|
||||||||||
| PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
| SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD | |||||||||
java.lang.Object
|
+--java.awt.Component
|
+--java.awt.Container
|
+--java.awt.Panel
|
+--java.applet.Applet
|
+--MAExplorer
MicroArray Explorer main() class. See the MAExplorer Reference Manual for the details.
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/.
Gene,
GeneClass,
GeneGeneDist,
GeneList,
GipoTable,
GetParams,
MaeJavaAPI,
MaHybridSample,
MaInfoTable,
Maps,
MenuBarFrame,
PopupRegistry,
SampleSets,
SamplesTable,
ScrollableImageCanvas,
SpotData,
SpotFeatures,
StageNames,
StateScrollers,
Statistics,
UserState,
Util, Serialized Form| Inner classes inherited from class java.applet.Applet |
java.applet.Applet.AccessibleApplet |
| Inner classes inherited from class java.awt.Panel |
java.awt.Panel.AccessibleAWTPanel |
| Inner classes inherited from class java.awt.Container |
java.awt.Container.AccessibleAWTContainer |
| Inner classes inherited from class java.awt.Component |
java.awt.Component.AccessibleAWTComponent, java.awt.Component.AWTTreeLock |
| Field Summary | |
(package private) boolean |
abortFlag
Flag: set true by the STOP button. |
(package private) boolean |
addExprProfileFlag
set for EP ratios in gene REPORTS |
(package private) boolean |
addHP_XYstatFlag
set for HP_XY statistics in gene REPORTS |
(package private) boolean |
addOCLstatFlag
set for OCL statics statistics in gene REPORTS |
(package private) boolean |
allowNegQuantDataFlag
PARAM "allowNegQuantDataFlag" |
(package private) java.applet.Applet |
applet
"this" applet instance for MAExplorer main class |
(package private) boolean |
autoStateScrPopupFlag
Auto state-scroller popup windown assoc w/Filters |
(package private) boolean |
bkgdCorrectFlag
calc: I'= Intensity - background |
(package private) static java.lang.String |
browserTitle
browser title |
(package private) java.lang.String |
cacheDir
Standalone /Cache directory for saving data downloaded for array Web server. |
(package private) boolean |
cacheFIOflag
Flag: if enabled, it first checks the /Cache directory for all http:// codebase files and if not in the cache, it saves the file in the cache after reading it from the Web. |
(package private) static boolean |
CANVAS_WRAPAROUND_BUG
if debugging CANVAS_WRAPAROUND_BUG |
(package private) static int |
canvasHSize
PARAM "CanvasHorSize" |
(package private) static int |
canvasVSize
PARAM "CanvasVertSize" |
(package private) GeneGeneDist |
ccd
Global instance of Gene-Gene distances |
(package private) CompositeDatabase |
cdb
Global instance of composite database object |
(package private) Condition |
cdList
Global instance of condition list tables |
(package private) Config |
cfg
Global instance of Configuration and state variables including top level file, URL configs, etc. |
(package private) ConfigTable |
cfgDB
Global instance of configuration data from MaExplorerConfig.txt file |
(package private) java.lang.String |
classNameX
"HP-X 'set'" name for msListX[] HPs |
(package private) java.lang.String |
classNameY
"HP-Y 'set'" name for msListY[] HPs |
(package private) ClusterGenes |
clg
Global instance of Cluster Genes object |
(package private) GeneList |
clLst
Global instance of GeneList contains gene (clone) list tables |
(package private) ClusterSamples |
clstrSamp
Global instance of ClusterSamples class |
(package private) boolean |
clusterHP_EfilterFlag
filter genes by cluster HP-E |
(package private) boolean |
clusterOnFilteredCLflag
cluster on Filtered/All genes |
(package private) static java.lang.String |
codeBase
full codebase path for /mae/ on MAE svr |
(package private) static int |
COMPARE_ALL
range-compare mode: spot intensity of samples - ALL samples must comply |
(package private) static int |
COMPARE_ANY
range-compare mode: spot intensity of samples - ANY samples must comply |
(package private) static int |
COMPARE_AT_LEAST
range-compare mode: spot intensity of samples - AT LEAST n samples must comply |
(package private) static int |
COMPARE_AT_MOST
range-compare mode: spot intensity of samples - AT MOST n samples must comply |
(package private) static int |
COMPARE_PRODUCT
range-compare mode: spot intensity of samples - PRODUCT of samples must comply |
(package private) static int |
COMPARE_SUM
range-compare mode: spot intensity of samples - SUM samples must comply |
(package private) java.lang.String |
configFile
Default Configuration file: "MaExplorerConfig.txt" |
(package private) static boolean |
CONSOLE_FLAG
Debugging flag - Always TRUE |
(package private) float |
cr1
PARAM "CR1" MIN_RATIO range (i.e. |
(package private) float |
cr2
PARAM "CR2" MAX_RATIO range |
(package private) static int |
curHP
Current hybridized sample index for hps.msList[] |
(package private) static int |
curHP_X
Current HP-X sample index for hps.msList[] |
(package private) static int |
curHP_Y
Current HP-Y sample index for hps.msList[] |
(package private) static java.lang.String |
curPrjName
current project being requested |
(package private) int |
cvTestMode
CV test mode: SS_MODE_xxxx |
(package private) static java.lang.String |
date
startup date |
(package private) boolean |
dbESTviewerFlag
dbEST popup browser Mode |
(package private) static java.lang.String |
dbID
Unique Database ID ("DIDxxxxxx") - used as prefix for State/ files |
(package private) static boolean |
DBUG_CV_DISPLAY_EPLIST
if debugging display the CV of HP-EP samples as colors [0:1.0] lie for p-value display. |
(package private) static boolean |
DBUG_GENERIC_NORM_PLUGIN
[DEBUGGING] If debugging a plugin extending NormalizationPlugin, you may debug it in the MAExplorer core image by temporarily including in in the code. |
(package private) static boolean |
DBUG_GENOMIC_URLS_FLAG
debugging Genomic Menu/URLs |
(package private) static boolean |
DBUG_HCN
debugging HierClustNode lists |
(package private) static boolean |
DBUG_LOGIN
Debugging variablen - debugging CGI login locally |
(package private) static boolean |
DBUG_MAERlibr_ZIP_UPDATE
If debugging MAERlibr.zip file update. |
(package private) static boolean |
DBUG_MEDMINER_FLAG
debugging MedMiner Menu/URLs |
(package private) static boolean |
DBUG_NORM_PLUGIN
if debugging NormalizationPlugins using the PluginLoader |
(package private) static boolean |
DBUG_QUALCHK_QUANT_FLAG
debugging QualCheck |
(package private) static boolean |
DBUG_SET_EGL_FROM_DENDROGRAM
if debugging setting EGL set from subtree of HCN dendrogram |
(package private) static boolean |
DBUG_STANDALONE
debugging Stand-Alone code |
(package private) static boolean |
DBUG_TEST_PLUGIN_FLAG
Enable testing MAEPlugin from the intial menu without dynamic MAEPlugin loading of the class. |
(package private) static boolean |
DBUG_TEST_R_OR_SPLUS_CHECKBOX
Test the code to let the user switch between R or S-Plus as the statistics evaluation engine. |
(package private) static boolean |
DEBUG
General purpose debugging flag. |
(package private) static java.lang.String |
DEF_BASESERVER
Default microarray database server. |
(package private) static java.lang.String |
defDir
Default standalone directory (=null JWS hack) |
(package private) java.lang.String |
defSAprjName
Standalone current project DB name |
(package private) static java.lang.String |
defSAwebAddr
Default standalone assoc. |
(package private) static java.lang.String |
defStartupFile
Default standalone .mae startup file |
(package private) int |
detValueSpotTestMode
