Class MJAcondition

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

public class MJAcondition

extends MJAbase

MAExplorer Open Java API class to access MJAcondition methods and data structures. This contains methods for manipulating condition lists of samples and ordered lists of condition lists. Conditions are sets of samples. You may also have ordered lists of conditions. The latter would be the case in an ordered list of conditions (eg. cell cycle points) with replicate samples in each condition.

List of methods available to Plugin-writers
 --------------- Lists of Condition Lists --------------- 
 getMaxCondListSize() - get maximum # of samples condition list can hold
 getMaxNbrSamplesInDB() - get maximum # of samples database list can hold
 getMaxNbrCondParams() - get maximum # of condition parameters DB may hold
 getNbrCondLists() - get # of active condition lists 
 getCondListsNames() - get list of active condition lists names
 getCondListsSizes() - get list of active condition lists sizes
 createNewCondList() - create new named condition list
 isCondList() - tests if this is a name of a condition list
 removeCondList() - remove named condition list if it exists
 renameCondList() - rename userListName if it exists to newListName.
 addSampleToCondList() - add sample to named condition list
 removeSampleFromCondList() - remove sample from named condition list
 removeAllSamplesFromCondList() - Remove all samples from cond list.
 isSampleInCondList() - is sample in named condition list?
 getCondListLength() - get # of samples in the condition list
 getSamplesInCondList() - get list of sample numbers in named condition 
 getSampleNamesInCondList() - get list of sample names for named condition 
 getAllSampleNamesInDB() - get list of all sample names in the database
 getSampleNbrByCondNameAndSampleName() - get sample number by sample name & condition name.
 getListCondListsStr() - get list of Conditions pretty-print string
 updateListCondLists() - update existing Condition list window if active.
 popupAllConditionsReport() - popup a report showing list of all conditions
 popupListConditionReport() - popup a report showing list of samples for condition

 --------------- get Lists of Ordered Condition Lists ---------------
 getMaxOrderedCondListSize() - get max # condition lists an ordered cond. list can hold
 getNbrOrderedCondLists() - get # of active ordered condition lists
 getOrderedCondListsNames() - get list of active ordered condition lists names
 getOrderedCondListsSizes() - get list of active ordered condition lists sizes
 getOrderedCondNamesInCondList() - get a list of all conditions in order cond list

 --------------- manipulate Lists of Ordered Condition Lists ---------------
 createNewNamedOrderedCondList() - create new named ordered list of conditions
 removeNamedOrderedCondList() - remove named ordered list of conditions
 isConditionInOrderedCondList() - test if condition is in named ordered condition list.
 getConditionIdxInOrderedCondList() - get condition index in named ordered condition list.   
 addConditionToOrderedCondList() - add condition list to named ordered condition list.
 rmvConditionFromOrderedCondList() - remove condition list from named ordered condition list.
 getNamedOrderedCondListIdx() - lookup named ordered condition list index
 getConditionsInOrderedCondList() - get list of names conditions in OCL
 getAllCondNames()- get a list of all condition names.
 isOrderedCondList() - tests if this is a name of an ordered condition list
 removeAllCondsFromOrderedCondList() - Remove all conditions from condList
 setCondInOrderedCondList() - replace existing conditions with new list
 popupListOCLReport() - popup a report showing list of conds for OCL
 popupAllOCLsReport() - popup a report showing list of all OCLs
 getCurOCL() - return the name of the current OCL if it exists
 setCurOCL() - set the name of the current OCL

 --------------- ordered conditions parameters -----------------------------
 getMaxNbrOCLParams() - return max number of Ordered Condition List parameters.
 getOrderedCondParamNames() - return list of Ordered condition paramter names. 
 setOclParamNames() - set list of ocl parameter names for all conditions
 setOclParamValues() - set list of ocl parameter values for specific condition

