Merge pull request #1579 from opencobra/develop

Develop

Author: rmtfleming

.gitignore

@@ -82,6 +82,8 @@ sampleCbModelTmp.mat
 test/verifiedTests/analysis/testEnumerateOptimal/MILPProblem.mat
 test/verifiedTests/analysis/testThermo/MILPProblem.mat
 test/verifiedTests/design/MILPProblem.mat
+test/verifiedTests/design/testOptForce/TestOptForceM/
+test/verifiedTests/reconstruction/testModelBorgifier/SRP065497_taxonomy_abundances_v3.0.tsv
 
 # shared libraries
 *.so
@@ -167,4 +169,11 @@ docs/source/_static/json/functions.json
 
 # videos
 *.flv
-*.mp4
+*.mp4
+
+# external modules (legacy)
+external/Smith-Decomposition/
+external/gaimc/
+external/lusol/
+external/pdco/
+.DS_Store

.gitmodules

@@ -20,7 +20,7 @@
 	ignore = dirty
 [submodule "test/models"]
 	path = test/models
-	url = https://github.com/LCSB-BioCore/COBRA.models
+	url = https://github.com/opencobra/COBRA.models
 	ignore = dirty
 [submodule "external/analysis/Volume-and-Sampling"]
 	path = external/analysis/Volume-and-Sampling
@@ -38,14 +38,6 @@
 	path = papers
 	url = https://github.com/opencobra/COBRA.papers.git
 	ignore = dirty
-[submodule "external/base/utilities/rdir"]
-	path = external/base/utilities/rdir
-	url = https://github.com/LCSB-BioCore/rdir.git
-	ignore = dirty
-[submodule "external/analysis/mptoolbox"]
-	path = external/analysis/mptoolbox
-	url = https://github.com/LCSB-BioCore/mptoolbox.git
-	ignore = dirty
 [submodule "external/analysis/octave-networks-toolbox"]
 	path = external/analysis/octave-networks-toolbox
 	url = https://github.com/aeolianine/octave-networks-toolbox.git

deprecated/_modelManipulationOri/addDemandReactionOri.m

@@ -0,0 +1,35 @@
+function [model,rxnNames] = addDemandReactionOri(model,metaboliteNameList, addRxnGeneMat)
+% addDemandReaction adds demand reactions for a set of metabolites
+% The reaction names for the demand reactions will be DM_[metaboliteName]
+%
+% model = addDemandReaction(model,metaboliteNameList)
+%
+% INPUTS
+% model                 COBRA model structure
+% metaboliteNameList    List of metabolite names (cell array)
+% addRxnGeneMat         Adds rxnGeneMat to model structure (default = true)
+%
+% OUTPUTS
+% model                 COBRA model structure with added demand reactions
+% rxnNames              List of added reactions
+%
+% Markus Herrgard 5/8/07
+% Ines Thiele 03/09 - Corrected reaction coefficient for demand reaction
+% Ines Thiele 08/03/2015, made rxnGeneMat optional
+if ~exist('addRxnGeneMat','var')
+    addRxnGeneMat = 1;
+end
+
+if (~iscell(metaboliteNameList))
+    tmp = metaboliteNameList;
+    clear metaboliteNameList;
+    metaboliteNameList{1} = tmp;
+end
+
+for i = 1:length(metaboliteNameList)
+    rxnName = ['DM_' metaboliteNameList{i}];
+    rxnNames{i}=rxnName;
+    metaboliteList = {metaboliteNameList{i}};
+%     [model,rxnIDexists] = addReaction(model,rxnName,metaboliteList,stoichCoeffList,revFlag,lowerBound,upperBound,objCoeff,subSystem,grRule,geneNameList,systNameList,checkDuplicate, addRxnGeneMat)
+    model = addReactionOri(model,rxnName,metaboliteList,-1,false,0,1000,0,'Demand','',[],[],0, addRxnGeneMat);
+end

deprecated/_modelManipulationOri/addExchangeRxnOri.m

@@ -0,0 +1,34 @@
+function [newModel,AddedExchRxn] = addExchangeRxn(model,metList,lb,ub)
+%addExchangeRxn adds exchange reactions
+%
+% newModel = addExchangeRxn(model,metList,lb,ub)
+%
+%INPUTS
+% model         Cobra model structure
+% metList       List of metabolites
+%
+%OPTIONAL INPUTS
+% lb            Array of lower bounds
+% ub            Array of upper bounds
+%
+%OUTPUT
+% newModel      COBRA model with added exchange reactions
+%
+% Ines Thiele 02/2009
+
+if nargin < 3
+    lb = ones(length(metList),1)*min(model.lb);
+end
+if nargin < 4
+    ub = ones(length(metList),1)*max(model.ub);
+end
+Revs = zeros(length(metList),1);
+Revs(lb<0) = 1;
+
+newModel = model;
+AddedExchRxn = '';
+for i = 1 : length(metList)
+    [newModel,rxnIDexists] = addReactionOri(newModel,strcat('EX_',metList{i}),metList(i),-1,Revs(i),...
+        lb(i),ub(i));
+    AddedExchRxn=[AddedExchRxn;strcat('EX_',metList(i))];
+end