Spot (Detection Value) test mode: SS_MODE_xxxx |
(package private) boolean |
dieFlag
Flag: call quit() if flag set to exit run(). |
(package private) java.lang.String |
docCodeBase
codebase where the documentation Reference Manual is kept |
(package private) boolean |
doGCflag
Flag: run the Garbage Collector. |
(package private) static int |
DRAW_BIN
Plotting types - draw histogram bin |
(package private) static int |
DRAW_BOX
Plotting types - draw box symbol in scatter plot |
(package private) static int |
DRAW_CIRCLE
Plotting types - draw circle symbol in scatter plot |
(package private) static int |
DRAW_PLUS
Plotting types - draw plus symbol in scatter plot |
(package private) DryRotException |
dryRotExcept
Global instance of DryRotException class |
(package private) java.lang.String |
dryrotLogStr
List of dryrot messages if any occur. |
(package private) boolean |
dualXYpseudoPlotFlag
Flag: plot mean HP-X in F1, HP-Y in F2 pseudoimg |
(package private) DrawPseudoImage |
dwPI
Global instance of draw pseudo image |
(package private) java.lang.String |
dynFileSeparator
dynamic paths separator, "/" or "|", depends on OS and if using URL from Stand-Alone |
(package private) static int |
EDIT_ADD
Edited Gene List mouse click action mode: ADD gene on click |
(package private) static int |
EDIT_NOP
Edited Gene List mouse click action mode: NO-OP |
(package private) static int |
EDIT_RMV
Edited Gene List mouse click action mode: REMOVE gene on click |
(package private) int |
editMode
EGL mode for 'edited gene list': EDIT_xxxx |
(package private) EditedGeneList |
egl
Global instance of edit editedCL gene (clone) list |
(package private) EventMenu |
em
Global instance of handle MenuItem and MenuItemCheckbox events |
(package private) boolean |
enableFIOcachingFlag
Flag: stand-alone PARAM "enableFIOcaching" |
(package private) boolean |
F_TestOCLFilterFlag
filter genes passing current OCL (Ordered Condition List) F-test |
(package private) Filter |
fc
Global instance of data Filter gene operations |
(package private) static java.lang.String |
fileBasePath
either Applet or file I/O or standalone |
(package private) java.lang.String |
fileSeparator
paths, "/" or "|", depends on OS |
(package private) FileIO |
fio
Global instance of file and URL I/O |
(package private) boolean |
flickerXYflag
Flicker HP-X and HP-Y in run() loop |
(package private) boolean |
gangSpotFlag
Flag: report f1 or f1&f2 (ganged) |
(package private) GeneClass |
gct
Global instance of Gene Class table |
(package private) boolean |
genBankViewerFlag
GenBank popup browser Mode |
(package private) Gene |
gene
Global instance of Gene |
(package private) boolean |
geneClassMbrFilterFlag
filter genes by GeneClass mbrshp |
(package private) boolean[] |
genomicViewerFlag
holds sGenomicMenu[cfg.nGenomicMenus] menu flags |
(package private) GipoTable |
gipo
Global instance of GIPO table mapping genes to other data |
(package private) GenNormalizationPlugin |
gnp
Only while debugging: if DBUG_GENERIC_NORM_PLUGIN is set for use with TestPlugin. |
(package private) int |
goodSpotTestMode
Good Spot (QualChk) test mode: SS_MODE_xxxx |
(package private) GetParams |
gp
Global instance of contains set of applet/configuration PARAM parsers |
(package private) GridCoords |
grcd
Global instance of share grid coordinate mapper |
(package private) static int |
HIER_CLUST_NEXT_MIN_LNKG
Hierarchical clustering mode: next-minimum cluster linkage |
(package private) static int |
HIER_CLUST_PGMA_LNKG
Hierarchical clustering mode: Average-arithmetic linkage |
(package private) static int |
HIER_CLUST_PGMC_LNKG
Hierarchical clustering mode: Average-centroid linkage |
(package private) int |
hierClustMode
Hier.Clustering linkage mode: HIER_CLUST_xxxxx |
(package private) boolean |
hierClustUnWtAvgFlag
use UPGMA or WPGMA for computing the average node vector when hierarchical clustering. |
(package private) static double[] |
histRatioBin
preloaded set of legal ratios in [1/100 : 100] |
(package private) SampleSets |
hps
Global instance of HP-X, HP-Y and HP-E sets and lists |
(package private) int |
iHPnbr
# of entries in "image#" PARAM list. |
(package private) java.lang.String[] |
iImageFile
image files to read allocated [MAX_HYB_SAMPLES+1] |
(package private) MaInfoTable |
infoDB
Global instance of depricated "MaExplorerInfo.txt" DB list of .info data for entire DB. |
(package private) boolean |
intensFilterFlag
filter genes by intensity threshold |
(package private) ArrayScroller |
is
Global instance of ArrayScroller obj to hold pseudoarray image scrollable canvas |
(package private) java.lang.String[] |
iSampleName
HP name from "image*" [1:iHPnbr] allocated [MAX_HYB_SAMPLES+1] |
(package private) boolean |
isAppletFlag
Flag: cleared if enter through standalone main() |
(package private) boolean |
isLoggedInFlag
set if valid login has been performed |
(package private) boolean |
isWinPCflag
Flag: set to TRUE if any Windows PC |
(package private) boolean |
isWorkingMAE
Flag indicating whether using the Working server (mae/) or not |
(package private) boolean |
isZscoreFlag
Flag: is using one of the Zscore normalizations |
(package private) static java.lang.String |
javaHome
Standalone getProperties("java.home") |
(package private) boolean |
killAppletFlag
Flag: set if do "Quit". |
(package private) boolean |
KS_TestXYsetsFilterFlag
filter genes passing HP-X/-Y sets KS-test |
(package private) int |
LECBdebug
Developer debug flag. |
(package private) boolean |
locusLinkViewerFlag
LocusLink LocusID page popup browser Mode |
(package private) boolean |
lowRangeZoomFlag
Scale pseudoarray image by 1/100 to zoom low-range values |
(package private) boolean |
mAdbViewerFlag
mAdb Clone page popup browser Mode |
(package private) boolean |
madeChangesFlag
made changes to DB so may want to SAVE DB |
(package private) static java.lang.String |
MAE_STARTUP_FILE
Default empty .mae startup database |
(package private) java.lang.String |
maeServerBase
top level codebase for MAE server |
(package private) static java.lang.String |
maeTitleVer
Compiled MAExplorer title with version number |
(package private) int[] |
mapHPtoMenuName
index of snHPName[] corresponding to iSampleName[] entry allocated [MAX_HYB_SAMPLES+1]. |
(package private) static int |
MARKER_CIRCLE
pseudoarray canvas - draw circle of size radius |
(package private) static int |
MARKER_CURRENT
pseudoarray canvas - draw Current object |
(package private) static int |
MARKER_GENES
pseudoarray canvas - draw all spots in gene list |
(package private) static int |
MARKER_KMEANS_CLUSTER
pseudoarray canvas - draw K-means cluster # |
(package private) static int |
MARKER_NONE
pseudoarray canvas - No overlay |
(package private) static int |
MARKER_PLUS
pseudoarray canvas - draw 5x5 plus |
(package private) static int |
MARKER_SQUARE
pseudoarray canvas - draw square of size radius |
(package private) static int |
MASTER_CLONE_ID
Master masterIDmode Mode - clone ID |
(package private) static int |
MASTER_DBEST3
Master masterIDmode Mode - dbEST 3' ID |
(package private) static int |
MASTER_DBEST5
Master masterIDmode Mode - dbEST 5' ID |
(package private) static int |
MASTER_GENBANK
Master masterIDmode Mode - GenBank ID |
(package private) static int |
MASTER_GENBANK3
Master masterIDmode Mode - GenBank 3' ID |
(package private) static int |
MASTER_GENBANK5
Master masterIDmode Mode - GenBank 5' ID |
(package private) static int |
MASTER_GENE_NAME
