Merge pull request #433 from SysBioChalmers/devel

RAVEN 2.7.4

.gitattributes

@@ -5,6 +5,7 @@
 # Mark as binary to prevent EOL changes. Also no need to track 
 mafft.bat  binary
 mafft/  binary
+mafft binary
 # Files/folders that should not be included when downloading repo as ZIP
 .gitattributes	export-ignore
 .gitignore	export-ignore

INIT/runINIT.m

@@ -283,7 +283,7 @@
 prob.b=zeros(size(prob.a,1), 1);
 prob.ub=[prob.bux; prob.buc];
 prob.osense=1;
-prob.csense=char(1,zeros(size(prob.a,1)));
+prob.csense=char(zeros(1,size(prob.a,1)));
 prob.csense(:)='E';
 
 %We still don't know which of the presentMets that can be produced. Go

core/addRxns.m

@@ -60,7 +60,7 @@
 %                    interpreted
 %                    1 - The metabolites are matched to model.mets. New
 %                        metabolites (if allowed) are added to
-%                        "compartment"
+%                        "compartment" (default)
 %                    2 - The metabolites are matched to model.metNames and
 %                        all metabolites are assigned to "compartment". Any
 %                        new metabolites that are added will be assigned
@@ -101,6 +101,16 @@
 %   Usage: newModel=addRxns(model,rxnsToAdd,eqnType,compartment,...
 %                           allowNewMets,allowNewGenes)
 
+if nargin<3
+    eqnType=1;
+elseif ~isnumeric(eqnType)
+    EM='eqnType must be numeric';
+    dispEM(EM);
+elseif ~ismember(eqnType,[1 2 3])
+    EM='eqnType must be 1, 2, or 3';
+    dispEM(EM);
+end    
+
 if nargin<4
     compartment=[];
 else
@@ -139,17 +149,6 @@
     return;
 end
 
-%Check the input
-if isfield(rxnsToAdd,'stoichCoeffs')
-    eqnType=1;
-elseif ~isnumeric(eqnType)
-    EM='eqnType must be numeric';
-    dispEM(EM);
-elseif ~ismember(eqnType,[1 2 3])
-    EM='eqnType must be 1, 2, or 3';
-    dispEM(EM);
-end
-
 if eqnType==2 || (eqnType==1 && allowNewMets==true)
     compartment=char(compartment);
     if ~ismember(compartment,model.comps)
@@ -518,18 +517,18 @@
 if eqnType==1
     [I, J]=ismember(mets,model.mets);
     if ~all(I)
-        if allowNewMets==true | isstr(allowNewMets)
+        if allowNewMets==true || ischar(allowNewMets)
             %Add the new mets
             metsToAdd.mets=mets(~I);
             metsToAdd.metNames=metsToAdd.mets;
             metsToAdd.compartments=compartment;
-            if isstr(allowNewMets)
+            if ischar(allowNewMets)
                 newModel=addMets(newModel,metsToAdd,true,allowNewMets);
             else
                 newModel=addMets(newModel,metsToAdd,true);
             end
         else
-            EM='One or more equations contain metabolites that are not in model.mets. Set allowNewMets to true to allow this function to add metabolites or use addMets to add them before calling this function';
+            EM='One or more equations contain metabolites that are not in model.mets. Set allowNewMets to true to allow this function to add metabolites or use addMets to add them before calling this function. Are you sure that eqnType=1?';
             dispEM(EM);
         end
     end
@@ -553,11 +552,11 @@
     [I, J]=ismember(t1,t2);
 
     if ~all(I)
-        if allowNewMets==true | isstr(allowNewMets)
+        if allowNewMets==true || ischar(allowNewMets)
             %Add the new mets
             metsToAdd.metNames=mets(~I);
             metsToAdd.compartments=compartment;
-            if isstr(allowNewMets)
+            if ischar(allowNewMets)
                 newModel=addMets(newModel,metsToAdd,true,allowNewMets);
             else
                 newModel=addMets(newModel,metsToAdd,true);
@@ -603,11 +602,11 @@
     [I, J]=ismember(t1,t2);
 