 ------------------------- Set Lists of Conditions ----------------
 setNbrCondLists() - Set # of active condition lists 
 setCondListsNames() - Set list of active condition lists names
 setCondListsSizes() - Set list of active condition lists sizes
 setCondListLength() - Set # of samples in the condition list 
 setSamplesInCondList() - Set list of sample numbers in named condition.
 setSampleNamesInCondList() - Set list of sample names in named condition.
 getCurCondition() - return the name of the current condition if it exists
 setCurCondition() - set the name of the current condition

 ------------------------- set-theoretic methods ----------------------------
 union() - compute resultCond= Union (Condition 1, Condition 2)
 intersection() - compute resultCond= Intersection (Condition 1, Condition 2)
 difference() - compute resultCond = difference (Condition 1 - Condition 2)

 ------------------------- get condition parameter methods ------------------
 getNbrCondParams() - get the number of condition parameters
 getCondParamNames() - get list of condition parameter names for all conditions
 getOrderedCondParamValues() - return list of Ordered condition paramter values. 

 ------------------------- set condition parameter methods ------------------ 
 setCondParamNames() - set list of condition parameter names for all conditions
 setCondParamValues() - set list of parameter values for specific condition
 
 

 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: 2003/02/18 18:02:33 $   $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




 boolean
addConditionToOrderedCondList(java.lang.String condName,
                              java.lang.String oCondListName)



          addConditionToOrderedCondList() - add condition to named ordered condition list.



 boolean
addSampleToCondList(int sampleNbr,
                    java.lang.String condName)



          addSampleToCondList() - add sample to named condition list



 boolean
createNewCondList(java.lang.String condName)



          createNewCondList() - create new named condition list



 boolean
createNewNamedOrderedCondList(java.lang.String oCondListName)



          createNewNamedOrderedCondList() - create new named ordered condition list
 of conditions if it does not already exist - in which case do nothing.



 boolean
difference(java.lang.String cond1Name,
           java.lang.String cond2Name,
           java.lang.String resultCondName)



          difference() - compute resultCond = difference (Condition 1 - Condition 2)



 java.lang.String[]
getAllCondNames()



          getAllCondNames()- get a list of all condition names.



 java.lang.String[]
getAllSampleNamesInDB()



          getAllSampleNamesInDB() - get list of all sample names in the database



 int
getConditionIdxInOrderedCondList(java.lang.String cdName,
                                 java.lang.String oCondListName)



          getConditionIdxInOrderedCondList() - get condition index in named ordered condition list.



 java.lang.String[]
getConditionsInOrderedCondList(java.lang.String oCondListName)



          getConditionsInOrderedCondList() - get list of names conditions in OCL



 int
getCondListLength(java.lang.String condName)



          getCondListLength() - get # of samples in the condition list



 java.lang.String[]
getCondListsNames()



          getCondListsNames() - get list of active condition lists names



 int[]
getCondListsSizes()



          getCondListsSizes() - get list of active condition lists sizes



 java.lang.String[]
getCondParamNames()



          getCondParamNames() - get list of condition parameter names for all conditions



 java.lang.String[]
getCondParamValues(java.lang.String condName)



          getCondParamValues() - get list of parameter values for specific condition



 java.lang.String
getCurCondition()



           



 java.lang.String
getCurOCL()



           



 java.lang.String
getListCondListsStr()



          getListCondListsStr() - get list of Conditions pretty-print string



 int
getMaxCondListSize()



          getMaxCondListSize() - get maximum # of samples condition list can hold



 int
getMaxNbrCondParams()



          getMaxNbrCondParams() - get maximum # of condition parameters DB may hold



 int
getMaxNbrOCLParams()



          getMaxNbrOCLParams() - return max number of Ordered Condition List parameters.