Master masterNameMode Mode - gene name |
(package private) static int |
MASTER_GENERIC_ID
Master masterIDmode Mode - generic ID |
(package private) static int |
MASTER_LOCUSLINK
Master masterIDmode Mode - LocusLink ID |
(package private) static int |
MASTER_OMIM
Master masterIDmode Mode - OMIM ID |
(package private) static int |
MASTER_SWISS_PROT
Master masterIDmode Mode - SwissProt ID |
(package private) static int |
MASTER_UG_ID
Master masterIDmode Mode - UniGene ID |
(package private) static int |
MASTER_UG_NAME
Master masterNameMode Mode - UniGene name |
(package private) java.lang.String |
masterGeneName
either "GeneName", "UGclusterName, etc" |
(package private) int |
masterIDmode
either MASTER_CLONE_ID or MASTER_GENBANK or MASTER_GENBANK5 or MASTER_GENBANK3 or MASTER_UG_ID, MASTER_SWISS_PROT, MASTER_GENERIC_ID |
(package private) java.lang.String |
masterIDname
either "CloneID", "UniGeneID, GenBank, etc" |
(package private) int |
masterNameMode
either MASTER_GENE_NAME or MASTER_UG_NAME |
static int |
MAX_COND_PARAM
maximum number of Condition parameters |
(package private) static int |
MAX_CONDITION_LISTS
Max # of named sample condition lists. |
(package private) static int |
MAX_HYB_SAMPLES
Max # of hybridized array samples to load at one time |
(package private) int |
MAX_INTENSITY
maximum # intensity values of .quant data |
(package private) static int |
MAX_ORDERED_COND_LISTS
maximum number of # of ordered condition lists slots available. |
(package private) static int |
MAX_PROJECTS
Maximum # of projects for project lists |
(package private) static float |
MAX_RATIO
maximum ratio for histogram of ratios histRatioBin[] |
(package private) static int |
MAX_RATIO_HIST
# of bins in histRatioBin[] |
(package private) int |
maxPreloadImgs
PARAM max # images to preload set from "maxPreloadImages" |
(package private) MenuBarFrame |
mbf
Global instance of Frame based MenuBar |
(package private) boolean |
medMinerViewerFlag
MedMiner gene page popup browser Mode |
(package private) static float |
MIN_RATIO
Minimum ratio for histogram of ratios histRatioBin[] |
static MaeJavaAPI |
mja
Global instance of MaeJavaAPI Gather/Scatter API for MAEPlugins |
(package private) Maps |
mp
Global instance of lookup table maps populated elsewhere |
(package private) boolean |
mReady
Flag set when done initialization and ready to analyze |
(package private) static MaHybridSample |
ms
Current hybridized sample |
(package private) static MaHybridSample |
msPrev
Previous (last current) hybridized sample for garbage collection |
(package private) static MaHybridSample |
msX
Current HP-X hybridized sample |
(package private) static MaHybridSample |
msY
Current HP-Y hybridized sample |
(package private) static int |
N_CONST_FILES
# of files always read: MaExplorerConfig.txt GIPO-xxx.txt Samples.txt MaExplorerInfo.txt [DEPRICATED] |
(package private) static int |
N_EST_QUANT_FILES
default est # .quant files to load |
(package private) static boolean |
NEVER
Debugging flag - Always FALSE |
(package private) int |
nFilesRead
# of files read so far |
(package private) int |
nFilesTotal
# files always read + # .quant files. |
(package private) boolean |
noMsgReportFlag
PARAM "noMsgReporting" |
(package private) boolean |
normByCalDNAflag
normalize by Calibration DNA set |
(package private) boolean |
normByGeneSetFlag
normalize by 'user gene set' |
(package private) boolean |
normByHousekeepGenesFlag
normalize by housekeeping genes |
(package private) boolean |
normByLogMedianFlag
normalize by HP log of median |
(package private) boolean |
normByMedianFlag
normalize by HP median |
(package private) boolean |
normByZscoreFlag
normalize by HP Zscore |
(package private) boolean |
normByZscoreMeanAbsDevLogFlag
norm. |
(package private) boolean |
normByZscoreMeanStdDevLogFlag
norm by Zscore log intens,stdDev. |
(package private) boolean |
normHCbyRatioHPflag
set true if normalize Hier-Clustering dataV[h] by dataV[iDataV] else norm by HP[h] msListE[h].maQ.maxRI |
(package private) java.lang.String |
normName
name of normalization method |
(package private) java.lang.String |
normNameDisp
name of norm. |
(package private) int |
nValidPrj
# of login verified projects |
(package private) OverlayMap |
olmap
Global instance of scatterplot named overlay maps |
(package private) boolean |
omimViewerFlag
OMIM popup browser Mode |
private boolean |
onceOnlyFlag
flag to prevent multiple instances |
(package private) static java.lang.String |
osName
operating system Windows, SUNOS, etc |
(package private) java.lang.String |
otherUserName
access other user name from Dialog |
(package private) int |
pHeight
working size of pseudoarray image |
(package private) java.awt.Image |
pImage
pseudo grayscale microarray image based on .quantspot intensity data. |
(package private) boolean |
pirViewerFlag
PIR page popup browser Mode |
(package private) static int |
PLOT_CLUSTER_GENES
Popup plot mode: cluster similar genes plot |
(package private) static int |
PLOT_CLUSTER_HIER
Popup plot mode: hierarchical cluster genes plot |
(package private) static int |
PLOT_CLUSTER_HYBSAMPLES
Popup plot mode: cluster HP-samples plot |
(package private) static int |
PLOT_CLUSTERGRAM
Popup plot mode: clustergram genes plot |
(package private) static int |
PLOT_EXPR_PROFILE
Popup plot mode: expression profile plot |
(package private) static int |
PLOT_F1_F2_INTENS
Popup plot mode: current F1 vs F2, or Cy3 vs Cy5 scatter plot |
(package private) static int |
PLOT_F1_F2_MVSA
Popup plot mode: M vs A scatter plot of current sample |
(package private) static int |
PLOT_HIST_F1F2_RATIO
Popup plot mode: current HP F1/F2 ratio histogram plot |
(package private) static int |
PLOT_HIST_HP_XY_RATIO
Popup plot mode: HP-X/HP-Y ratio histogram plot |
(package private) static int |
PLOT_HIST_HP_XY_SETS_RATIO
Popup plot mode: HP-X 'set' / HP-Y 'set' ratio histogram plot |
(package private) static int |
PLOT_HP_XY_INTENS
Popup plot mode: HP-X vs HP-Y, or HP-X 'set' vs HP-Y 'set' scatter plot |
(package private) static int |
PLOT_INTENS_HIST
Popup plot mode: current HP intensity histogram plot |
(package private) static int |
PLOT_KMEANS_CLUSTERGRAM
Popup plot mode: k-means cluster genes plot |
(package private) static int |
PLOT_PSEUDO_F1F2_IMG
Pseudoarray image plot mode: display current F1/F2 (Cy3/Cy5) ratios as [green:black:red] |
(package private) static int |
PLOT_PSEUDO_F1F2_RYG_IMG
Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:yellow:red] |
(package private) static int |
PLOT_PSEUDO_HP_EP_CV_VALUE_IMG
Pseudoarray image plot mode: display HP_EP 'list' CV coefficient of variation [0.0:1.0] as [black:white] |
(package private) static int |
PLOT_PSEUDO_HP_XY_IMG
Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:black:red] |
(package private) static int |
PLOT_PSEUDO_HP_XY_P_VALUE_IMG
Pseudoarray image plot mode: display X,Y 'sets' p-Value [0.0:1.0] as [black:white] |
(package private) static int |
PLOT_PSEUDO_HP_XY_RYG_IMG
Pseudoarray image plot mode: display HP-X/HP-Y ratios as [green:yellow:red] |
(package private) static int |
PLOT_PSEUDOIMG
Pseudoarray image plot mode: Grayscale display current HP intensity |
(package private) int |
plotImageMode
Pseudo array image plot mode: PLOT_xxxx_IMAGE |
(package private) static java.lang.String |
pluginsDir
Standalone /Plugins directory where optional MAEPlugins may be found |
(package private) int |
posQuantTestMode
positive Quant data test mode: SS_MODE_xxxx |
