Class MJAgeometry

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

public class MJAgeometry

extends MJAbase

MAExplorer Open Java API class to access MJAgeometry methods and data structures. Note: GID is the Grid coordinates ID, MID is Master gene ID, FGRC is (Field,Grid,Row,Col) spot location. Access geometry description of the arrays.

List of methods available to Plugin-writers

 
 getMaxGenes() - get number of genes in the database
 getMaps() - get Hashtablelist of a array geometry and MAExplorer maps
 getNbrMasterIDs() - get the number of Master Gene IDs
 getNbrGridIDs() - get the number of genes
 getNbrSpots() - get the number of Nbr Spots in entire array
 getMaxFields() - get the number of Max replicate grid Fields
 getMaxGrids() - get the number of Max Grids in the array
 getMaxGridRows() - get the number of rows/grid in the array
 getMaxGridCols() - get the number of columns/grid in the array
 getMasterGeneIDMap() - get the map of mid to gene.
 getGridIndexMap() - get the map of mid to gene.
 getFGRCtoGIDmap() - get map of [field][grid][grid_row][grid_col]'s to gids 
 getGIDtoFGRCmap() - get the map of GIDs to FGRC 5-tuples
 getMIDtoGIDmap() - get the map from MIDs to GIDs
 getGIDtoMIDmap() - get the map from GIDs to MIDs 
 getGIDtoGangGIDmap() - get the map from GIDs to Ganged GIDs
 lookupMIDtoGID() - lookup MID given the GID
 lookupGIDtoMID() - lookup GID given the MID
 lookupGIDtoGangGID() - lookup ganged GID given the GID

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 20:21:43 $ $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[][][][]	getFGRCtoGIDmap() getFGRCtoGIDmap() - get map of [field][grid][grid_row][grid_col] to gid (GridCoords index GID).
int[][]	getGIDtoFGRCmap() getGIDtoFGRCmap() - get the map of GIDs to FGRC 5-tuples Each map entry is {gid, field, grid, row, column}
int[]	getGIDtoGangGIDmap() getGIDtoGangGIDmap() - get the map from GIDs to Ganged GIDs
int[]	getGIDtoMIDmap() getGIDtoMIDmap() - get the map from GIDs to MIDs
int[]	getGridIndexMap() getGridIndexMap() - get the map of mid to gene.
java.util.Hashtable	getMaps() getMaps() - get Hashtable list of a MAExplorer maps
int[]	getMasterGeneIDMap() getMasterGeneIDMap() - get the map of mid to gene.
int	getMaxFields() getMaxFields() - get the number of Max replicate grid Fields
int	getMaxGenes() getMaxGenes() - get number of genes in the database
int	getMaxGridCols() getMaxGridCols() - get the number of columns/grid in the array
int	getMaxGridRows() getMaxGridRows() - get the number of rows/grid in the array
int	getMaxGrids() getMaxGrids() - get the number of Max Grids in the array not counting replicate fields.
int[]	getMIDtoGIDmap() getMIDtoGIDmap() - get the map from MIDs to GIDs
int	getNbrGridIDs() getNbrGridIDs() - get the number of genes
int	getNbrMasterIDs() getNbrMasterIDs() - get the number of Master Gene IDs
int	getNbrSpots() getNbrSpots() - get the number of Nbr Spots in entire array
int	lookupGIDtoGangGID(int gid) lookupGIDtoGangGID() - lookup ganged GID given the GID
int	lookupGIDtoMID(int gid) lookupGIDtoMID() - lookup GID given the MID
int	lookupMIDtoGID(int mid) lookupMIDtoGID() - lookup MID given the GID

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

getMaxGenes

public final int getMaxGenes()

getMaxGenes() - get number of genes in the database

Returns:

value else null if not found.

