refactor: char, string and cell array input

.gitattributes

@@ -3,7 +3,8 @@
 # Use MATLAB style diff
 *.m text diff=matlab
 # Mark as binary to prevent EOL changes. Also no need to track 
-mafft-linux*/*  binary
+mafft.bat  binary
+mafft/  binary
 # Files/folders that should not be included when downloading repo as ZIP
 .gitattributes	export-ignore
 .gitignore	export-ignore

INIT/getINITModel.m

@@ -109,6 +109,8 @@
 
 if nargin<3
     celltype=[];
+else
+    celltype=char(celltype);
 end
 if nargin<4
     hpaData=[];
@@ -121,6 +123,8 @@
 end
 if nargin<7
     taskFile=[];
+else
+    taskFile=char(taskFile);
 end
 if nargin<8 || isempty(useScoresForTasks)
     useScoresForTasks=true;

INIT/runINIT.m

@@ -67,24 +67,17 @@
 if isempty(rxnScores)
     rxnScores=zeros(numel(model.rxns),1);
 end
-if nargin<3
+if nargin<3 || isempty(presentMets)
     presentMets={};
+else
+    presentMets=convertCharArray(presentMets);
 end
-if isempty(presentMets)
-    presentMets={};
-end
-presentMets=presentMets(:);
-if nargin<4
-    essentialRxns={};
-end
-if isempty(essentialRxns)
+if nargin<4 || isempty(essentialRxns)
     essentialRxns={};
+else
+    essentialRxns=convertCharArray(essentialRxns);
 end
-essentialRxns=essentialRxns(:);
-if nargin<5
-    prodWeight=0.5;
-end
-if isempty(prodWeight)
+if nargin<5 || isempty(prodWeight)
     prodWeight=0.5;
 end
 if nargin<6

core/FSEOF.m

@@ -23,6 +23,9 @@
 %
 %   Usage: targets=FSEOF(model,biomassRxn,targetRxn,iterations,coefficient,outputFile)
 
+biomassRxn=char(biomassRxn);
+targetRxn=char(targetRxn);
+
 if nargin<4
     iterations=10;
     coefficient=0.9;
@@ -96,6 +99,7 @@
 %Generating output
 formatSpec='%s\t%s\t%s\t%s\t%s\t%s\t%s\n';
 if output == 1    %Output to a file
+    outputFile=char(outputFile);
     fid=fopen(outputFile,'w');
     fprintf(fid,formatSpec,'Slope','rowID','Enzyme ID','Enzyme Name','Subsystems','Direction','Gr Rule');
 else              %Output to screen

core/addExchangeRxns.m

@@ -23,11 +23,14 @@
 
 if nargin<3
     mets=model.mets;
+elseif ~islogical(mets) && ~isnumeric(mets)
+    mets=convertCharArray(mets);
 end
-reactionType=upper(reactionType);
 J=getIndexes(model,mets,'mets',false);
 mets=model.mets(J);
 
+reactionType=char(upper(reactionType));
+
 %Production is positive for OUT and BOTH
 if strcmp(reactionType,'IN')
     I=speye(numel(model.mets));

core/addGenesRaven.m

@@ -32,11 +32,8 @@
 if ~isfield(genesToAdd,'genes')
     EM='genes is a required field in genesToAdd';
     dispEM(EM);
-end
-
-if ~iscellstr(genesToAdd.genes)
-    EM='genesToAdd.genes must be a cell array of strings';
-    dispEM(EM);
+else
+    genesToAdd.genes=convertCharArray(genesToAdd.genes);
 end
 
 %Number of genes
@@ -68,14 +65,11 @@
 
 %Some more checks and if they pass then add each field to the structure
 if isfield(genesToAdd,'geneShortNames')
+    genesToAdd.geneShortNames=convertCharArray(genesToAdd.geneShortNames);
     if numel(genesToAdd.geneShortNames)~=nGenes
         EM='genesToAdd.geneShortNames must have the same number of elements as genesToAdd.genes';
         dispEM(EM);
     end
-    if ~iscellstr(genesToAdd.geneShortNames)
-        EM='genesToAdd.geneShortNames must be a cell array of strings';
-        dispEM(EM);
-    end
     %Add empty field if it doesn't exist
     if ~isfield(newModel,'geneShortNames')
         newModel.geneShortNames=largeFiller;

core/addMets.m

@@ -58,6 +58,8 @@
 end
 if nargin<4
     prefix='m_';
+else
+    prefix=char(prefix);
 end
 