(package private) boolean |
presentViewFlag
Flag: use larger fonts, thicker lines, circles, plus, etc. |
(package private) boolean |
previousStartupState
Flag that indicates if the startup .mae file exists in PREVIOUS database |
(package private) static boolean |
PRINT_MEM_TIMES
print memory times at key places |
(package private) static java.lang.String |
prjListFile
Standalone Sample DB project list DB file |
(package private) java.lang.String |
proxyServer
base addr PARAM "proxyServer" |
(package private) static int |
PSEUDOIMG_HEIGHT
(600x900) size of pseudoarray image canvas |
(package private) static int |
PSEUDOIMG_WIDTH
(600x900) size of pseudoarray image canvas |
(package private) PopupRegistry |
pur
Global instance of holds popup registry of all active popup windows and update handlers. |
(package private) int |
pWidth
working size of pseudoarray image |
(package private) static int |
QUALTYPE_ALPHA
QualCheck type: Alphabetic codes |
(package private) static int |
QUALTYPE_PROP_CODE
QualCheck type: uses MAE Gene.xxxx prop QualCheck codes |
(package private) static int |
QUALTYPE_THR
QualCheck type: Uses [qualThr] QualCheck continuous data |
(package private) int |
qualTypeMode
spot quality type mode: QUALTYPE_xxxx |
(package private) float |
r1
PARAM "R1" MIN_RATIO range (HP-X/HP-Y) |
(package private) float |
r2
PARAM "R2" MAX_RATIO range |
(package private) static int |
RANGE_INSIDE
rangeMode: Inside [v1:v2] for testing |
(package private) static int |
RANGE_OUTSIDE
rangeMode: Outsiide [v1:v2] for testing |
(package private) boolean |
ratioCy3Cy5FilterFlag
filter genes by Cy3/Cy5 ratio threshold |
(package private) int |
ratioCy3Cy5RangeMode
Cy3/Cy5 range restriction for threshold mode: RANGE_INSIDE, RANGE_OUTSIDE |
(package private) boolean |
ratioFilterFlag
filter genes by ratio threshold |
(package private) boolean |
ratioMedianCorrectionFlag
enable cy3/cy5 ratio median correction |
(package private) int |
ratioRangeMode
Ratio range restriction for threshold mode: RANGE_INSIDE, RANGE_OUTSIDE |
(package private) int |
reportMode
Report type mode: RPT_xxxx. |
(package private) java.lang.String |
reportRatioStr
either "F1/F2", "Cy3/Cy5", or "Cy5/Cy3" |
(package private) boolean |
reuseGUIframeFlag
Flag: set if reuse main GUI frame |
(package private) boolean |
reuseXYcoordsFlag
Flag: reuse HP[1] Quant xy coords for speedup |
(package private) static int |
RPT_FMT_DYN
Report format mode: dynamic spreadsheet report |
(package private) static int |
RPT_FMT_TAB_DELIM
Report format mode: tab-delimited report as TextArea |
(package private) static int |
RPT_NONE
Report mode: no report |
(package private) static int |
RPT_TBL_ALL_GENES_CLUSTER
Report mode: all genes clustering statistics |
(package private) static int |
RPT_TBL_CALIB_DNA_STAT
Report mode: array samples Calibration DNA statistics |
(package private) static int |
RPT_TBL_CUR_GENE_CLUSTER
Report mode: current gene clustering statistics |
(package private) static int |
RPT_TBL_EDITED_GENE_LIST
Report mode: Edited Gene List |
(package private) static int |
RPT_TBL_EXPR_PROFILE
Report mode: expression profiles of filtered genes [CHECK] |
(package private) static int |
RPT_TBL_FILTERED_GENES
Report mode: data Filtered genes |
(package private) static int |
RPT_TBL_GENE_CLASS
Report mode: genes in current GencClass |
(package private) static int |
RPT_TBL_HIER_CLUSTER
Report mode: hierarchical clusters gene statistics |
(package private) static int |
RPT_TBL_HIGH_F1F2
Report mode: highest N current HP F1/F2 ratio genes |
(package private) static int |
RPT_TBL_HIGH_RATIO
Report mode: highest N HP-X/HP-Y ratio genes |
(package private) static int |
RPT_TBL_HP_DB_INFO
Report mode: array report of extra Info samples data (DEPRICATED) |
(package private) static int |
RPT_TBL_HP_HP_CORR
Report mode: HP vs HP correlation coefficient for only filtered genes |
(package private) static int |
RPT_TBL_HP_MN_VAR_STAT
Report mode: array samples mean and variance statistics |
(package private) static int |
RPT_TBL_HP_XY_SET_STAT
Report mode: array samples set statistics |
(package private) static int |
RPT_TBL_KMEANS_CLUSTER
Report mode: K-means clustering statistics |
(package private) static int |
RPT_TBL_LOW_F1F2
Report mode: lowest N current HP F1/F2 ratio genes |
(package private) static int |
RPT_TBL_LOW_RATIO
Report mode: lowest N HP-X/HP-Y ratio genes |
(package private) static int |
RPT_TBL_MAE_PRJ_DB
Report mode: project database |
(package private) static int |
RPT_TBL_MN_KMEANS_CLUSTER
Report mode: mean clusters for K-means clusters statistics |
(package private) static int |
RPT_TBL_NAMED_GENES
Report mode: all named genes |
(package private) static int |
RPT_TBL_NORMALIZATION_GENE_LIST
Report mode:Normalization gene list statistics |
(package private) static int |
RPT_TBL_OCL_STAT
Report mode: Ordered Condition List gene statistics |
(package private) static int |
RPT_TBL_SAMPLES_DB_INFO
Report mode: array report of SamplesDB |
(package private) static int |
RPT_TBL_SAMPLES_WEB_LINKS
Report mode: array report with active Web links |
(package private) java.lang.String |
rptFontSize
Report font size: "8pt", "10pt", or "12pt" |
(package private) int |
runLoopDelayMsec
Flicker delay for run() loop delay also used for flicker |
(package private) java.lang.Thread |
runT
main thread for run() |
(package private) static java.lang.String |
saCodeBase
Stand-alone PARAM "saCodeBase" overrides default |
(package private) SamplesTable |
sampDB
The "Samples.txt" database list of the H.P.s in the entire database. |
(package private) int |
sampleIntensityRangeMode
Sample intensity range mode for threshold: RANGE_INSIDE, RANGE_OUTSIDE |
(package private) boolean |
scaleDataToMaxIntensFlag
normalize to maximum intensity |
(package private) int |
scrHeight
Horizontal screen size |
(package private) int |
scrWidth
Horizontal screen size |
(package private) SpotData |
sd
Global instance of spot data object |
(package private) SpotFeatures |
sf
Global instance of spot feature info |
(package private) StageNames |
sg
Global instance of Staging names for menus etc |
(package private) boolean |
showEGLflag
Display Flag: show edited gene list |
(package private) float |
sit1
PARAM "SI1" 0 or MIN_INTENSITY (spot Intens.) |
(package private) float |
sit2
PARAM "SI2" MAX_INTENSITY |
(package private) java.lang.String[] |
snHPDatabaseFileID
(opt) list of DB file ID [1:snHPnbr] |
(package private) java.lang.String[] |
snHPFullStageText
list for buildingn menus [1:snHPnbr] |
(package private) java.lang.String[] |
snHPMenuText
list for building menus [1:snHPnbr] |
(package private) java.lang.String[] |
snHPName
slist of tage HP name [1:snHPnbr] |
(package private) int |
snHPnbr
# of entries in the Stage name list |
(package private) java.lang.String[] |
snHPSampleID
list of free form sample names [1:snHPnbr] |
(package private) java.lang.String[] |
snImageFile
list of image files to read [1:snHPnbr] |
(package private) boolean[] |
snNeedLogin
(opt) sample requires login |
(package private) java.lang.String[] |
snPrjName
list of Project names [1:snHPnbr] |
(package private) boolean[] |
snSwapCy5Cy3Data
swap (Cy3,Cy5) field data for (Cy5,Cy3) for this HP |
(package private) boolean |
sortedGeneAndCloneIDListsFlag
true if alphaList[] geneNames and numericList[] gene xxxx_IDs are sorted |
(package private) int |
spotIntensCompareMode
Spot Intensity compare mode for threshold: COMPARE_xxxx |
