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java.lang.Object | +--MJAbase | +--MJAgeometry
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/.
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 |
public final int getMaxGenes()
null
if not found.public final java.util.Hashtable getMaps()
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
null
if not found or error, else return list.public final int getNbrMasterIDs()
public final int getNbrGridIDs()
public final int getNbrSpots()
public final int getMaxFields()
public final int getMaxGrids()
public final int getMaxGridRows()
public final int getMaxGridCols()
public final int[] getMasterGeneIDMap()
public final int[] getGridIndexMap()
public final int[][][][] getFGRCtoGIDmap()
public final int[][] getGIDtoFGRCmap()
public final int[] getMIDtoGIDmap()
public final int[] getGIDtoMIDmap()
public final int[] getGIDtoGangGIDmap()
public final int lookupMIDtoGID(int mid)
public final int lookupGIDtoMID(int gid)
public final int lookupGIDtoGangGID(int gid)
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