 int
getMaxNbrSamplesInDB()



          getMaxNbrSamplesInDB() - get maximum # of samples database list can hold



 int
getMaxOrderedCondListSize()



          getMaxOrderedCondListSize() - get maximum # of condition lists that an
 ordered condition list can hold



 int
getNamedOrderedCondListIdx(java.lang.String oCondListName)



          getNamedOrderedCondListIdx() - get named ordered condition list index



 int
getNbrCondLists()



          getNbrCondLists() - get # of active condition lists



 int
getNbrCondParams()



          getNbrCondParams() - get the number of condition parameters



 int
getNbrOrderedCondLists()



          getNbrOrderedCondLists() - get # of active ordered condition lists



 java.lang.String[]
getOrderedCondListsNames()



          getOrderedCondListsNames() - get list of active ordered condition lists names



 int[]
getOrderedCondListsSizes()



          getOrderedCondListsSizes() - get list of active ordered condition lists sizes



 java.lang.String[]
getOrderedCondNamesInCondList(java.lang.String orderedCondListName)



          getOrderedCondNamesInCondList() - get a list of all condition names in ordered cond list



 java.lang.String[]
getOrderedCondParamNames()



          getOrderedCondParamNames() - return list of Ordered condition paramter names.



 java.lang.String[]
getOrderedCondParamValues(java.lang.String oclName)



          getOrderedCondParamValues() - return list of Ordered condition paramter values.



 java.lang.String[]
getSampleNamesInCondList(java.lang.String condName)



          getSampleNamesInCondList() - get list of sample names in named condition.



 int
getSampleNbrByCondNameAndSampleName(java.lang.String condName,
                                    java.lang.String sampleName)



          getSampleNbrByCondNameAndSampleName() - get sample number by sample name and condition name.



 int[]
getSamplesInCondList(java.lang.String condName)



          getSamplesInCondList() - get list of sample numbers in named condition.



 boolean
intersection(java.lang.String cond1Name,
             java.lang.String cond2Name,
             java.lang.String resultCondName)



          intersection() - compute resultCond= Intersection (Condition 1, Condition 2)



 boolean
isConditionInOrderedCondList(java.lang.String condName,
                             java.lang.String oCondListName)



          isConditionInOrderedCondList() - test if condition is in named ordered condition list.



 boolean
isCondList(java.lang.String condName)



          isCondList() - tests if this is a name of a condition list



 boolean
isOrderedCondList(java.lang.String condName)



          isOrderedCondList() - tests if this is a name of an ordered condition list



 boolean
isSampleInCondList(int sampleNbr,
                   java.lang.String condName)



          isSampleInCondList() - is sample in named condition list?



 void
popupAllConditionsReport()



          popupAllConditionsReport() - popup a report showing list of all conditions



 void
popupAllOCLsReport()



          popupAllOCLsReport() - popup a report showing list of all OCLs



 void
popupListConditionReport(java.lang.String condName)



          popupListConditionReport() - popup a report showing list of samples for condition



 void
popupListOCLReport(java.lang.String orderedCondListName)



           



 boolean
removeAllCondsFromOrderedCondList(java.lang.String oCondListName)



          removeAllCondsFromOrderedCondList() - Remove all conditions from condList



 boolean
removeAllSamplesFromCondList(java.lang.String condListName)



          removeAllSamplesFromCondList() - Remove all samples from cond list.



 boolean
removeCondList(java.lang.String condName)



          removeCondList() - remove named condition list if it exists
 and also remove it from any ordered condition lists it
 may appear in.



 boolean
removeNamedOrderedCondList(java.lang.String oCondListName)



          removeNamedOrderedCondList() - remove existing named ordered list of
 conditions the ordered list exists.



 boolean
removeSampleFromCondList(int sampleNbr,
                         java.lang.String condName)



          removeSampleFromCondList() - remove sample from named condition list



 boolean
renameCondList(java.lang.String oldConditionName,
               java.lang.String newConditionName,
               boolean useExactMatchOnOldNameFlag)



          renameCondList() - rename userListName if it exists to newListName.