(package private) boolean |
spotIntensFilterFlag
filter genes by spot Intensity threshold |
(package private) int |
spotIntensRangeMode
Spot intensity range mode for thresholds RANGE_OUTSIDE, RANGE_INSIDE |
(package private) int |
spotIntensTestMode
spot intensity test mode: SS_MODE_xxxx |
(package private) int |
spotRad
PARAM "SpotRadius" |
(package private) static int |
SS_MODE_ELIST
HP data Filter subset mode: F1F2 HP-E list - hps.msListE[] |
(package private) static int |
SS_MODE_MS
HP data Filter subset mode: F1F2 current HP - mae.ms |
(package private) static int |
SS_MODE_XANDY_SETS
HP data Filter subset mode: F1F2 HP-X AND HP-Y sets - hps.msListX(Y)[] |
(package private) static int |
SS_MODE_XORY_SETS
HP data Filter subset mode: F1F2 HP-X or HP-Y sets - hps.msListX(Y)[] |
(package private) static int |
SS_MODE_XSET
HP data Filter subset mode: F1F2 HP-X sets - hps.msListX[] |
(package private) static int |
SS_MODE_XY
HP data Filter subset mode: F1F2 HP-X and HP-Y - mae.msX and mae.msY |
(package private) static int |
SS_MODE_YSET
HP data Filter subset mode: F1F2 HP-Y sets - hps.msListY[] |
(package private) static java.lang.String |
startupDir
Standalone startup Directory where startupFile is found |
(package private) static java.lang.String |
startupFile
Standalone startup DB .mae file |
(package private) static boolean |
startupFileExistsFlag
Flag that indicates if the database startup .mae file exists |
(package private) Statistics |
stat
Global instance of parametric & non-parametric stats |
(package private) StateScrollers |
stateScr
holds popup state scrollers - note: created in MenuBarFrame! |
(package private) boolean |
swapRowsColsFlag
PARAM flip array rows & columns |
(package private) boolean |
swissProtViewerFlag
Swiss-Prot page popup browser Mode |
(package private) float |
t1
PARAM "I1" 0 or MIN_INTENSITY (gene "intens") |
(package private) float |
t2
PARAM "I2" MAX_INTENSITY |
(package private) int |
tblFmtMode
Report table format mode: RPT_FMT_xxxx |
(package private) boolean |
testGenericNormPluginFlag
If DBUG_GENERIC_NORM_PLUGIN, then debug GenericNormalizationPlugin within the code. |
(package private) boolean |
tTestXYfilterFlag
filter genes passing HP-X/-Y t-test |
(package private) boolean |
tTestXYsetsFilterFlag
filter genes passing HP-X/-Y sets t-test |
(package private) boolean |
uniGeneViewerFlag
UniGene popup browser Mode |
(package private) boolean |
updatePseudoImgFlag
update pseudo image - not saved in the State |
(package private) UserState |
us
Global instance of User State methods |
(package private) boolean |
useClusterCountsDispFlag
show gene clusters count |
(package private) boolean |
useClusterDistCacheFlag
use cluster cache else recompute each time |
(package private) boolean |
useClusterDistFlag
cluster distance thresholding |
(package private) boolean |
useCorrCoeffFlag
use correlation coeffieient instead of Euclidian distance when clustering |
(package private) boolean |
useCVmeanElseMaxFlag
use mean of CV else use max in CV filter |
(package private) boolean |
useCy5OverCy3Flag
PARAM "useCy5/Cy3" else Cy3/Cy5 |
(package private) boolean |
useDetValueSpotDataFlag
filter genes with Spot (Detection value) data |
(package private) boolean |
useDichromasyFlag
PARAM "useDichromasy" alt. |
(package private) boolean |
useDiffFilterFlag
filter genes by abs diff(HP-X,HP-Y) |
(package private) boolean |
useEditedCLflag
filter genes on Edited Gene List |
(package private) boolean |
useEPoverlayFlag
Flag: Plot EP list as overlay 2Dplot else scrollable Grid of EPs |
(package private) boolean |
useEPrawIntensValFlag
use Raw intensity for EP ratios in gene REPORTS |
(package private) boolean |
useGeneSetFilterFlag
filter genes by useGeneSet mbrship |
(package private) boolean |
useGoodGeneCLflag
filter by genes in Good Genes List |
(package private) boolean |
useGoodSpotDataFlag
filter genes with Good Spot (QualChk) data |
(package private) boolean |
useGoodSpotsForGlobalStatsFlag
use Good Spots data for computing global array statistics for normalization purposes on a per array basis, otherwise use all spot data. |
(package private) boolean |
useHierClusterDispFlag
show hierarchical clusters |
(package private) boolean |
useHighRatiosFilterFlag
"Use highest X/Y ratios filter" |
(package private) boolean |
useHPxySetDataFlag
use HP-X,Y 'sets msListX/Y else HP-X,HP-Y msX/Y |
(package private) boolean |
useIntensHistCLflag
filter genes on Intensity hist bin |
(package private) boolean |
useKmeansClusterCntsDispFlag
show K-means clusters |
(package private) boolean |
useLowRatiosFilterFlag
"Use lowest X/Y ratios filter" |
(package private) boolean |
useLSQmagNormFlag
norm geneEPvect[] to 1.0 for clustering |
(package private) boolean |
useMeanHPeListDataFlag
[TODO] use mean HP-E 'list' data else single current HP sample data |
(package private) boolean |
useMedianForKmeansClusteringFlag
set true if use median instead of means of clusters in K-means clustering. |
(package private) boolean |
useMouseOverFlag
PARAM "useMouseOver" for popup tracking balloons |
(package private) boolean |
useOnlyGenesWithNonZeroDensityFlag
filter by genes with non-zero intensity - problem when do log() transform |
(package private) boolean |
usePosQuantDataFlag
filter genes with positive quant data |
(package private) boolean |
usePseudoXYcoordsFlag
PARAM use Pseudo XY coords else actual |
(package private) boolean |
useRatioDataFlag
PARAM "useRatioData" Cy3/Cy5 else Intensity |
(package private) boolean |
useRatioHistCLflag
filter genes on Ratio histogram bin |
(package private) boolean |
useReplicateGenesFlag
filter by genes with at least 1 replicate |
(package private) boolean |
useRLOloggingFlag
Flag: use time-stamped RLO logging files folders, else just Report/ |
(package private) java.lang.String |
userName
Dialog: current user login name |
(package private) java.lang.String |
userPasswd
Dialog: current user password |
(package private) int |
userStateIdx
current user state index |
(package private) java.lang.String |
userStateName
current user state name |
(package private) boolean |
useShortClusterDistCacheFlag
use short else float cluster cache, can save memory if really needed |
(package private) boolean |
useSimGeneClusterDispFlag
show a cluster of similar genes for current gene |
(package private) boolean |
useSPLUSasComputingEngineFlag
Flag: Use S-PLUS, else R, as computing engine |
(package private) boolean |
useSpotCVfilterFlag
filter by Spot CV filter is enabled |
(package private) boolean |
useWebDBflag
Flag: stand-alone PARAM "useWebDB" try WebDB before local directories |
(package private) Util |
util
Global instance of Utility class |
(package private) java.lang.String[] |
validPrj
[0:n-1] login verified projects |
(package private) static java.lang.String |
VERSION
Compiled Version constant for use in version comparison etc. |
(package private) static java.lang.String |
verStr
Compiled Date/Revision constants |
(package private) boolean |
viewFilteredSpotsFlag
Flag: show Filtered spots |
(package private) static int |
X_AXIS
Code for assigning current HP to X-axis |
(package private) static int |
Y_AXIS
Code for assigning current HP to X-axis |
| Fields inherited from class java.applet.Applet |
accessibleContext, serialVersionUID, stub |
| Fields inherited from class java.awt.Panel |
base, nameCounter |
| Fields inherited from class java.awt.Container |
