RAVEN 2.11.0

.gitattributes

@@ -10,3 +10,4 @@ mafft binary
 .gitattributes	export-ignore
 .gitignore	export-ignore
 .github	export-ignore
+*.mat filter=lfs diff=lfs merge=lfs -text

INIT/runINIT.m

@@ -1,4 +1,4 @@
-function [outModel, deletedRxns, metProduction, fValue]=runINIT(model,rxnScores,presentMets,essentialRxns,prodWeight,allowExcretion,noRevLoops)
+function [outModel, deletedRxns, metProduction, fValue]=runINIT(model,rxnScores,presentMets,essentialRxns,prodWeight,allowExcretion,noRevLoops,params)
 % runINIT
 %	Generates a model using the INIT algorithm, based on proteomics and/or
 %   transcriptomics and/or metabolomics and/or metabolic tasks. This is the 
@@ -38,6 +38,7 @@
 %                   problem significantly more computationally intensive to
 %                   solve (two more integer constraints per reversible reaction)
 %                   (optional, default false)
+%   params          parameter structure for use by optimizeProb
 %
 %   outModel        the resulting model structure
 %   deletedRxns     reactions which were deleted by the algorithm

core/FSEOF.m

@@ -119,7 +119,12 @@
         A2=char(model.rxns(num));                         %enzyme ID
         A3=char(model.rxnNames(num));                     %enzyme Name
         if isfield(model,'subSystems') && ~isempty(model.subSystems{num});
-            A4=char(strjoin(model.subSystems{num,1},';'));                   %Subsystems
+            if ~any(cellfun(@(x) iscell(x), model.subSystems));
+                subSys = cellfun(@(x) {x}, model.subSystems, 'uni', 0);
+            else
+                subSys = model.subSystems;
+            end
+            A4=char(strjoin(subSys{num},';'));                   %Subsystems
         else
             A4='';
         end

core/addExchangeRxns.m

@@ -63,8 +63,8 @@
 end
 if isfield(model,'subSystems')
     fillerSub = filler;
-    if iscell(model.subSystems(1,1))
-        fillerSub = repmat({fillerSub},numel(J),1);
+    if any(cellfun(@(x) iscell(x), model.subSystems))
+        fillerSub(:)={{''}};
     end
     model.subSystems=[model.subSystems;fillerSub];
 end

core/addRxns.m

@@ -227,10 +227,12 @@
 nOldRxns=numel(model.rxns);
 filler=cell(nRxns,1);
 filler(:)={''};
-cellfiller=cellfun(@(x) cell(0,0),filler,'UniformOutput',false);
+cellfiller=cell(nRxns,1);
+cellfiller(:)={{''}};
 largeFiller=cell(nOldRxns,1);
 largeFiller(:)={''};
-celllargefiller=cellfun(@(x) cell(0,0),largeFiller,'UniformOutput',false);
+largeCellFiller=cell(nOldRxns,1);
+largeCellFiller(:)={{''}};
 
 %***Add everything to the model except for the equations.
 if numel(rxnsToAdd.equations)~=nRxns
@@ -350,24 +352,45 @@
 end
 
 if isfield(rxnsToAdd,'subSystems')
-    if numel(rxnsToAdd.subSystems)~=nRxns
-        EM='rxnsToAdd.subSystems must have the same number of elements as rxnsToAdd.rxns';
-        dispEM(EM);
+    % Has to be cell array
+    if ischar(rxnsToAdd.subSystems)
+        rxnsToAdd.subSystems = {rxnsToAdd.subSystems};
+    end
+    % If all nested cells are 1x1, then unnest
+    if all(cellfun(@(x) iscell(x) && isscalar(x), rxnsToAdd.subSystems))
+        rxnsToAdd.subSystems = transpose([rxnsToAdd.subSystems{:}]);
     end
-    for i=1:numel(rxnsToAdd.subSystems)
-        if ischar(rxnsToAdd.subSystems{i})
-            rxnsToAdd.subSystems{i}=rxnsToAdd.subSystems(i);
+    % Cell array should now be as simple as possible. Check if it is nested
+    subSysRxnsNested = any(cellfun(@(x) iscell(x), rxnsToAdd.subSystems));
+    if isfield(newModel,'subSystems')
+        subSysModelNested = any(cellfun(@(x) iscell(x), newModel.subSystems));
+    else
+        subSysModelNested = subSysRxnsNested;
+        if subSysRxnsNested
+            newModel.subSystems=largeCellFiller;
+        else
+            newModel.subSystems=largeFiller;
         end
     end
-    %Fill with standard if it doesn't exist
-    if ~isfield(newModel,'subSystems')
-        newModel.subSystems=celllargefiller;
+    if subSysRxnsNested && ~subSysModelNested
+        % Make all existing subSystems nested
+        newModel.subSystems = cellfun(@(x) {x}, newModel.subSystems, 'uni', 0);
+    elseif ~subSysRxnsNested && subSysModelNested
+        rxnsToAdd.subSystems = cellfun(@(x) {x}, rxnsToAdd.subSystems, 'uni', 0);
+    end
+    if numel(rxnsToAdd.subSystems)~=nRxns
+        EM='rxnsToAdd.subSystems must have the same number of elements as rxnsToAdd.rxns';
+        dispEM(EM);
     end
     newModel.subSystems=[newModel.subSystems;rxnsToAdd.subSystems(:)];
 else
-    %Fill with standard if it doesn't exist
+    %Fill with standard if it does not exist
     if isfield(newModel,'subSystems')
-        newModel.subSystems=[newModel.subSystems;cellfiller];
+        if any(cellfun(@(x) iscell(x), newModel.subSystems))
+            newModel.subSystems=[newModel.subSystems;cellfiller];
+        else
+            newModel.subSystems=[newModel.subSystems;filler];
+        end
     end
 end
 if isfield(rxnsToAdd,'rxnMiriams')