 boolean
rmvConditionFromOrderedCondList(java.lang.String condName,
                                java.lang.String oCondListName)



          rmvConditionFromOrderedCondList() -  remove condition from named ordered condition list.



 boolean
setCondInOrderedCondList(java.lang.String oCondListName,
                         java.lang.String[] newConds,
                         int nNewCond)



          setCondInOrderedCondList() - replace existing conditions with new list



 boolean
setCondListLength(int nSamples,
                  java.lang.String condName)



          setCondListLength() - Set # of samples in the condition list



 boolean
setCondListsNames(java.lang.String[] activeCondList,
                  int size)



          setCondListsNames() - Set list of active condition lists names



 boolean
setCondListsSizes(int[] newListSizes)



          setCondListsSizes() - Set list of active condition lists sizes



 boolean
setCondParamNames(java.lang.String[] newParamNames)



          setCondParamNames() - set list of condition parameter names for all conditions.



 boolean
setCondParamValue(java.lang.String condName,
                  java.lang.String[] newParamValues)



          setCondParamValue() - set list of parameter values for specific condition
 NOTE: the # of parameter values must match the number of parameter names.



 boolean
setCurCondition(java.lang.String newCurCondName)



           



 boolean
setCurOCL(java.lang.String newCurOCLname)



           



 boolean
setNbrCondLists(int nCondListsNew)



          setNbrCondLists() - Set # of active condition lists



 boolean
setOclParamNames(java.lang.String[] newParamNames)



          setOclParamNames() - set list of ocl parameter names for all conditions.



 boolean
setOclParamValue(java.lang.String oclName,
                 java.lang.String[] newParamValues)



          setOclParamValue() - set list of ocl parameter values for specific condition
 NOTE: the # of parameter values must match the number of parameter names.



 boolean
setSamplesInCondList(java.lang.String condListName,
                     java.lang.String[] sampleNames,
                     int nNewSamples)



          setSamplesInCondList() - Set list of sample numbers in named condition.



 boolean
union(java.lang.String cond1Name,
      java.lang.String cond2Name,
      java.lang.String resultCondName)



          union() - compute resultCond= Union (Condition 1, Condition 2)



 void
updateListCondLists()



          updateListCondLists() - update existing Condition list window if active.


 
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



getMaxCondListSize
public final int getMaxCondListSize()

getMaxCondListSize() - get maximum # of samples condition list can hold

Returns:
value





getMaxNbrSamplesInDB
public final int getMaxNbrSamplesInDB()

getMaxNbrSamplesInDB() - get maximum # of samples database list can hold

Returns:
value





getMaxNbrCondParams
public final int getMaxNbrCondParams()

getMaxNbrCondParams() - get maximum # of condition parameters DB may hold

Returns:
value





getNbrCondLists
public final int getNbrCondLists()

getNbrCondLists() - get # of active condition lists

Returns:
value





getCondListsNames
public final java.lang.String[] getCondListsNames()

getCondListsNames() - get list of active condition lists names

Returns:
value, null if no lists.





getCondListsSizes
public final int[] getCondListsSizes()

getCondListsSizes() - get list of active condition lists sizes

Returns:
value, null if no lists.





createNewCondList
public final boolean createNewCondList(java.lang.String condName)

createNewCondList() - create new named condition list

Parameters:
condName - is the name of the new condition list
Returns:
false if failed. It returns true if it succeeds
         or the condition list already exists.





isCondList
public final boolean isCondList(java.lang.String condName)

isCondList() - tests if this is a name of a condition list

Parameters:
condName - is the name of the condition list
Returns:
true if it is.





removeCondList
public final boolean removeCondList(java.lang.String condName)

removeCondList() - remove named condition list if it exists
 and also remove it from any ordered condition lists it
 may appear in.