     if ~all(I)
-        if allowNewMets==true | isstr(allowNewMets)
+        if allowNewMets==true || ischar(allowNewMets)
             %Add the new mets
             metsToAdd.metNames=metNames(~I);
             metsToAdd.compartments=compartments(~I);
-            if isstr(allowNewMets)
+            if ischar(allowNewMets)
                 newModel=addMets(newModel,metsToAdd,true,allowNewMets);
             else
                 newModel=addMets(newModel,metsToAdd,true);

core/changeRxns.m

@@ -13,7 +13,7 @@
 %                    interpreted
 %                    1 - The metabolites are matched to model.mets. New
 %                        metabolites (if allowed) are added to
-%                        "compartment"
+%                        "compartment" (default)
 %                    2 - The metabolites are matched to model.metNames and
 %                        all metabolites are assigned to "compartment". Any
 %                        new metabolites that are added will be assigned
@@ -53,7 +53,7 @@
 %
 %   Usage: model=changeRxns(model,rxns,equations,eqnType,compartment,allowNewMets)
 
-if nargin<4 & isfield(equations,'stoichCoeffs')
+if nargin<4
     eqnType=1;
 end
 
@@ -65,7 +65,6 @@
 end
 
 rxns=convertCharArray(rxns);
-equations=convertCharArray(equations);
 compartment=char(compartment);
 
 %Find the indexes of the reactions and throw an error if they aren't all
@@ -86,7 +85,7 @@
     rxnsToChange.mets=equations.mets;
     rxnsToChange.stoichCoeffs=equations.stoichCoeffs;
 else
-    rxnsToChange.equations=equations;
+    rxnsToChange.equations=convertCharArray(equations);
 end
 if isfield(model,'rxnNames')
     rxnsToChange.rxnNames=model.rxnNames(J);

core/getGenesFromGrRules.m

@@ -1,9 +1,9 @@
-function [genes,rxnGeneMat] = getGenesFromGrRules(grRules)
+function [genes,rxnGeneMat] = getGenesFromGrRules(grRules, originalGenes)
 %getGenesFromGrRules  Extract gene list and rxnGeneMat from grRules array.
 %
 % USAGE:
 %
-%   [genes,rxnGeneMat] = getGenesFromGrRules(grRules);
+%   [genes,rxnGeneMat] = getGenesFromGrRules(grRules, originalGenes);
 %
 % INPUTS:
 %
@@ -12,6 +12,7 @@
 %               NOTE: Boolean operators can be text ("and", "or") or
 %                     symbolic ("&", "|"), but there must be a space
 %                     between operators and gene names/IDs.
+%   originalGenes     The original gene list from the model as reference
 %
 % OUTPUTS:
 %
@@ -24,6 +25,11 @@
 %
 
 
+% handle input arguments
+if nargin < 2
+    originalGenes = [];
+end
+
 % check if the grRules use written or symbolic boolean operators
 if any(contains(grRules,{'&','|'}))
     % fix some potential missing spaces between parentheses and &/|
@@ -50,10 +56,16 @@
 nonEmpty = ~cellfun(@isempty,rxnGenes);
 genes = unique([rxnGenes{nonEmpty}]');
 
+if ~isempty(originalGenes)
+    if ~isequal(sort(originalGenes), sort(genes))
+        error('The grRules and original gene list are inconsistent!');
+    else
+        genes = originalGenes;
+    end
+end
+
 % construct new rxnGeneMat (if requested)
 if nargout > 1
     rxnGeneCell = cellfun(@(rg) ismember(genes,rg),rxnGenes,'UniformOutput',false);
     rxnGeneMat = sparse(double(horzcat(rxnGeneCell{:})'));
-end
-
-
+end

doc/INIT/runINIT.html

@@ -388,7 +388,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0283 prob.b=zeros(size(prob.a,1), 1);
 0284 prob.ub=[prob.bux; prob.buc];
 0285 prob.osense=1;
-0286 prob.csense=char(1,zeros(size(prob.a,1)));
+0286 prob.csense=char(zeros(1,size(prob.a,1)));
 0287 prob.csense(:)=<span class="string">'E'</span>;
 0288 
 0289 <span class="comment">%We still don't know which of the presentMets that can be produced. Go</span>