core/addTransport.m

@@ -134,11 +134,15 @@
         model.eccodes=[model.eccodes;filler];
     end
     if isfield(model,'subSystems')
-        ssFiller=filler;
+        isNested = any(cellfun(@(x) iscell(x), model.subSystems));
+        ssFiller = filler;
         if isRev==1
-            ssFiller(:)={{['Transport between ' fromComp ' and ' toComps{i}]}};
+            ssFiller(:) = {['Transport between ' fromComp ' and ' toComps{i}]};
         else
-            ssFiller(:)={{['Transport from ' fromComp ' to ' toComps{i}]}};
+            ssFiller(:) = {['Transport from ' fromComp ' to ' toComps{i}]};
+        end
+        if isNested
+            ssFiller = cellfun(@(x) {x}, ssFiller, 'uni', 0);
         end
         model.subSystems=[model.subSystems;ssFiller];
     end

core/checkModelStruct.m

@@ -175,11 +175,11 @@ function checkModelStruct(model,throwErrors,trimWarnings)
     end
 end
 if isfield(model,'subSystems')
-    for i=1:numel(model.subSystems)
-        if ~iscell(model.subSystems{i,1})
-            EM='The "subSystems" field must be a cell array';
+    isNested  = any(cellfun(@(x) iscell(x), model.subSystems));
+    isCellStr = any(cellfun(@(x) ischar(x), model.subSystems));
+    if ~xor(isNested,isCellStr)
+        EM='The "subSystems" field must be a cell array of chars, *or* a cell array of cell arrays of chars';
             dispEM(EM,throwErrors);
-        end
     end
 end
 if isfield(model,'eccodes')

core/compareMultipleModels.m

@@ -92,16 +92,6 @@
 fprintf('*** Done \n\n')
 
 
-%% Flatten models' subSystems field
-% Convert from cell array of cells to cell array of strings
-% NOTE: this function currently only recognizes one subSystem per reaction;
-%       additional subSystems will be ignored!
-for i = 1:numel(models)
-    cells = cellfun(@iscell,models{i}.subSystems);
-    models{i}.subSystems(cells) = cellfun(@(s) s{1}, models{i}.subSystems(cells), 'UniformOutput', false);
-end
-
-
 %% Compare models structure & function based on high-dimensional methods
 % Compare number of reactions in each subsystem in each model using a heatmap
 field = 'subSystems';
@@ -110,6 +100,16 @@
     fprintf('\nWARNING: At least one model does not contain the field "subSystems". \n')
     fprintf('         Skipping subsystem comparison. \n\n')
 else
+    %% Flatten model subSystems field
+    % Convert from cell array of cells to cell array of strings
+    % NOTE: this function currently only recognizes one subSystem per reaction;
+    %       additional subSystems will be ignored!
+    for i = 1:numel(models)
+        if any(cellfun(@(x) iscell(x), models{i}.subSystems));
+            cells = cellfun(@iscell,models{i}.subSystems);
+            models{i}.subSystems(cells) = cellfun(@(s) s{1}, models{i}.subSystems(cells), 'UniformOutput', false);
+        end
+    end
     [id,compMat] = compareModelField(models,field);
     compStruct.subsystems.ID = id;
     compStruct.subsystems.matrix = compMat;

core/copyToComps.m

@@ -25,24 +25,26 @@
 %
 % Usage: model=copyToComps(model,toComps,rxns,deleteOriginal,compNames,compOutside)
 
