extractMiriam

 extractMiriam
   This function unpacks the information kept in metMiriams, rxnMiriams,
   geneMiriams or compMiriams to make the annotation more
   human-readable. The obtained cell array looks the same like in Excel
   format, just the columns are split to have particular miriam name in
   corresponding column

   modelMiriams                a miriam structure (e.g. model.metMiriams)
                               for one or multiple metabolites
   miriamNames                 cell array with miriam names to be
                               extracted (optional, default 'all', meaning
                               that annotation for all miriam names found
                               in modelMiriams will be extracted)

   miriams                     a cell array with extracted miriams. if
                               several miriam names are requested, the
                               corresponding information is saved in
                               different columns. if there are several ids
                               available for the same entity (metabolite,
                               gene, reaction or compartment), they are
                               concatenated into one column. the total
                               number of column represent the number of
                               unique miriam names per entity
   extractedMiriamNames        cell array with extracted miriam names

   Usage: miriam=extractMiriam(modelMiriams,miriamName)

0001 function [miriams,extractedMiriamNames]=extractMiriam(modelMiriams,miriamNames)
0002 % extractMiriam
0003 %   This function unpacks the information kept in metMiriams, rxnMiriams,
0004 %   geneMiriams or compMiriams to make the annotation more
0005 %   human-readable. The obtained cell array looks the same like in Excel
0006 %   format, just the columns are split to have particular miriam name in
0007 %   corresponding column
0008 %
0009 %   modelMiriams                a miriam structure (e.g. model.metMiriams)
0010 %                               for one or multiple metabolites
0011 %   miriamNames                 cell array with miriam names to be
0012 %                               extracted (optional, default 'all', meaning
0013 %                               that annotation for all miriam names found
0014 %                               in modelMiriams will be extracted)
0015 %
0016 %   miriams                     a cell array with extracted miriams. if
0017 %                               several miriam names are requested, the
0018 %                               corresponding information is saved in
0019 %                               different columns. if there are several ids
0020 %                               available for the same entity (metabolite,
0021 %                               gene, reaction or compartment), they are
0022 %                               concatenated into one column. the total
0023 %                               number of column represent the number of
0024 %                               unique miriam names per entity
0025 %   extractedMiriamNames        cell array with extracted miriam names
0026 %
0027 %   Usage: miriam=extractMiriam(modelMiriams,miriamName)
0028 
0029 if nargin<2 || (ischar(miriamNames) && strcmp(miriamNames,'all'))
0030     extractAllTypes=true;
0031 else
0032     extractAllTypes=false;
0033     miriamNames=convertCharArray(miriamNames);
0034 end
0035 
0036 %The annotation for all miriam names should be extracted
0037 if extractAllTypes
0038     miriamNames={''};
0039     for i=1:numel(modelMiriams)
0040         if ~isempty(modelMiriams{i,1})
0041             for j=1:numel(modelMiriams{i,1}.name)
0042                 miriamNames{numel(miriamNames)+1,1}=modelMiriams{i,1}.name{j};
0043             end
0044         end
0045     end
0046     miriamNames=sort(unique(miriamNames));
0047 end
0048 
0049 %Aggregate the final cell array table with extracted miriam information
0050 miriams=cell(numel(modelMiriams),0);
0051 for i=1:numel(miriamNames)
0052     miriams=[miriams, extractMiriamType(modelMiriams,miriamNames{i})];
0053 end
0054 extractedMiriamNames=miriamNames;
0055 
0056 end
0057 
0058 function miriams=extractMiriamType(modelMiriams,miriamName)
0059 %Create an empty cell array for ids vector
0060 tempMiriams = cell([size(modelMiriams,1) 1]);
0061 %Firstly obtain the list of relevant miriam ids. Several entries may have
0062 %several miriam ids, such ids are kept in additional columns
0063 for i=1:numel(modelMiriams)
0064     if (~isempty(modelMiriams{i,1})) && any(strcmp(modelMiriams{i,1}.name,miriamName))
0065         for j=1:numel(modelMiriams{i,1}.name)
0066             if strcmp(modelMiriams{i,1}.name(j),miriamName)
0067                 tempMiriams(i,j) = modelMiriams{i,1}.value(j);
0068             end
0069         end
0070     else
0071         modelMiriams{i,1} = '';
0072     end
0073 end
0074 
0075 %Concatenate multiple ids per miriam name in one column with semicolon as
0076 %separator
0077 miriams = cell([size(tempMiriams,1) 1]);
0078 notEmpty=~cellfun(@isempty,tempMiriams);
0079 for i=1:size(miriams)
0080     miriams{i}=strjoin(tempMiriams(i,notEmpty(i,:)),{'; '});
0081 end
0082 end