RAVEN 2.10.4

Author: edkerk

INIT/ftINIT.m

@@ -54,9 +54,7 @@
 %   useScoresForTasks   true if the calculated reaction scored should be 
 %                       used as weights when fitting to tasks (optional, default
 %                       true)
-%   paramsFT            parameter structure as used by getMILPParams. This
-%                       is for the fitTasks step. For the INIT algorithm,
-%                       see params (optional, default [])
+%   paramsFT            *obsolete option*
 %   verbose             if true, the MILP progression will be shown. 
 %                       (optional, default false)
 %

INIT/ftINITFillGaps.m

@@ -23,7 +23,7 @@
 %                       reference tModel. 
 %                       The solver will try to maximize the sum of the
 %                       scores for the included reactions
-%   params              parameter structure as used by getMILPParams
+%   params              *obsolete option*
 %   verbose             if true, the MILP progression will be shown. 
 %
 %   addedRxns           the rxns added

INIT/ftINITFillGapsForAllTasks.m

@@ -18,7 +18,7 @@
 %                   reactions (optional, default is -1 for all reactions)
 %   taskStructure   structure with the tasks, as from parseTaskList. If
 %                   this is supplied then inputFile is ignored
-%   params          parameter structure as used by getMILPParams
+%   params          *obsolete option*
 %   verbose         if true, the MILP progression will be shown. 
 %
 %

INIT/ftINITFillGapsMILP.m

@@ -12,7 +12,7 @@
 %                 with the same number of elements as reactions in the model,
 %                 of a vector of indexes for the reactions that should be
 %                 minimized (optional, default model.rxns)
-%   params        parameter structure as used by getMILPParams (optional)
+%   params        *obsolete option*
 %   scores        vector of weights for the reactions. Negative scores
 %                 should not have flux. Positive scores are not possible in this
 %                 implementation, and they are changed to max(scores(scores<0)).

INIT/getINITModel.m

@@ -1,10 +1,10 @@
-function [model, metProduction, essentialRxnsForTasks, addedRxnsForTasks, deletedDeadEndRxns, deletedRxnsInINIT, taskReport]=getINITModel(refModel, tissue, celltype, hpaData, arrayData, metabolomicsData, taskFile, useScoresForTasks, printReport, taskStructure, params, paramsFT)
+function [model, metProduction, essentialRxnsForTasks, addedRxnsForTasks, deletedDeadEndRxns, deletedRxnsInINIT, taskReport]=getINITModel(refModel, tissue, celltype, hpaData, arrayData, metabolomicsData, taskFile, useScoresForTasks, printReport, taskStructure)
 % getINITModel_legacy
 %   Generates a model using the INIT algorithm, based on proteomics and/or
 %   transcriptomics and/or metabolomics and/or metabolic tasks. This is the original 
 %   implementation of tINIT, which is replaced by ftINIT.
 %
-%   Input:
+% Input:
 %   refModel            a model structure. The model should be in the
 %                       closed form (no exchange reactions open). Import
 %                       using import(filename,false). If the model is not
@@ -53,15 +53,8 @@
 %                       as an alternative way to define tasks when Excel
 %                       sheets are not suitable. Overrides taskFile (optional,
 %                       default [])
-%   params              parameter structure as used by getMILPParams. This is
-%                       for the INIT algorithm. For the the MILP problems
-%                       solved to fit tasks, see paramsFT (optional, default [])
-%   paramsFT            parameter structure as used by getMILPParams. This is
-%                       for the fitTasks step. For the INIT algorithm, see
-%                       params (optional, default [])
 %
-%
-%   Output:
+% Output:
 %   model                   the resulting model structure
 %   metProduction           array that indicates which of the
 %                           metabolites in metabolomicsData that could be

INIT/runINIT.m

@@ -1,4 +1,4 @@
-function [outModel, deletedRxns, metProduction, fValue]=runINIT(model,rxnScores,presentMets,essentialRxns,prodWeight,allowExcretion,noRevLoops,params)
+function [outModel, deletedRxns, metProduction, fValue]=runINIT(model,rxnScores,presentMets,essentialRxns,prodWeight,allowExcretion,noRevLoops)
 % runINIT
 %	Generates a model using the INIT algorithm, based on proteomics and/or
 %   transcriptomics and/or metabolomics and/or metabolic tasks. This is the 
@@ -38,8 +38,6 @@
 %                   problem significantly more computationally intensive to
 %                   solve (two more integer constraints per reversible reaction)
 %                   (optional, default false)
-%   params          parameter structure as used by getMILPParams (optional,
-%                   default [])
 %
 %   outModel        the resulting model structure
 %   deletedRxns     reactions which were deleted by the algorithm

core/consumeSomething.m

@@ -19,7 +19,7 @@
 %                   fluxes instead of the sum. Slower, but can be
 %                   used if the sum gives too many fluxes (optional, default
 %                   false)
-%   params          parameter structure as used by getMILPParams (optional)
+%   params          *obsolete option*
 %   ignoreIntBounds	true if internal bounds (including reversibility)
 %                   should be ignored. Exchange reactions are not affected.
 %                   This can be used to find unbalanced solutions which are

core/fillGaps.m

@@ -1,4 +1,4 @@
-function [newConnected, cannotConnect, addedRxns, newModel, exitFlag]=fillGaps(model,models,allowNetProduction,useModelConstraints,supressWarnings,rxnScores,params)
+function [newConnected, cannotConnect, addedRxns, newModel, exitFlag]=fillGaps(model,models,allowNetProduction,useModelConstraints,supressWarnings,rxnScores)
 % fillGaps
 %   Uses template model(s) to fill gaps in a model
 %
@@ -24,7 +24,6 @@
 %                       The solver will try to maximize the sum of the
 %                       scores for the included reactions (optional, default
 %                       is -1 for all reactions)
-%   params              parameter structure as used by getMILPParams (optional)
 %
 %   newConnected        cell array with the reactions that could be
 %                       connected. This is not calulated if

core/fitTasks.m

@@ -1,4 +1,4 @@
-function [outModel, addedRxns]=fitTasks(model,refModel,inputFile,printOutput,rxnScores,taskStructure,params)
+function [outModel, addedRxns]=fitTasks(model,refModel,inputFile,printOutput,rxnScores,taskStructure)
 % fitTasks
 %   Fills gaps in a model by including reactions from a reference model,
 %   so that the resulting model can perform all the tasks in a task list
@@ -17,7 +17,6 @@
 %                   reactions (optional, default is -1 for all reactions)
 %   taskStructure   structure with the tasks, as from parseTaskList. If
 %                   this is supplied then inputFile is ignored (optional)
-%   params          parameter structure as used by getMILPParams (optional)
 %
 %
 %   Output:

core/getMinNrFluxes.m

@@ -8,7 +8,7 @@
 %                 with the same number of elements as reactions in the model,
 %                 of a vector of indexes for the reactions that should be
 %                 minimized (optional, default model.rxns)
-%   params        parameter structure as used by getMILPParams (optional)
+%   params        *obsolete option*
 %   scores        vector of weights for the reactions. Negative scores
 %                 should not have flux. Positive scores are not possible in this
 %                 implementation, and they are changed to max(scores(scores<0)).