 newModel=model;
@@ -69,35 +71,19 @@
 %Check some stuff regarding the required fields
 if ~isfield(metsToAdd,'mets')
     metsToAdd.mets=generateNewIds(newModel,'mets',prefix,numel(metsToAdd.metNames));
+else
+    metsToAdd.mets=convertCharArray(metsToAdd.mets);
 end
 if ~isfield(metsToAdd,'metNames')
     metsToAdd.metNames=metsToAdd.mets;
+else
+    metsToAdd.metNames=convertCharArray(metsToAdd.metNames);
 end
 if ~isfield(metsToAdd,'compartments')
     EM='compartments is a required field in metsToAdd';
     dispEM(EM);
-end
-if ischar(metsToAdd.mets)
-    metsToAdd.mets={metsToAdd.mets};
-elseif ~iscellstr(metsToAdd.mets)
-    EM='metsToAdd.mets must be a cell array of strings';
-    dispEM(EM);
-end
-if ischar(metsToAdd.metNames)
-    metsToAdd.metNames={metsToAdd.metNames};
-elseif ~iscellstr(metsToAdd.metNames)
-    EM='metsToAdd.metNames must be a cell array of strings';
-    dispEM(EM);
-end
-if ~iscellstr(metsToAdd.compartments)
-    if ischar(metsToAdd.compartments)
-        temp=cell(numel(metsToAdd.mets),1);
-        temp(:)={metsToAdd.compartments};
-        metsToAdd.compartments=temp;
-    else
-        EM='metsToAdd.compartments must be a cell array of strings';
-        dispEM(EM);
-    end
+else
+    metsToAdd.compartments=convertCharArray(metsToAdd.compartments);
 end
 
 %Number of metabolites
@@ -193,14 +179,11 @@
 end
 
 if isfield(metsToAdd,'inchis')
+    metsToAdd.inchis=convertCharArray(metsToAdd.inchis);
     if numel(metsToAdd.inchis)~=nMets
         EM='metsToAdd.inchis must have the same number of elements as metsToAdd.mets';
         dispEM(EM);
     end
-    if ~iscellstr(metsToAdd.inchis)
-        EM='metsToAdd.inchis must be a cell array of strings';
-        dispEM(EM);
-    end
     %Add empty field if it doesn't exist
     if ~isfield(newModel,'inchis')
         newModel.inchis=largeFiller;
@@ -214,14 +197,11 @@
 end
 
 if isfield(metsToAdd,'metFormulas')
+    metsToAdd.metFormulas=convertCharArray(metsToAdd.metFormulas);
     if numel(metsToAdd.metFormulas)~=nMets
         EM='metsToAdd.metFormulas must have the same number of elements as metsToAdd.mets';
         dispEM(EM);
     end
-    if ~iscellstr(metsToAdd.metFormulas)
-        EM='metsToAdd.metFormulas must be a cell array of strings';
-        dispEM(EM);
-    end
     %Add empty field if it doesn't exist
     if ~isfield(newModel,'metFormulas')
         newModel.metFormulas=largeFiller;
@@ -255,14 +235,11 @@
 end
 
 if isfield(metsToAdd,'metNotes')
+    metsToAdd.metNotes=convertCharArray(metsToAdd.metNotes);
     if numel(metsToAdd.metNotes)~=nMets
         EM='metsToAdd.metNotes must have the same number of elements as metsToAdd.mets';
         dispEM(EM);
     end
-    if ~iscellstr(metsToAdd.metNotes)
-        EM='metsToAdd.metNotes must be a cell array of strings';
-        dispEM(EM);
-    end
     %Add empty field if it doesn't exist
     if ~isfield(newModel,'metNotes')
         newModel.metNotes=largeFiller;

core/addRxns.m

@@ -103,16 +103,20 @@
 
 if nargin<4
     compartment=[];
+else
+    compartment=char(compartment);
 end
 if nargin<5
     allowNewMets=false;
+elseif ~islogical(allowNewMets)
+    allowNewMets=char(allowNewMets);
 end
 if nargin<6
     allowNewGenes=false;
 end
 
 if allowNewGenes & isfield(rxnsToAdd,'grRules')
-    genesToAdd.genes = strjoin(rxnsToAdd.grRules);
+    genesToAdd.genes = strjoin(convertCharArray(rxnsToAdd.grRules));
     genesToAdd.genes = regexp(genesToAdd.genes,' |)|(|and|or','split'); % Remove all grRule punctuation
     genesToAdd.genes = genesToAdd.genes(~cellfun(@isempty,genesToAdd.genes));  % Remove spaces and empty genes
     genesToAdd.genes = setdiff(unique(genesToAdd.genes),model.genes); % Only keep new genes
@@ -147,10 +151,7 @@
 end
 
 if eqnType==2 || (eqnType==1 && allowNewMets==true)
-    if ~ischar(compartment)
-        EM='compartment must be a string';
-        dispEM(EM);
-    end
+    compartment=char(compartment);
     if ~ismember(compartment,model.comps)
         EM='compartment must match one of the compartments in model.comps';
         dispEM(EM);
@@ -160,7 +161,8 @@
 if ~isfield(rxnsToAdd,'rxns')
     EM='rxns is a required field in rxnsToAdd';
     dispEM(EM);
-elseif iscell(rxnsToAdd.rxns)
+else
+    rxnsToAdd.rxns=convertCharArray(rxnsToAdd.rxns);
     %To fit with some later printing
     rxnsToAdd.rxns=rxnsToAdd.rxns(:);
 end
@@ -174,30 +176,16 @@
     dispEM(EM);
 end
 