-if nargin<3
-    rxns=model.rxns;
-elseif ~islogical(rxns) && ~isnumeric(rxns)
-    rxns=convertCharArray(rxns);
+arguments
+    model (1,1) struct
+    toComps {emptyOrTextOrCellOfText}
+    rxns = model.rxns
+    deleteOriginal {emptyOrLogicalScalar} = false
+    compNames {emptyOrTextOrCellOfText} = toComps
+    compOutside {emptyOrTextOrCellOfText} = '';
 end
-if nargin<4
-    deleteOriginal=false;
+
+if nargin >= 3 && ~islogical(rxns) && ~isnumeric(rxns)
+    rxns = convertCharArray(rxns);
 end
-if nargin<5
-    compNames=toComps;
-else
+if nargin >= 5
     compNames=convertCharArray(compNames);
 end
-if nargin<6
-    compOutside=cell(numel(toComps),1);
-    compOutside(:)={''};
-else
+if nargin >= 6
     compOutside=convertCharArray(compOutside);
+    if length(compOutside) ~= length(compNames)
+        error('compOutside and compNames should be of equal size.');
+    end
 end
 
 originalID=model.id;
@@ -79,15 +81,20 @@
         modelToAdd.compMiriams=modelToAdd.compMiriams(J);
     end
     modelToAdd.metComps=ones(numel(modelToAdd.mets),1);
-
+    if isfield(modelToAdd,'metFrom')
+        modelToAdd = rmfield(modelToAdd,'metFrom');
+    end
+    if isfield(modelToAdd,'rxnFrom')
+        modelToAdd = rmfield(modelToAdd,'rxnFrom');
+    end
+    if isfield(modelToAdd,'geneFrom')
+        modelToAdd = rmfield(modelToAdd,'geneFrom');
+    end
+
     %Merge the models
-    model=mergeModels({model;modelToAdd},'metNames');
+    model=mergeModels({model;modelToAdd},'metNames',[],true);
 end
 
-model=rmfield(model,'rxnFrom');
-model=rmfield(model,'metFrom');
-model=rmfield(model,'geneFrom');
-
 if deleteOriginal==true
     model=removeReactions(model,rxns,true,true,true); %Also delete unused compartments
 end

core/findRAVENroot.m

@@ -1,23 +1,27 @@
 function [ravenPath, prevDir] = findRAVENroot()
 % findRAVENroot
-%   Finds the root of the RAVEN directory, by searching for the path to
+%   Finds the root of the RAVEN directory, first by  by searching for the path to
 %   RAVEN2.png. Can also record the current directory, in case a function will
 %   use the ravenPath to navigate to a precise folder, and it should return to
 %   the previous directory afterwards. See e.g. optimizeProb calling glpk.
 
 ST=dbstack('-completenames');
 prevDir = pwd();
-ravenPath = ST(strcmp({ST.name},'findRAVENroot')).file;
-rootFound = 0;
-while rootFound == 0
-    isRoot = isfile(fullfile(ravenPath,'RAVEN2.png'));
-    if isRoot
-        rootFound = 1;
-    else
-        ravenPathOld = ravenPath;
-        ravenPath = fileparts(ravenPath);
-        if strcmp(ravenPathOld,ravenPath)
-            error('Cannot find the RAVEN root directory. Make sure you have not removed the RAVEN2.png file from your RAVEN installation.')
+if ispref('RAVEN','ravenPath')
+    ravenPath = getpref('RAVEN','ravenPath');
+else
+    ravenPath = ST(strcmp({ST.name},'findRAVENroot')).file;
+    rootFound = 0;
+    while rootFound == 0
+        isRoot = isfile(fullfile(ravenPath,'RAVEN2.png'));
+        if isRoot
+            rootFound = 1;
+        else
+            ravenPathOld = ravenPath;
+            ravenPath = fileparts(ravenPath);
+            if strcmp(ravenPathOld,ravenPath)
+                error('Cannot find the RAVEN root directory. Make sure you have not removed the RAVEN2.png file from your RAVEN installation.')
+            end
         end
     end
 end

core/fitTasks.m

@@ -34,7 +34,7 @@
 %   the result.
 %
 % Usage: [outModel, addedRxns]=fitTasks(model,refModel,inputFile,printOutput,...
-%           rxnScores,taskStructure,params)
+%           rxnScores,taskStructure)
 
 if nargin<4
     printOutput=true;
@@ -48,9 +48,6 @@
 if nargin<6
     taskStructure=[];
 end
-if nargin<7
-    params=[];
-end
 
 if isempty(taskStructure) && ~isfile(inputFile)
     error('Task file %s cannot be found',string(inputFile));
@@ -266,9 +263,9 @@
             %Only do gap-filling if it cannot be solved
             failed=false;
             try
-                [~, ~, newRxns, newModel, exitFlag]=fillGaps(tModel,refModel,false,true,supressWarnings,rxnScores,params);
+                [~, ~, newRxns, newModel, exitFlag]=fillGaps(tModel,refModel,false,true,supressWarnings,rxnScores);
                 if exitFlag==-2
-                    EM=['"[' taskStructure(i).id '] ' taskStructure(i).description '" was aborted before reaching optimality. Consider increasing params.maxTime\n'];
+                    EM=['"[' taskStructure(i).id '] ' taskStructure(i).description '" was aborted before reaching optimality.\n'];
                     dispEM(EM,false);
                 end
             catch