 [TODO]

Parameters:
condName - is the name of the condition list to delete
Returns:
false if failed. It returns true if it succeeds
         or the condition list already exists.





addSampleToCondList
public final boolean addSampleToCondList(int sampleNbr,
                                         java.lang.String condName)

addSampleToCondList() - add sample to named condition list

Parameters:
sampleNbr - is the sample to add to the condition list
condName - is the name of the condition list
Returns:
true if succeed, false if problem or the condition does not exist





removeSampleFromCondList
public final boolean removeSampleFromCondList(int sampleNbr,
                                              java.lang.String condName)

removeSampleFromCondList() - remove sample from named condition list

Parameters:
sampleNbr - is the sample to remove from the condition list
condName - is the name of the condition list
Returns:
true if succeed





removeAllSamplesFromCondList
public boolean removeAllSamplesFromCondList(java.lang.String condListName)

removeAllSamplesFromCondList() - Remove all samples from cond list.

Parameters:
condListName - name of condition list to remove all samples.
Returns:
true if ok, false if not found or problem





renameCondList
public final boolean renameCondList(java.lang.String oldConditionName,
                                    java.lang.String newConditionName,
                                    boolean useExactMatchOnOldNameFlag)

renameCondList() - rename userListName if it exists to newListName.

Parameters:
oldConditionName - name of existing condition to be renamed
newConditionName - is the new name to call that condition
useExactMatchOnOldNameFlag - will match just first part of old name
Returns:
true if successful.





isSampleInCondList
public final boolean isSampleInCondList(int sampleNbr,
                                        java.lang.String condName)

isSampleInCondList() - is sample in named condition list?

Parameters:
sampleNbr - is the sample to test in the condition list
condName - is the name of the condition list
Returns:
true if it is





getCondListLength
public final int getCondListLength(java.lang.String condName)

getCondListLength() - get # of samples in the condition list

Parameters:
condName - is the name of the condition list
Returns:
# of samples in condition list, -1 if failed.





getSamplesInCondList
public final int[] getSamplesInCondList(java.lang.String condName)

getSamplesInCondList() - get list of sample numbers in named condition.
 NOTE: for N samples, the values are in the range of [1:N], not [0:N-1].

Parameters:
condName - is the name of the condition list
Returns:
list of sample numbers if succeed, else null





getSampleNamesInCondList
public final java.lang.String[] getSampleNamesInCondList(java.lang.String condName)

getSampleNamesInCondList() - get list of sample names in named condition.

Parameters:
condName - is the name of the condition list
Returns:
list of sample names if succeed, else null





getAllSampleNamesInDB
public final java.lang.String[] getAllSampleNamesInDB()

getAllSampleNamesInDB() - get list of all sample names in the database

Returns:
list of sample names if succeed, else null





getSampleNbrByCondNameAndSampleName
public final int getSampleNbrByCondNameAndSampleName(java.lang.String condName,
                                                     java.lang.String sampleName)

getSampleNbrByCondNameAndSampleName() - get sample number by sample name and condition name.

Parameters:
condName - is the name of the condition list
sampleName - is the name of the sample
Returns:
sample # if found, else -1





getListCondListsStr
public final java.lang.String getListCondListsStr()

getListCondListsStr() - get list of Conditions pretty-print string



updateListCondLists
public final void updateListCondLists()

updateListCondLists() - update existing Condition list window if active.



popupAllConditionsReport
public final void popupAllConditionsReport()

popupAllConditionsReport() - popup a report showing list of all conditions



popupListConditionReport
public final void popupListConditionReport(java.lang.String condName)

popupListConditionReport() - popup a report showing list of samples for condition

Parameters:
condName - is the condition that will be used to generate a report





getMaxOrderedCondListSize
public final int getMaxOrderedCondListSize()

getMaxOrderedCondListSize() - get maximum # of condition lists that an
 ordered condition list can hold

Returns:
value





getNbrOrderedCondLists
public final int getNbrOrderedCondLists()

getNbrOrderedCondLists() - get # of active ordered condition lists

Returns:
value





getOrderedCondListsNames
public final java.lang.String[] getOrderedCondListsNames()

getOrderedCondListsNames() - get list of active ordered condition lists names

Returns:
value, null if no lists.