component, containerListener, containerSerializedDataVersion, dbg, dispatcher, layoutMgr, listeningBoundsChildren, listeningChildren, maxSize, ncomponents, printing, printingThreads |
| Fields inherited from class java.awt.Component |
actionListenerK, adjustmentListenerK, appContext, background, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, changeSupport, componentListener, componentListenerK, componentOrientation, componentSerializedDataVersion, containerListenerK, cursor, dropTarget, enabled, eventMask, focusListener, focusListenerK, font, foreground, graphicsConfig, hasFocus, height, hierarchyBoundsListener, hierarchyBoundsListenerK, hierarchyListener, hierarchyListenerK, incRate, inputMethodListener, inputMethodListenerK, isInc, isPacked, itemListenerK, keyListener, keyListenerK, LEFT_ALIGNMENT, locale, LOCK, metrics, minSize, mouseListener, mouseListenerK, mouseMotionListener, mouseMotionListenerK, name, nameExplicitlySet, newEventsOnly, ownedWindowK, parent, peer, peerFont, popups, prefSize, privateKey, RIGHT_ALIGNMENT, textListenerK, TOP_ALIGNMENT, valid, visible, width, windowClosingException, windowListenerK, x, y |
| Fields inherited from interface java.awt.image.ImageObserver |
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
| Constructor Summary | |
MAExplorer()
|
|
| Method Summary | |
(package private) void |
chkIfCache()
chkIfCache() - check if set up to cache from Web DB. |
(package private) void |
cleanup()
cleanup() - close up what needs to be closed and GC all structures Reset to initial state so can restart it... |
private void |
clearDynamicState()
clearDynamicState() - reset dynamic state variables in MAE instance. |
(package private) MaHybridSample |
createSample(int hpNbr,
java.lang.String hpName,
java.lang.String sampleID,
java.lang.String databaseFileID,
java.lang.String oImageName,
java.lang.String oMenuName,
java.lang.String fullStageText,
java.lang.String projectName,
boolean needLoginFlag,
boolean swapCy5Cy3DataFlag)
createSample() - create and return a MaHybridSample hybridized sample object. |
void |
destroy()
destroy() - destroy this class |
(package private) void |
destroy2()
destroy2() - destroy this class, but clean up the mess of statics first. |
private void |
destroyStaticState()
destroyStaticState() - reset static state variables in MAE instance |
private boolean |
doAnyLoginsRequired()
doAnyLoginsRequired() - do any Web server logins required for PARAM images that access a Web server database of primary MAExplorer data. |
void |
init()
init() - allocate,clear state, read PARAMs, build GUI and start things off. |
(package private) void |
logDRYROTerr(java.lang.String msg)
logDRYROTerr() - add the dryrot error to the dryrotLogStr and log it by printing it to the system log. |
static void |
main(java.lang.String[] args)
main() - for MAExplorer started by standalone application. |
void |
paint(java.awt.Graphics g)
paint() - generate viewable scrollable pseudoarray image with overlays. |
(package private) int |
percentDone()
percentDone() - estimate percent of files done loading |
(package private) void |
quit()
quit() - kill this application or Applet |
(package private) boolean |
readListOfSampleDataFiles()
readListOfSampleDataFiles() - populate msList[1:nHP] data structures by reading the data files up to maxPreloadImgs. |
(package private) void |
resetDefaultstate()
resetDefaultstate() - Reinitialize global user state. |
(package private) void |
resetImageAndState()
resetImageAndState() - Re initialize whenever restart |
void |
run()
run() - main loop which does checking for various things [1] Check if want to repaint based on spot list change. |
void |
start()
start() - (re)create GUI if needed, read PARAMs & start run thread. |
void |
stop()
stop() - stop the thread. |
void |
update(java.awt.Graphics g)
update() - redraw graphics |
| Methods inherited from class java.applet.Applet |
getAccessibleContext, getAppletContext, getAppletInfo, getAudioClip, getAudioClip, getCodeBase, getDocumentBase, getImage, getImage, getLocale, getParameter, getParameterInfo, isActive, newAudioClip, play, play, resize, resize, setStub, showStatus |
| Methods inherited from class java.awt.Panel |
|
| Methods inherited from class java.awt.Container |
add, add, add, add, add, addContainerListener, addImpl, adjustListeningChildren, applyOrientation, checkGD, countComponents, createChildHierarchyEvents, createHierarchyEvents, deliverEvent, dispatchEventImpl, dispatchEventToSelf, doLayout, eventEnabled, findComponentAt, findComponentAt, findComponentAt, getAccessibleAt, getAccessibleChild, getAccessibleChildrenCount, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents_NoClientCode, getComponents, getInsets, getLayout, getListeners, getMaximumSize, getMinimumSize, getMouseEventTarget, getPreferredSize, getWindow, initIDs, insets, invalidate, invalidateTree, isAncestorOf, layout, lightweightPaint, lightweightPrint, list, list, locate, minimumSize, nextFocus, numListening, paintComponents, paintHeavyweightComponents, paramString, postProcessKeyEvent, postsOldMouseEvents, preferredSize, preProcessKeyEvent, print, printComponents, printHeavyweightComponents, processContainerEvent, processEvent, proxyEnableEvents, proxyRequestFocus, readObject, remove, remove, removeAll, removeContainerListener, removeNotify, setFocusOwner, setFont, setLayout, transferFocus, validate, validateTree, writeObject |
| Methods inherited from class java.awt.Component |
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addPropertyChangeListener, addPropertyChangeListener, areInputMethodsEnabled, bounds, checkImage, checkImage, checkWindowClosingException, coalesceEvents, contains, contains, createImage, createImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, getAccessibleIndexInParent, getAccessibleStateSet, getBackground, getBounds, getBounds, getColorModel, getComponentOrientation, getCursor, getDropTarget, getFont_NoClientCode, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getInputContext, getInputMethodRequests, getLocation, getLocation, getLocationOnScreen_NoTreeLock, getLocationOnScreen, getName, getNativeContainer, getParent_NoClientCode, getParent, getPeer, getSize, getSize, getToolkit, getToolkitImpl, getTreeLock, getWidth, getWindowForObject, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isDisplayable, isDoubleBuffered, isEnabled, isEnabledImpl, isFocusTraversable, isLightweight, isOpaque, isRecursivelyVisible, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, resetGC, reshape, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setForeground, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, show, show, size, toString, transferFocus |
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, registerNatives, wait, wait, wait |
| Field Detail |
static final java.lang.String VERSION
static final java.lang.String maeTitleVer
static final java.lang.String verStr
static boolean DBUG_TEST_PLUGIN_FLAG
static final boolean DBUG_TEST_R_OR_SPLUS_CHECKBOX
static final boolean DBUG_MAERlibr_ZIP_UPDATE
static final java.lang.String MAE_STARTUP_FILE
static final java.lang.String DEF_BASESERVER
private boolean onceOnlyFlag
static boolean CONSOLE_FLAG
static boolean NEVER
static final boolean DEBUG
static final boolean DBUG_LOGIN
static final boolean DBUG_HCN
static final boolean DBUG_STANDALONE
static boolean DBUG_GENOMIC_URLS_FLAG
static final boolean DBUG_QUALCHK_QUANT_FLAG
static final boolean DBUG_MEDMINER_FLAG
