Class MJApopupRegistry

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

public class MJApopupRegistry

extends MJAbase

MAExplorer Open Java API class to access MJApopupRegistry methods and data structures. Access the Popup Registry.

List of methods available to Plugin-writers

 addUniquePopupWindowToReg() - register popupWindowInstance window with keyName
 addPopupWindowToReg() - register popupWindowInstance window with keyName
 removePopupByKey() - remove popupWindowInstance by keyName
 doesPopupExistByKey() - does popup Window Instance exist by keyName
 doesUniquePopupExistByKey() - does unique popupWindow exist by keyName
 invokeUpdateCurGene() - invoke popup updates with current gene and mouseKeyMods
 invokeUpdateFilter() - invoke registered popups updates for data filter changed   
 invokeUpdateSlider() - invoke registered popups updates for slider state data changed
 invokeUnvokeUpdateLabels() - invoke registered popups updates for sample labels, etc data changed
 chkOtherCurGeneEffects() - check for other current gene effects when change MID
 updateCurGeneInImageAndReg() - update current gene in PseudoArray image and registry
 setWaitCursor() - set wait cursor ON/OFF to clock or standard cursor

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: 2002/10/14 20:19:25 $ $Revision: $

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	addPopupWindowToReg(MAEUpdateListener maePluginInstance, java.lang.String keyName, int propBits) addPopupWindowToReg() - register instance of MAEPlugin window with keyName
int	addUniquePopupWindowToReg(MAEUpdateListener popupWindowInstance, java.lang.String keyName, int propBits) addUniquePopupWindowToReg() - register popupWindowInstance window with keyName
boolean	chkOtherCurGeneEffects(int mid, int mouseKeyMods) chkOtherCurGeneEffects() - check for other current gene effects when change MID
boolean	doesPopupExistByKey(java.lang.String keyName) doesPopupExistByKey() - does instance of registered MAEPlugin exist by keyName
boolean	doesUniquePopupExistByKey(java.lang.String keyName) doesUniquePopupExistByKey() - does unique instance of registered MAEPlugin exist by keyName
boolean	invokeUpdateCurGene(java.lang.Object maepluginInstance, int mid, int mouseKeyMods) invokeUpdateCurGene() - invoke updates for registered popups and plugins for current gene.
boolean	invokeUpdateFilter() invokeUpdateFilter() - invoke registered plugins updates for data filter changed
boolean	invokeUpdateLabels() invokeUnvokeUpdateLabels() - invoke registered plugins updates for sample labels, etc data changed
boolean	invokeUpdateSlider() invokeUpdateSlider() - invoke registered plugins updates for slider state data changed
boolean	removePopupByKey(java.lang.String keyName) removePopupByKey() - remove instance of MAEPlugin by keyName
boolean	setWaitCursor(boolean status) setWaitCursor() - set wait cursor ON/OFF to clock or standard cursor
boolean	updateCurGeneInImageAndReg(int mid) updateCurGeneInImageAndReg() - update current gene in PseudoArray image and registry If the current gene is defined (i.e.

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

addUniquePopupWindowToReg

public final int addUniquePopupWindowToReg(MAEUpdateListener popupWindowInstance,
                                           java.lang.String keyName,
                                           int propBits)

addUniquePopupWindowToReg() - register popupWindowInstance window with keyName

Parameters:

popupWindowInstance - instance of popup window

keyName - key name associated with popupWindowInstance

propBits - property bits associated with popupWindowInstance

Returns:

number of objects of this type, -1 if failed.

addPopupWindowToReg

public final int addPopupWindowToReg(MAEUpdateListener maePluginInstance,
                                     java.lang.String keyName,
                                     int propBits)

addPopupWindowToReg() - register instance of MAEPlugin window with keyName

Parameters:

maePluginInstance - instance of MAEPlugin

keyName - key name associated with maePluginInstance

propBits - property bits associated with maePluginInstance

Returns:

number of objects of this type, -1 if failed.

removePopupByKey

public final boolean removePopupByKey(java.lang.String keyName)

removePopupByKey() - remove instance of MAEPlugin by keyName

Parameters:

keyName - key name associated with registered instance of MAEPlugin

Returns:

true if succeed, else false if problem

doesPopupExistByKey

public final boolean doesPopupExistByKey(java.lang.String keyName)

doesPopupExistByKey() - does instance of registered MAEPlugin exist by keyName

Parameters:

keyName - key name associated with popup Window Instance

Returns:

true if popup exists.

doesUniquePopupExistByKey

public final boolean doesUniquePopupExistByKey(java.lang.String keyName)

doesUniquePopupExistByKey() - does unique instance of registered MAEPlugin exist by keyName

Parameters:

keyName - key name associated with popup Window Instance

Returns:

true if unique popup exists.

invokeUpdateCurGene

public final boolean invokeUpdateCurGene(java.lang.Object maepluginInstance,
                                         int mid,
                                         int mouseKeyMods)

invokeUpdateCurGene() - invoke updates for registered popups and plugins for current gene. The effect of the updates depending on mouseKeyMods specified.

 mouseKeyMods         Effect
  none                   set current gene
  InputEvent.CTRL_MASK   set current gene and add it to Edited Gene List
  InputEvent.SHIFT_MASK  set current gene and remove it from Edited Gene List

Parameters:

maepluginInstance - (opt) instance of plugin to avoid calling if not null (specify 'this' to avoid calling oneself)

mid - current gene if required

mouseKeyMods - mouse key modifier bits associated with mouse press

Returns:

true if succeed, false if failed for any reason.

invokeUpdateFilter

public final boolean invokeUpdateFilter()

invokeUpdateFilter() - invoke registered plugins updates for data filter changed

Returns:

true if succeed, else false if any error

invokeUpdateSlider

public final boolean invokeUpdateSlider()

invokeUpdateSlider() - invoke registered plugins updates for slider state data changed

Returns:

true if succeed, else false if any error

invokeUpdateLabels

public final boolean invokeUpdateLabels()

invokeUnvokeUpdateLabels() - invoke registered plugins updates for sample labels, etc data changed

Returns:

true if succeed, else false if any error

chkOtherCurGeneEffects

public final boolean chkOtherCurGeneEffects(int mid,
                                            int mouseKeyMods)

chkOtherCurGeneEffects() - check for other current gene effects when change MID

 mouseKeyMods         Effect
  none                   set current gene
  InputEvent.CTRL_MASK   set current gene and add it to Edited Gene List
  InputEvent.SHIFT_MASK  set current gene and remove it from Edited Gene List

Parameters:

mid - current gene if required

mouseKeyMods - bits associated with mouse press

Returns:

true if succeed, else false if any error

updateCurGeneInImageAndReg

public final boolean updateCurGeneInImageAndReg(int mid)

updateCurGeneInImageAndReg() - update current gene in PseudoArray image and registry If the current gene is defined (i.e. not -1), then check and update the following if they are enabled:

    1. modifying the 'editable gene list',
    2. poping up a web browser on external GenBank data (if enabled),
    3. change the gene used in the 'single' expression profile plot,
    4. update cluster algorithms and redraw overlays in pseudoarray image.

Parameters:

mid - current gene if required (-1 if not)

Returns:

true if succeed, else false if any error

setWaitCursor

public final boolean setWaitCursor(boolean status)

setWaitCursor() - set wait cursor ON/OFF to clock or standard cursor

Parameters:

status - turn clock (ON) or standard cursor (OFF)

Returns:

false if method was not found or method failed, otherwise the flag returned by the method.