getOrderedCondListsSizes
public final int[] getOrderedCondListsSizes()

getOrderedCondListsSizes() - get list of active ordered condition lists sizes

Returns:
value, null if no lists.





getOrderedCondNamesInCondList
public final java.lang.String[] getOrderedCondNamesInCondList(java.lang.String orderedCondListName)

getOrderedCondNamesInCondList() - get a list of all condition names in ordered cond list

Returns:
value if found, else null





createNewNamedOrderedCondList
public final boolean createNewNamedOrderedCondList(java.lang.String oCondListName)

createNewNamedOrderedCondList() - create new named ordered condition list
 of conditions if it does not already exist - in which case do nothing.

Parameters:
oCondListName - is the name of the ordered condition list
Returns:
true if created new ordered condList, false if list already exists.





removeNamedOrderedCondList
public final boolean removeNamedOrderedCondList(java.lang.String oCondListName)

removeNamedOrderedCondList() - remove existing named ordered list of
 conditions the ordered list exists.

Parameters:
oCondListName - is the name of the ordered condition list
Returns:
true if removed named condList, false if does not exist.





isConditionInOrderedCondList
public final boolean isConditionInOrderedCondList(java.lang.String condName,
                                                  java.lang.String oCondListName)

isConditionInOrderedCondList() - test if condition is in named ordered condition list.

Parameters:
cdName - is condition to test
oCondListName - is the name of the ordered condition list
Returns:
true if the condition is in the ordered condition list





getConditionIdxInOrderedCondList
public final int getConditionIdxInOrderedCondList(java.lang.String cdName,
                                                  java.lang.String oCondListName)

getConditionIdxInOrderedCondList() - get condition index in named ordered condition list.

Parameters:
cdName - is condition to test
oCondListName - is the name of the ordered condition list
Returns:
index if found, else -1





addConditionToOrderedCondList
public final boolean addConditionToOrderedCondList(java.lang.String condName,
                                                   java.lang.String oCondListName)

addConditionToOrderedCondList() - add condition to named ordered condition list.
 The ordered condition list is a list of unique conditions.
 If the ordered condition list or condition does not exist, then fail. 
 The list must be created (or removed) separately.

Parameters:
cdName - is condition to add
oCondListName - is the name of the ordered condition list
Returns:
true if successful
See Also: 
addConditionToOrderedCondList(java.lang.String, java.lang.String)





rmvConditionFromOrderedCondList
public final boolean rmvConditionFromOrderedCondList(java.lang.String condName,
                                                     java.lang.String oCondListName)

rmvConditionFromOrderedCondList() -  remove condition from named ordered condition list.
 The ordered condition list is a list of conditions. 
 If the ordered condition list or condition does not exist, then fail. 
 The list must be created (or removed) separately.

Parameters:
cdName - is condition list to remove
oCondListName - is the name of the ordered condition list
Returns:
true if condition list removed from the ordered condition list.
See Also: 
Condition#lookupCondListIdxByName, 
Condition#rmvConditionFromOrderedCondList





getNamedOrderedCondListIdx
public final int getNamedOrderedCondListIdx(java.lang.String oCondListName)

getNamedOrderedCondListIdx() - get named ordered condition list index

Parameters:
oCondListName - is the name of the ordered condition list
Returns:
index if found, else -1





getConditionsInOrderedCondList
public final java.lang.String[] getConditionsInOrderedCondList(java.lang.String oCondListName)

getConditionsInOrderedCondList() - get list of names conditions in OCL

Parameters:
oCondListName - is the name of the ordered condition list
Returns:
list of conditions in OCL if found, else null





getAllCondNames
public final java.lang.String[] getAllCondNames()

getAllCondNames()- get a list of all condition names.