static final boolean PRINT_MEM_TIMES
static final boolean DBUG_SET_EGL_FROM_DENDROGRAM
static final boolean CANVAS_WRAPAROUND_BUG
static final boolean DBUG_NORM_PLUGIN
static final boolean DBUG_GENERIC_NORM_PLUGIN
GenNormalizationPlugin gnp
static final boolean DBUG_CV_DISPLAY_EPLIST
int LECBdebug
java.applet.Applet applet
static final int PSEUDOIMG_WIDTH
static final int PSEUDOIMG_HEIGHT
static final int X_AXIS
static final int Y_AXIS
static final int MAX_PROJECTS
static final int MAX_HYB_SAMPLES
static final int MAX_CONDITION_LISTS
public static final int MAX_COND_PARAM
static final int MAX_ORDERED_COND_LISTS
static final int N_EST_QUANT_FILES
static final int N_CONST_FILES
static boolean startupFileExistsFlag
boolean previousStartupState
java.lang.String configFile
ArrayScroller is
ClusterGenes clg
CompositeDatabase cdb
Condition cdList
Config cfg
ConfigTable cfgDB
GridCoords grcd
DrawPseudoImage dwPI
EditedGeneList egl
EventMenu em
FileIO fio
Filter fc
Gene gene
GeneClass gct
GeneGeneDist ccd
GeneList clLst
GipoTable gipo
GetParams gp
public static MaeJavaAPI mja
MaInfoTable infoDB
Maps mp
MenuBarFrame mbf
OverlayMap olmap
PopupRegistry pur
SampleSets hps
SamplesTable sampDB
SpotData sd
SpotFeatures sf
StageNames sg
StateScrollers stateScr
Statistics stat
UserState us
Util util
ClusterSamples clstrSamp
DryRotException dryRotExcept
static MaHybridSample ms
static MaHybridSample msPrev
static MaHybridSample msX
static MaHybridSample msY
static int curHP
static int curHP_X
static int curHP_Y
java.lang.String classNameX
java.lang.String classNameY
int scrWidth
int scrHeight
static java.lang.String dbID
static java.lang.String date
static java.lang.String osName
static java.lang.String codeBase
static java.lang.String saCodeBase
java.lang.String proxyServer
java.lang.String maeServerBase
static java.lang.String fileBasePath
java.lang.String docCodeBase
java.lang.String fileSeparator
java.lang.String dynFileSeparator
java.lang.String defSAprjName
static java.lang.String defDir
static java.lang.String defStartupFile
static java.lang.String defSAwebAddr
static java.lang.String startupDir
static java.lang.String startupFile
static java.lang.String prjListFile
java.lang.String cacheDir
static java.lang.String pluginsDir
static java.lang.String javaHome
boolean reuseGUIframeFlag
boolean isWinPCflag
static java.lang.String browserTitle
java.lang.String otherUserName
java.lang.String userName
java.lang.String userPasswd
static java.lang.String curPrjName
java.lang.String[] validPrj
int nValidPrj
boolean isLoggedInFlag
java.lang.String userStateName
int userStateIdx
java.awt.Image pImage
int pWidth
int pHeight
int MAX_INTENSITY
static final float MIN_RATIO
static final float MAX_RATIO
static final double[] histRatioBin
static final int MAX_RATIO_HIST
static final int MARKER_NONE
static final int MARKER_PLUS
static final int MARKER_CIRCLE
static final int MARKER_SQUARE
static final int MARKER_GENES
static final int MARKER_CURRENT
static final int MARKER_KMEANS_CLUSTER
static final int MASTER_GENE_NAME
static final int MASTER_UG_NAME
static final int MASTER_CLONE_ID
static final int MASTER_GENBANK
static final int MASTER_GENBANK5
static final int MASTER_GENBANK3
static final int MASTER_UG_ID
static final int MASTER_DBEST5
static final int MASTER_DBEST3
static final int MASTER_SWISS_PROT
static final int MASTER_LOCUSLINK
static final int MASTER_OMIM
static final int MASTER_GENERIC_ID
static final int QUALTYPE_ALPHA
static final int QUALTYPE_PROP_CODE
static final int QUALTYPE_THR
static final int DRAW_PLUS
static final int DRAW_CIRCLE
static final int DRAW_BOX
static final int DRAW_BIN
static final int RANGE_INSIDE
static final int RANGE_OUTSIDE
static final int COMPARE_ALL
static final int COMPARE_ANY
static final int COMPARE_PRODUCT
static final int COMPARE_SUM
static final int COMPARE_AT_MOST
static final int COMPARE_AT_LEAST
static final int SS_MODE_MS
static final int SS_MODE_XY
static final int SS_MODE_XSET
static final int SS_MODE_YSET
static final int SS_MODE_XORY_SETS
static final int SS_MODE_XANDY_SETS
static final int SS_MODE_ELIST
static final int EDIT_NOP
static final int EDIT_ADD
static final int EDIT_RMV
static final int PLOT_PSEUDOIMG
static final int PLOT_PSEUDO_HP_XY_RYG_IMG
static final int PLOT_PSEUDO_F1F2_RYG_IMG
static final int PLOT_PSEUDO_F1F2_IMG
static final int PLOT_PSEUDO_HP_XY_IMG
static final int PLOT_PSEUDO_HP_XY_P_VALUE_IMG
static final int PLOT_PSEUDO_HP_EP_CV_VALUE_IMG
static final int PLOT_F1_F2_INTENS
static final int PLOT_HP_XY_INTENS
static final int PLOT_F1_F2_MVSA
static final int PLOT_INTENS_HIST
static final int PLOT_HIST_F1F2_RATIO
static final int PLOT_HIST_HP_XY_RATIO
static final int PLOT_HIST_HP_XY_SETS_RATIO
static final int PLOT_EXPR_PROFILE
static final int PLOT_CLUSTER_GENES
static final int PLOT_CLUSTER_HIER
static final int PLOT_CLUSTER_HYBSAMPLES
static final int PLOT_CLUSTERGRAM
static final int PLOT_KMEANS_CLUSTERGRAM
static final int HIER_CLUST_PGMA_LNKG
static final int HIER_CLUST_PGMC_LNKG
static final int HIER_CLUST_NEXT_MIN_LNKG
static final int RPT_NONE
static final int RPT_TBL_HIGH_RATIO
static final int RPT_TBL_LOW_RATIO
static final int RPT_TBL_HIGH_F1F2
static final int RPT_TBL_LOW_F1F2
static final int RPT_TBL_FILTERED_GENES
static final int RPT_TBL_GENE_CLASS
static final int RPT_TBL_NAMED_GENES
static final int RPT_TBL_SAMPLES_DB_INFO
static final int RPT_TBL_HP_DB_INFO
static final int RPT_TBL_SAMPLES_WEB_LINKS
static final int RPT_TBL_EXPR_PROFILE
static final int RPT_TBL_HP_XY_SET_STAT
static final int RPT_TBL_CUR_GENE_CLUSTER
static final int RPT_TBL_ALL_GENES_CLUSTER
static final int RPT_TBL_KMEANS_CLUSTER
static final int RPT_TBL_MN_KMEANS_CLUSTER
static final int RPT_TBL_EDITED_GENE_LIST
static final int RPT_TBL_NORMALIZATION_GENE_LIST
static final int RPT_TBL_HP_HP_CORR
static final int RPT_TBL_CALIB_DNA_STAT
static final int RPT_TBL_HP_MN_VAR_STAT
static final int RPT_TBL_HIER_CLUSTER
static final int RPT_TBL_MAE_PRJ_DB
static final int RPT_TBL_OCL_STAT
static final int RPT_FMT_TAB_DELIM
static final int RPT_FMT_DYN
int maxPreloadImgs
java.lang.String[] iSampleName
java.lang.String[] iImageFile
int iHPnbr
int snHPnbr
int[] mapHPtoMenuName
java.lang.String[] snHPName
java.lang.String[] snHPSampleID
java.lang.String[] snHPDatabaseFileID
java.lang.String[] snImageFile
java.lang.String[] snHPMenuText
java.lang.String[] snHPFullStageText
java.lang.String[] snPrjName
boolean[] snNeedLogin
boolean[] snSwapCy5Cy3Data
boolean sortedGeneAndCloneIDListsFlag
int nFilesRead
int nFilesTotal
int runLoopDelayMsec
java.lang.Thread runT
int spotRad
static int canvasHSize
static int canvasVSize
float sit1
float sit2
float t1
float t2
float r1
float r2
float cr1
float cr2
java.lang.String rptFontSize
java.lang.String dryrotLogStr
boolean showEGLflag
boolean mReady
boolean isWorkingMAE
int plotImageMode
int editMode
int hierClustMode
int qualTypeMode
int posQuantTestMode
int goodSpotTestMode
int detValueSpotTestMode
int reportMode
int tblFmtMode
int spotIntensTestMode
int spotIntensRangeMode
int spotIntensCompareMode
int sampleIntensityRangeMode
int ratioRangeMode
int ratioCy3Cy5RangeMode
int cvTestMode
boolean isAppletFlag
boolean useWebDBflag
boolean enableFIOcachingFlag
boolean cacheFIOflag
boolean madeChangesFlag
boolean useCy5OverCy3Flag
boolean useMouseOverFlag
boolean flickerXYflag
boolean lowRangeZoomFlag
boolean isZscoreFlag
boolean useEPoverlayFlag