-if ~iscellstr(rxnsToAdd.rxns) && ~ischar(rxnsToAdd.rxns)
-    %It could also be a string, but it's not encouraged
-    EM='rxnsToAdd.rxns must be a cell array of strings';
-    dispEM(EM);
-else
-    rxnsToAdd.rxns=cellstr(rxnsToAdd.rxns);
-end
-
 %Normal case: equations provided
 if isfield(rxnsToAdd,'equations')
-    if ~iscellstr(rxnsToAdd.equations) && ~ischar(rxnsToAdd.equations)
-        %It could also be a string, but it's not encouraged
-        EM='rxnsToAdd.equations must be a cell array of strings';
-        dispEM(EM);
-    else
-        rxnsToAdd.equations=cellstr(rxnsToAdd.equations);
-    end
-
+    rxnsToAdd.equations=convertCharArray(rxnsToAdd.equations);
+
     %Alternative case: mets+stoichiometry provided
 else
     %In the case of 1 rxn added (array of strings + vector), transform to
     %cells of length=1:
     if iscellstr(rxnsToAdd.mets)
-        rxnsToAdd.mets = {rxnsToAdd.mets};
+        rxnsToAdd.mets={rxnsToAdd.mets};
     end
     if isnumeric(rxnsToAdd.stoichCoeffs)
         rxnsToAdd.stoichCoeffs = {rxnsToAdd.stoichCoeffs};
@@ -257,6 +245,7 @@
 newModel.rxns=[newModel.rxns;rxnsToAdd.rxns(:)];
 
 if isfield(rxnsToAdd,'rxnNames')
+    rxnsToAdd.rxnNames=convertCharArray(rxnsToAdd.rxnNames);
     if numel(rxnsToAdd.rxnNames)~=nRxns
         EM='rxnsToAdd.rxnNames must have the same number of elements as rxnsToAdd.rxns';
         dispEM(EM);
@@ -340,6 +329,7 @@
 end
 
 if isfield(rxnsToAdd,'eccodes')
+    rxnsToAdd.eccodes=convertCharArray(rxnsToAdd.eccodes);
     if numel(rxnsToAdd.eccodes)~=nRxns
         EM='rxnsToAdd.eccodes must have the same number of elements as rxnsToAdd.rxns';
         dispEM(EM);
@@ -414,6 +404,7 @@
     end
 end
 if isfield(rxnsToAdd,'grRules')
+    rxnsToAdd.grRules=convertCharArray(rxnsToAdd.grRules);
     if numel(rxnsToAdd.grRules)~=nRxns
         EM='rxnsToAdd.grRules must have the same number of elements as rxnsToAdd.rxns';
         dispEM(EM);
@@ -431,6 +422,7 @@
 end
 
 if isfield(rxnsToAdd,'rxnFrom')
+    rxnsToAdd.rxnFrom=convertCharArray(rxnsToAdd.rxnFrom);
     if numel(rxnsToAdd.rxnFrom)~=nRxns
         EM='rxnsToAdd.rxnFrom must have the same number of elements as rxnsToAdd.rxns';
         dispEM(EM);
@@ -448,6 +440,7 @@
 end
 
 if isfield(rxnsToAdd,'rxnNotes')
+    rxnsToAdd.rxnNotes=convertCharArray(rxnsToAdd.rxnNotes);
     if numel(rxnsToAdd.rxnNotes)~=nRxns
         EM='rxnsToAdd.rxnNotes must have the same number of elements as rxnsToAdd.rxns';
         dispEM(EM);
@@ -465,6 +458,7 @@
 end
 
 if isfield(rxnsToAdd,'rxnReferences')
+    rxnsToAdd.rxnReferences=convertCharArray(rxnsToAdd.rxnReferences);
     if numel(rxnsToAdd.rxnReferences)~=nRxns
         EM='rxnsToAdd.rxnReferences must have the same number of elements as rxnsToAdd.rxns';
         dispEM(EM);
@@ -482,6 +476,7 @@
 end
 
 if isfield(rxnsToAdd,'pwys')
+    rxnsToAdd.pwys=convertCharArray(rxnsToAdd.pwys);
     if numel(rxnsToAdd.pwys)~=nRxns
         EM='rxnsToAdd.pwys must have the same number of elements as rxnsToAdd.rxns';
         dispEM(EM);