name if exists

Returns:

value else null if not found.

getProject

public final java.lang.String getProject()

getProject() - get current project associated with database

Returns:

value else null if not found.

getRatioString

public final java.lang.String getRatioString()

getRatioString() - get "F1/F2", "Cy3/Cy5" or "Cy5/Cy3", or user-defined channels "channel1/channel2" etc. as a string. The string is used to display ratio data labels in plots and reports.

Returns:

value else null if not found.

getMaeCurProjectPath

public final java.lang.String getMaeCurProjectPath()

getMaeCurProjectPath() - get path of current project MAExplorer session. The project contains the {MAE/ Quant/ Config/ State/ Report/ Cache/} sub directories.

Returns:

value

getMaeBrowserTitle

public final java.lang.String getMaeBrowserTitle()

getMaeBrowserTitle() - get current browser MAExplorer title.

Returns:

value

getMaeDatabaseTitle

public final java.lang.String getMaeDatabaseTitle()

getMaeDatabaseTitle() - get current MAExplorer database title.

Returns:

value

getMaeDbSubsetTitle

public final java.lang.String getMaeDbSubsetTitle()

getMaeDbSubsetTitle() - get current MAExplorer DB subset title.

Returns:

value

getFlourescentLabel1Name

public final java.lang.String getFlourescentLabel1Name()

getFlourescentLabel1Name() - get current fluorescent label 1 name.

Returns:

value

getFlourescentLabel2Name

public final java.lang.String getFlourescentLabel2Name()

getFlourescentLabel2Name() - get current fluorescent label 1 name.

Returns:

value

getReportFontSize

public final java.lang.String getReportFontSize()

getReportFontSize() - get current Report font size

Returns:

value which is "8pt", "10pt", or "12pt"

getReportFontFamily

public final java.lang.String getReportFontFamily()

getReportFontFamily() - get current Report font family

Returns:

value which is "Ariel", "Sans Serif", "Courier", etc.

getGEOplatformID

public final java.lang.String getGEOplatformID()

getGEOplatformID() - get current GEO platform ID for this database

Returns:

GEO platform ID of the form "GPInnn" (nnn is #) if it exists

getListOfGEOplatformsURL

public final java.lang.String getListOfGEOplatformsURL()

getListOfGEOplatformsURL() - get URL for list of current GEO platforms

Returns:

URL of list of GEO platforms if it exists, else null

getFullGEOplatformDataTableURL

public final java.lang.String getFullGEOplatformDataTableURL()

getFullGEOplatformDataTableURL() - get URL for current full GEO platform data table

Returns:

URL for current full GEO platform data table if it exists, else null

setGEOplatformID

public final boolean setGEOplatformID(java.lang.String newGeoPlatformID)

setGEOplatformID() - set current GEO platform ID for this database. The GEO platform ID is of the form "GPInnn" (nnn is #)

Parameters:

newGeoPlatformID - is the new value

Returns:

true if succeed

setListOfGEOplatformsURL

public final boolean setListOfGEOplatformsURL(java.lang.String newListOfGEOplatformsURL)

setListOfGEOplatformsURL() - set URL for list of current GEO platforms

Parameters:

newListOfGEOplatformsURL - is the new URL of list of GEO platforms

Returns:

true if succeed

setFullGEOplatformDataTableURL

public final boolean setFullGEOplatformDataTableURL(java.lang.String newFullGEOplatformDataTableURL)

setFullGEOplatformDataTableURL() - set URL for current full GEO platform data table

Parameters:

newFullGEOplatformDataTableURL - is the new URL for current full GEO platform data table

Returns:

true if succeed

getPosQuantTestMode

public final int getPosQuantTestMode()

getPosQuantTestMode() - get positive Quant data test mode: SS_MODE_xxxx

Returns:

value else null if not found.

getSpotIntensTestMode

public final int getSpotIntensTestMode()

getSpotIntensTestMode() - get spot intensity test mode: SS_MODE_xxxx

Returns:

value else null if not found.

getCVtestMode

public final int getCVtestMode()

getCVtestMode() - get Coefficient of Variation (CV) test mode: SS_MODE_xxxx

Returns:

value else null if not found.

getGoodSpotTestMode

public final int getGoodSpotTestMode()

getGoodSpotTestMode() - get Good Spot (QualCheck) test mode: SS_MODE_xxxx

Returns:

value else null if not found.

getReportTestMode

public final int getReportTestMode()

getReportTestMode() - get Report type mode: 'RPT_xxxx'

Returns:

value else null if not found.

getTblFmtMode

public final int getTblFmtMode()

getTblFmtMode() - get Report table format mode: RPT_FMT_xxxx

Returns:

value else null if not found.

getSpotIntensRangeMode

public final int getSpotIntensRangeMode()

getSpotIntensRangeMode() - get Spot intensity range restriction mode for filter: RANGE_xxxx

Returns:

value else null if not found.

getSpotIntensCompareMode

public final int getSpotIntensCompareMode()

getSpotIntensCompareMode() - get Spot Intensity compare restriction mode for filter: COMPARE_xxxx

Returns:

value else null if not found.

getSampleIntensRangeMode

public final int getSampleIntensRangeMode()

getSampleIntensRangeMode() - get Sample intensity range restriction mode for filter: RANGE_xxxx

Returns:

value else null if not found.

getRatioRangeMode

public final int getRatioRangeMode()

getRatioRangeMode() - get Ratio range restriction for threshold mode: RANGE_xxxx

Returns:

value else null if not found.

getRatioCy3Cy5RangeMode

public final int getRatioCy3Cy5RangeMode()

getRatioCy3Cy5RangeMode() - get Cy3/Cy5 range restriction mode for threshold filter: RANGE_xxxx

Returns:

value else null if not found.

getPlotModeImage

public final int getPlotModeImage()

getPlotModeImage() - get pseudoarray image plot mode: PLOT_xxxx_IMAGE

Returns:

value else null if not found.

getEditMode

public final int getEditMode()

getEditMode() - get EGL mode for 'edited gene list': EDIT_xxxx

Returns:

value else null if not found.

getHierClustMode

public final int getHierClustMode()

getHierClustMode() - get hierarchical clustering linkage mode: HIER_CLUST_xxxxx

Returns:

value else null if not found.

lookupRangeModeName

public final java.lang.String lookupRangeModeName(int mode)

lookupRangeModeName() - lookup the inside/outside range Mode Name for values RANGE-xxxx. It will return one of ("inside", "outside", ""). If valid it appends the word "range".

Parameters:

mode - to look up

Returns:

string name if valid mode else return ""

lookupCompareModeName

public final java.lang.String lookupCompareModeName(int mode)

lookupCompareModeName() - lookup the compare-criteria Mode Name for values COMPARE-xxxx. It will return one of ("all", "any", "product", "sum", "at most", "at least", ""). If valid, it appends the word "samples".

Parameters:

mode - to look up

Returns:

string name if valid mode else return ""

lookupFilterSampleSubsetModeName

public final java.lang.String lookupFilterSampleSubsetModeName(int mode)

lookupFilterSampleSubsetModeName() - lookup the sample-subset Mode Name for values SS_MODE-xxxx. It will return one of ("current", "X and Y", "X set", "Y set", "X or Y sets", "E list"). If valid, it appends the word "samples".

Parameters:

mode - to look up

Returns:

string name if valid mode else return ""