boolean swapRowsColsFlag
boolean useRatioDataFlag
boolean useHPxySetDataFlag
boolean useMeanHPeListDataFlag
boolean allowNegQuantDataFlag
boolean updatePseudoImgFlag
boolean usePseudoXYcoordsFlag
boolean dualXYpseudoPlotFlag
boolean reuseXYcoordsFlag
boolean noMsgReportFlag
boolean dieFlag
boolean abortFlag
boolean doGCflag
boolean killAppletFlag
boolean viewFilteredSpotsFlag
boolean useDichromasyFlag
boolean gangSpotFlag
boolean presentViewFlag
boolean useSPLUSasComputingEngineFlag
boolean useRLOloggingFlag
java.lang.String masterGeneName
java.lang.String masterIDname
int masterNameMode
int masterIDmode
java.lang.String reportRatioStr
java.lang.String normNameDisp
java.lang.String normName
boolean useGoodSpotsForGlobalStatsFlag
boolean bkgdCorrectFlag
boolean ratioMedianCorrectionFlag
boolean normByHousekeepGenesFlag
boolean normByGeneSetFlag
boolean normByCalDNAflag
boolean normByZscoreFlag
boolean normByMedianFlag
boolean normByLogMedianFlag
boolean normByZscoreMeanStdDevLogFlag
boolean normByZscoreMeanAbsDevLogFlag
boolean scaleDataToMaxIntensFlag
boolean testGenericNormPluginFlag
boolean useCorrCoeffFlag
boolean hierClustUnWtAvgFlag
boolean normHCbyRatioHPflag
boolean useMedianForKmeansClusteringFlag
boolean genBankViewerFlag
boolean dbESTviewerFlag
boolean uniGeneViewerFlag
boolean omimViewerFlag
boolean mAdbViewerFlag
boolean locusLinkViewerFlag
boolean medMinerViewerFlag
boolean swissProtViewerFlag
boolean pirViewerFlag
boolean[] genomicViewerFlag
boolean useEPrawIntensValFlag
boolean addExprProfileFlag
boolean addHP_XYstatFlag
boolean addOCLstatFlag
boolean autoStateScrPopupFlag
boolean useLowRatiosFilterFlag
boolean useHighRatiosFilterFlag
boolean spotIntensFilterFlag
boolean intensFilterFlag
boolean ratioFilterFlag
boolean ratioCy3Cy5FilterFlag
boolean geneClassMbrFilterFlag
boolean useGeneSetFilterFlag
boolean useRatioHistCLflag
boolean useIntensHistCLflag
boolean useEditedCLflag
boolean useGoodGeneCLflag
boolean useReplicateGenesFlag
boolean useCVmeanElseMaxFlag
boolean tTestXYfilterFlag
boolean tTestXYsetsFilterFlag
boolean KS_TestXYsetsFilterFlag
boolean F_TestOCLFilterFlag
boolean useSpotCVfilterFlag
boolean clusterHP_EfilterFlag
boolean useDiffFilterFlag
boolean usePosQuantDataFlag
boolean useGoodSpotDataFlag
boolean useDetValueSpotDataFlag
boolean useOnlyGenesWithNonZeroDensityFlag
boolean clusterOnFilteredCLflag
boolean useClusterDistFlag
boolean useSimGeneClusterDispFlag
boolean useClusterCountsDispFlag
boolean useHierClusterDispFlag
boolean useKmeansClusterCntsDispFlag
boolean useLSQmagNormFlag
boolean useClusterDistCacheFlag
boolean useShortClusterDistCacheFlag
| Constructor Detail |
public MAExplorer()
| Method Detail |
public static void main(java.lang.String[] args)
args - is the command line arg listprivate void clearDynamicState()
private void destroyStaticState()
ClusterGenes.cleanup(),
CompositeDatabase.cleanup(),
Condition.cleanup(),
EventMenu.cleanup(),
GeneGeneDist.cleanup(),
GeneList.cleanup(),
HierClustNode.cleanup(),
Util.cleanup()void resetDefaultstate()
Config.getStateParamValues()public void init()
init in class java.applet.AppletComponent.repaint(),
CompositeDatabase,
CompositeDatabase.recalcNorms(java.lang.String, boolean),
CompositeDatabase.setOBJtoGID(int, MaHybridSample),
Config.getStateParamValues(),
Config.setupFullpathFilenames(),
Config.setupPathBase(MAExplorer),
Condition,
DrawPseudoImage,
EditedGeneList,
EventMenu,
EventMenu.setPlotState(java.awt.CheckboxMenuItem),
Filter,
Filter.computeWorkingGeneList(),
FileIO,
Gene,
GeneClass,
GeneClass.assignGeneNames2StaticGeneList(),
GeneClass.setCurrentGeneClassName(java.lang.String),
GeneClass.setupSpecialGeneLists(),
GeneClass.updateStdGenePartitions(),
GeneGeneDist,
GeneList,
GetParams,
GipoTable,
GipoTable.copyGBCTdataToStaticGeneDB(),
GipoTable.copyGeneNamesTableFile(),
GridCoords,
MaeJavaAPI,
MaeJavaAPI.initStateAndMJAchildren(MAExplorer),
Maps,
MaInfoTable,
MenuBarFrame,
MenuBarFrame.callAllStartupPlugins(),
MenuBarFrame.enableMenus(java.lang.String),
MenuBarFrame.redoMenuBar(),
Frame.setTitle(java.lang.String),
PopupRegistry,
SamplesTable,
SampleSets,
SamplesTable.readListOfSampleNames(),
Component.repaint(),
StageNames,
StageNames.getMenuTreeFromSamplesTable(MAExplorer),
SpotData,
SpotFeatures,
Statistics,
SimpleTable.freeTable(),
UserState,
Util,
Util.chkDirFinalSeparator(java.lang.String, java.lang.String),
Util.getRatioStr(),
Util.popupDryrotMsgsAndQuit(),
Util.popupViewer(java.net.URL, java.lang.String, java.lang.String),
Util.showMsg(java.lang.String),
Util.showMsg2(java.lang.String),
Util.showMsg3(java.lang.String),
doAnyLoginsRequired(),
clearDynamicState(),
destroy2(),
destroyStaticState(),
Applet.getParameter(java.lang.String),
readListOfSampleDataFiles(),
Component.repaint(),
resetDefaultstate()public void start()
start in class java.applet.Appletpublic void stop()
stop in class java.applet.Appletpublic void run()
run in interface java.lang.RunnableFileIO.logMsgln(java.lang.String),
PopupRegistry.checkStringPopupTimeouts(int),
Component.repaint(),
Util.sleepMsec(int),
destroy(),
stop()public void paint(java.awt.Graphics g)
paint in class java.awt.Containerg - is graphics contextArrayScroller.syncScrollerAccess()public void update(java.awt.Graphics g)
update in class java.awt.Containerg - is graphics contextprivate boolean doAnyLoginsRequired()
Util.popupDryrotMsgsAndQuit(),
Util.showMsg(java.lang.String),
UserState.validateUserProject(java.lang.String, java.lang.String, java.lang.String),
logDRYROTerr(java.lang.String)boolean readListOfSampleDataFiles()
Condition.addCondList(java.lang.String, MaHybridSample[], int, int),
GetParams.setDefParam(java.lang.String, boolean),
MenuBarFrame.setHP_XYlabels(),
MaHybridSample,
SampleSets.addHPtoDB(MaHybridSample, int),
SampleSets.setHPlistsFromPARAM(),
Util.popupDryrotMsgsAndQuit(),
UserState.restoreCondLists(),
createSample(int, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, boolean, boolean)MaHybridSample createSample(int hpNbr,
java.lang.String hpName,
java.lang.String sampleID,
java.lang.String databaseFileID,
java.lang.String oImageName,
java.lang.String oMenuName,
java.lang.String fullStageText,
java.lang.String projectName,
boolean needLoginFlag,
boolean swapCy5Cy3DataFlag)
hpNbr - is the sample numberhpName - is the sample file namesampleID - is the free-form name of the sampledatabaseFileID - is the optional database file ID (used with mAdb)oImageName - is the optional image file nameoMenuName - is the name of this sample as it appears in the menufullStageText - is the full text specification of this sampleprojectName - project this database belongs toneedLoginFlag - requires login to access data from Web server if needed.swapCy5Cy3DataFlag - set if swap Cy3 and Cy5 channels.MaHybridSamplevoid chkIfCache()
void resetImageAndState()
resetDefaultstate(),
GeneClass.setupSpecialGeneLists(),
Component.repaint()void quit()
Component.setVisible(boolean),
Window.dispose()int percentDone()
Util.showMsg3(java.lang.String)void cleanup()
destroyStaticState(),
FileIO.logMsgln(java.lang.String)public void destroy()
destroy in class java.applet.Appletdestroy2()void destroy2()
FileIO.closeLogFile(),
FileIO.logMsgln(java.lang.String),
cleanup()void logDRYROTerr(java.lang.String msg)
msg - is the dryrot message to printFileIO.logMsg(java.lang.String)
|
||||||||||
| PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
| SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD | |||||||||