Returns:
List of all condition names





isOrderedCondList
public final boolean isOrderedCondList(java.lang.String condName)

isOrderedCondList() - tests if this is a name of an ordered condition list

Parameters:
oCondName - is the name of the ordered condition list
Returns:
true if it is.
See Also: 
Condition#isOrderedCondList





removeAllCondsFromOrderedCondList
public final boolean removeAllCondsFromOrderedCondList(java.lang.String oCondListName)

removeAllCondsFromOrderedCondList() - Remove all conditions from condList

Parameters:
condListName - name of condion list
Returns:
true if success, false if problem
See Also: 
getOrderedCondNamesInCondList(java.lang.String), 
isOrderedCondList(java.lang.String), 
rmvConditionFromOrderedCondList(java.lang.String, java.lang.String)





setCondInOrderedCondList
public final boolean setCondInOrderedCondList(java.lang.String oCondListName,
                                              java.lang.String[] newConds,
                                              int nNewCond)

setCondInOrderedCondList() - replace existing conditions with new list

Parameters:
oCondListName - ordered condition list name
newConds - ordered list of conds
nNewCond - number of conditions in newConds
Returns:
true if success, false if problem
See Also: 
addConditionToOrderedCondList(java.lang.String, java.lang.String), 
isOrderedCondList(java.lang.String), 
removeAllCondsFromOrderedCondList(java.lang.String)





popupListOCLReport
public final void popupListOCLReport(java.lang.String orderedCondListName)





popupAllOCLsReport
public final void popupAllOCLsReport()

popupAllOCLsReport() - popup a report showing list of all OCLs



getCurOCL
public final java.lang.String getCurOCL()





setCurOCL
public final boolean setCurOCL(java.lang.String newCurOCLname)





getMaxNbrOCLParams
public final int getMaxNbrOCLParams()

getMaxNbrOCLParams() - return max number of Ordered Condition List parameters.

Returns:
number of ocl parameters





getOrderedCondParamNames
public final java.lang.String[] getOrderedCondParamNames()

getOrderedCondParamNames() - return list of Ordered condition paramter names.



getOrderedCondParamValues
public final java.lang.String[] getOrderedCondParamValues(java.lang.String oclName)

getOrderedCondParamValues() - return list of Ordered condition paramter values.

Parameters:
oclName - Ordered Condition List name
Returns:
return list of Ordered Condition List paramter values





setOclParamNames
public final boolean setOclParamNames(java.lang.String[] newParamNames)

setOclParamNames() - set list of ocl parameter names for all conditions.
 Note: this method will not check whether you have changed the order of names.
 However, you could change the name if the meaning does not change. 
 E.g., "State" could be changed to "Disease state".
 Also, new parameter names may be added and the condition parameter names are
 extended in the MAExplorer state.

 The number of parameters is the size of the newParamNames list.
 NOTE: the # of parameter values must match the number of parameter names.
 The names must be set prior to setting the values.

Parameters:
newParamNames - - is the list of new names to save.
Returns:
true if succeed in changing the parameter names





setOclParamValue
public final boolean setOclParamValue(java.lang.String oclName,
                                      java.lang.String[] newParamValues)

setOclParamValue() - set list of ocl parameter values for specific condition
 NOTE: the # of parameter values must match the number of parameter names.
 The names must be set prior to setting the values.

Parameters:
condName - - name of the condition to update its values
newParamValues - - is the list of new parameter values to save.
Returns:
true if succeed in changing the parameter values, else failed
 if the condition was not found or the # of parameter values was different
 than the previously set parameter names.





setNbrCondLists
public final boolean setNbrCondLists(int nCondListsNew)

setNbrCondLists() - Set # of active condition lists

Returns:
boolean





setCondListsNames
public final boolean setCondListsNames(java.lang.String[] activeCondList,
                                       int size)

setCondListsNames() - Set list of active condition lists names

Returns:
value, null if no lists.





