Class MJAreport

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

public class MJAreport

extends MJAbase

MAExplorer Open Java API class to access MJAreport methods and data structures.

List of methods available to Plugin-writers

 get_useEPrawIntensityValuesFlag() - use Raw intens for EP ratios in REPORTS
 set_useEPrawIntensityValuesFlag() - use Raw intens for EP ratios in REPORTS
 get_addExprProfileFlag() - add EP ratios in gene REPORTS
 set_addExprProfileFlag() - add EP ratios in gene REPORTS
 get_addHP_XYstatFlag() - add HP_XY statistics in gene REPORTS
 set_addHP_XYstatFlag() - add HP_XY statistics in gene REPORTS
 --------------------------- Create TextArea Reports -----------------
 readTextFromFile() - read text from text file.
 writeTextToFile() - save text string as text file.
 popupTextReport() - popup a repoot window with a scrollable text area
 updateTextReportText() - update text in popup report window
 closePopupTextReportWindow() - close Popup Report Window
 --------------------------- Create TextArea Reports -----------------

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: 2003/03/26 16:16:43 $ $Revision: 1.8 $

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

void	closePopupTextReportWindow(java.lang.Object obj) closePopupTextReportWindow() - close Popup Report Window
boolean	get_addExprProfileFlag() get_addExprProfileFlag() - get flag: add EP ratios in gene REPORTS
boolean	get_addHP_XYstatFlag() get_addHP_XYstatFlag() - get flag: add HP_XY statistics in gene REPORTS
boolean	get_useEPrawIntensityValuesFlag() get_useEPrawIntensityValuesFlag() - get flag: use Raw intensity for EP ratios in gene REPORTS
java.lang.Object	popupTextReport(java.lang.String inputStr, int nRows, int nCols, java.lang.String fontSize, java.lang.String title, int optReportMode, int optMode, java.lang.String popupName, int popupPropertyBits, java.lang.String defTxtFile) popupTextReport() - popup a report window with a scrollable text area
java.lang.String	readTextFromFile(java.lang.String textFileName) readTextFromFile() - read text from text file.
void	set_addExprProfileFlag(boolean value) set_addExprProfileFlag() - set flag: add EP ratios in gene REPORTS
void	set_addHP_XYstatFlag(boolean value) set_addHP_XYstatFlag() - set flag: add HP_XY statistics in gene REPORTS
void	set_useEPrawIntensityValuesFlag(boolean value) set_useEPrawIntensityValuesFlag() - set flag: use Raw intensity for EP ratios in gene REPORTS
void	updateTextReportText(java.lang.String textReport, java.lang.Object obj) updateTextReportText() - update text in popup report window
boolean	writeTextToFile(java.lang.String textFileName, java.lang.String textReport) writeTextToFile() - save text string as text file.

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

get_useEPrawIntensityValuesFlag

public final boolean get_useEPrawIntensityValuesFlag()

get_useEPrawIntensityValuesFlag() - get flag: use Raw intensity for EP ratios in gene REPORTS

Returns:

value

set_useEPrawIntensityValuesFlag

public final void set_useEPrawIntensityValuesFlag(boolean value)

set_useEPrawIntensityValuesFlag() - set flag: use Raw intensity for EP ratios in gene REPORTS

Parameters:

value - to set the flag

get_addExprProfileFlag

public final boolean get_addExprProfileFlag()

get_addExprProfileFlag() - get flag: add EP ratios in gene REPORTS

Returns:

value

set_addExprProfileFlag

public final void set_addExprProfileFlag(boolean value)

set_addExprProfileFlag() - set flag: add EP ratios in gene REPORTS

Parameters:

value - to set the flag

get_addHP_XYstatFlag

public final boolean get_addHP_XYstatFlag()

get_addHP_XYstatFlag() - get flag: add HP_XY statistics in gene REPORTS

Returns:

value

set_addHP_XYstatFlag

public final void set_addHP_XYstatFlag(boolean value)

set_addHP_XYstatFlag() - set flag: add HP_XY statistics in gene REPORTS

Parameters:

value - to set the flag

readTextFromFile

public final java.lang.String readTextFromFile(java.lang.String textFileName)

readTextFromFile() - read text from text file.

Parameters:

textFileName - full path name of text file

Returns:

text if suceed else null

writeTextToFile

public final boolean writeTextToFile(java.lang.String textFileName,
                                     java.lang.String textReport)

writeTextToFile() - save text string as text file.

Parameters:

textFileName - full path name of text file

textReport - text to save in file

Returns:

true if succeed.

popupTextReport

public final java.lang.Object popupTextReport(java.lang.String inputStr,
                                              int nRows,
                                              int nCols,
                                              java.lang.String fontSize,
                                              java.lang.String title,
                                              int optReportMode,
                                              int optMode,
                                              java.lang.String popupName,
                                              int popupPropertyBits,
                                              java.lang.String defTxtFile)

popupTextReport() - popup a report window with a scrollable text area

Parameters:

inputStr - is the initial text string to display

nRows - # of rows of text in the window

nCols - # of rows of text in the window

fontSize - is the font size: null or "8pt", "10pt", or "12pt"

title - for the window

optReportMode - report mode for adding extra buttons if if not 0

optMode - is the save the mode used when closing

popupName - name used by PopupRegistry to track this window

popupPropertyBits - forPopupRegistry to determine registry actions

defTxtFile - is text file name used as the default SAVE AS .txt file

Returns:

object representing this popup report window used for other calls.

updateTextReportText

public final void updateTextReportText(java.lang.String textReport,
                                       java.lang.Object obj)

updateTextReportText() - update text in popup report window

Parameters:

textReport - is new text to update in the report

obj - is the object returned by popupStringReport()

closePopupTextReportWindow

public final void closePopupTextReportWindow(java.lang.Object obj)

closePopupTextReportWindow() - close Popup Report Window