getMaps

public final java.util.Hashtable getMaps()

getMaps() - get Hashtable list of a MAExplorer maps

 The list returned is defined as:
 Name                - Value
 "NbrMasterIDs"       - int # of MIDs (Master IDs) in DB  and
                        MasterGeneIndexMap
 "NbrGridIDs"         - int # of GIDs (GridCoords Index) in DB
 "NbrSpots"           - int # of spots in the database and GridIndexMap
 "MaxFields"          - int number of microarray duplicate grid fields
 "MaxGrids"           - int number of microarray grids
 "MaxGridRows"        - int number of microarray grid rows
 "MaxGridCols"        - int number of microarray grid columns
 "MasterGeneIDMap"    - int[0:NbrMasterIDs]  Master gene ID (MID) list
 "GridIndexMap"       - int[0:NbrGridIDs] master Grid Index (GID) list
 "FGRCtoGIDmap"       - int [0:MaxFields][0:MaxGrids][0:MaxGridRows1]
                           [0:MaxGridCols] maps [f][g][r][c] to GID
 "GIDtoFGRCmap"       - int[0:NbrGridIDs][0:4] maps GID to a
                           list (gid,f,g,r,c)
 "MIDtoGIDmap"        - int[0:NbrMasterIDs] maps MID to GID
 "GIDtoMIDmap"        - int[0:NbrGridIDs] maps GID to MID
 "GIDtoGangGIDmap"    - int[0:NbrGridIDs] maps GID to Gang GID
 

Returns:

null if not found or error, else return list.

getNbrMasterIDs

public final int getNbrMasterIDs()

getNbrMasterIDs() - get the number of Master Gene IDs

Returns:

value

getNbrGridIDs

public final int getNbrGridIDs()

getNbrGridIDs() - get the number of genes

Returns:

value

getNbrSpots

public final int getNbrSpots()

getNbrSpots() - get the number of Nbr Spots in entire array

Returns:

value

getMaxFields

public final int getMaxFields()

getMaxFields() - get the number of Max replicate grid Fields

Returns:

value

getMaxGrids

public final int getMaxGrids()

getMaxGrids() - get the number of Max Grids in the array not counting replicate fields. The total # of grids is (MaxGrids * MaxFields).

Returns:

value

getMaxGridRows

public final int getMaxGridRows()

getMaxGridRows() - get the number of rows/grid in the array

Returns:

value

getMaxGridCols

public final int getMaxGridCols()

getMaxGridCols() - get the number of columns/grid in the array

Returns:

value

getMasterGeneIDMap

public final int[] getMasterGeneIDMap()

getMasterGeneIDMap() - get the map of mid to gene. Entries with -1 indicate there is no gene at that Master Gene ID location.

Returns:

value

getGridIndexMap

public final int[] getGridIndexMap()

getGridIndexMap() - get the map of mid to gene. Entries with -1 indicate there is no spot at that Grid Index location.

Returns:

value

getFGRCtoGIDmap

public final int[][][][] getFGRCtoGIDmap()

getFGRCtoGIDmap() - get map of [field][grid][grid_row][grid_col] to gid (GridCoords index GID).

Returns:

map [field][grid][grid_row][grid_col] to lookup gids

getGIDtoFGRCmap

public final int[][] getGIDtoFGRCmap()

getGIDtoFGRCmap() - get the map of GIDs to FGRC 5-tuples Each map entry is {gid, field, grid, row, column}

Returns:

map array[0:maxSpots][0:4] of 5-tuples.

getMIDtoGIDmap

public final int[] getMIDtoGIDmap()

getMIDtoGIDmap() - get the map from MIDs to GIDs

Returns:

map

getGIDtoMIDmap

public final int[] getGIDtoMIDmap()

getGIDtoMIDmap() - get the map from GIDs to MIDs

Returns:

map

getGIDtoGangGIDmap

public final int[] getGIDtoGangGIDmap()

getGIDtoGangGIDmap() - get the map from GIDs to Ganged GIDs

Returns:

value

lookupMIDtoGID

public final int lookupMIDtoGID(int mid)

lookupMIDtoGID() - lookup MID given the GID

Returns:

GID value or -1 if an error

lookupGIDtoMID

public final int lookupGIDtoMID(int gid)

lookupGIDtoMID() - lookup GID given the MID

Returns:

MID value or -1 if an error

lookupGIDtoGangGID

public final int lookupGIDtoGangGID(int gid)

lookupGIDtoGangGID() - lookup ganged GID given the GID

Returns:

value