setCondListsSizes
public final boolean setCondListsSizes(int[] newListSizes)

setCondListsSizes() - Set list of active condition lists sizes

Parameters:
newListSizes - new size of cond list
Returns:
boolean, false if problem





setCondListLength
public final boolean setCondListLength(int nSamples,
                                       java.lang.String condName)

setCondListLength() - Set # of samples in the condition list

Parameters:
condName - is the name of the condition list
Returns:
boolean, false if problem





setSamplesInCondList
public final boolean setSamplesInCondList(java.lang.String condListName,
                                          java.lang.String[] sampleNames,
                                          int nNewSamples)

setSamplesInCondList() - Set list of sample numbers in named condition.

Parameters:
condListName - is the name of the condition list
sampleNames - is list of sample names to be assigned to the condition
nNewSamples - number of new samples to be set
Returns:
boolean, false if problem or the condition does not exist





getCurCondition
public final java.lang.String getCurCondition()





setCurCondition
public final boolean setCurCondition(java.lang.String newCurCondName)





union
public final boolean union(java.lang.String cond1Name,
                           java.lang.String cond2Name,
                           java.lang.String resultCondName)

union() - compute resultCond= Union (Condition 1, Condition 2)

Parameters:
cond1Name - name of condition 1
cond2 - name of condition 2
resultCondName - name of computed Union (Conditon 1, Condition 2)
Returns:
true if succeed.





intersection
public final boolean intersection(java.lang.String cond1Name,
                                  java.lang.String cond2Name,
                                  java.lang.String resultCondName)

intersection() - compute resultCond= Intersection (Condition 1, Condition 2)

Parameters:
cond1Name - name of condition 1
cond2Name - name of condition 2
resultCondName - name of computed Union (Conditon 1, Condition 2)
Returns:
true if succeed.





difference
public final boolean difference(java.lang.String cond1Name,
                                java.lang.String cond2Name,
                                java.lang.String resultCondName)

difference() - compute resultCond = difference (Condition 1 - Condition 2)

Parameters:
cond1Name - name of condition 1
cond2Name - name of condition 2
resultCondName - name of computed Union (Conditon 1, Condition 2)
Returns:
true if succeed.





getNbrCondParams
public final int getNbrCondParams()

getNbrCondParams() - get the number of condition parameters

Returns:
true if succeed.





getCondParamNames
public final java.lang.String[] getCondParamNames()

getCondParamNames() - get list of condition parameter names for all conditions

Returns:
a list of names if succeed, else null.





getCondParamValues
public final java.lang.String[] getCondParamValues(java.lang.String condName)

getCondParamValues() - get list of parameter values for specific condition

Parameters:
condName - name of condition
Returns:
a list of names if succeed, else null.





setCondParamNames
public final boolean setCondParamNames(java.lang.String[] newParamNames)

setCondParamNames() - set list of condition parameter names for all conditions.
 Note: this method will not check whether you have changed the order of names.
 However, you could change the name if the meaning does not change. 
 E.g., "State" could be changed to "Disease state".
 Also, new parameter names may be added and the condition parameter names are
 extended in the MAExplorer state.

 The number of parameters is the size of the newParamNames list.
 NOTE: the # of parameter values must match the number of parameter names.
 The names must be set prior to setting the values.

Parameters:
newParamNames - - is the list of new names to save.
Returns:
true if succeed in changing the parameter names
See Also: 
#setCondParamValues





setCondParamValue
public final boolean setCondParamValue(java.lang.String condName,
                                       java.lang.String[] newParamValues)

setCondParamValue() - set list of parameter values for specific condition
 NOTE: the # of parameter values must match the number of parameter names.
 The names must be set prior to setting the values.

Parameters:
condName - - name of the condition to update its values
newParamValues - - is the list of new parameter values to save.
Returns:
true if succeed in changing the parameter values, else failed
 if the condition was not found or the # of parameter values was different
 than the previously set parameter names.
See Also: 
setCondParamNames(java.lang.String[])