QP objective check bypassed for large v

Author: rmtfleming

.gitattributes

@@ -2,6 +2,32 @@
 *.html  linguist-vendored=true
 *.gms   linguist-vendored=true
 
-*.mat -crlf -diff -merge
-*.mlx -crlf -diff -merge
-*.xlsx -crlf -diff -merge
+## https://nl.mathworks.com/help/matlab/matlab_prog/set-up-git-source-control.html#buhx2d6-1_3
+*.fig binary
+*.mat binary
+*.mdl binary
+*.mdlp binary
+*.mexa64 binary
+*.mexw64 binary
+*.mexmaci64 binary
+*.mlapp binary
+*.mldatx binary
+*.mlproj binary
+*.mlx binary
+*.p binary
+*.sfx binary
+*.sldd binary
+*.slreqx binary
+*.slmx binary
+*.sltx binary
+*.slxc binary
+*.slx binary merge=mlAutoMerge
+*.slxp binary
+
+## Other common binary file types
+*.docx binary
+*.exe binary
+*.jpg binary
+*.pdf binary
+*.png binary
+*.xlsx binary

src/base/solvers/solveCobraQP.m

@@ -1072,11 +1072,11 @@
         if ~isempty(solution.full)
             %set the value of the objective
             solution.obj = c'*solution.full + 0.5*solution.full'*F*solution.full;
-            if norm(solution.obj - f) > getCobraSolverParams('LP', 'feasTol')*100
-                warning('solveCobraQP: Objectives do not match. Switch to a different solver if you rely on the value of the optimal objective.')
-                fprintf('%s\n%g\n%s\n%g\n%s\n%g\n',['The optimal value of the objective from ' solution.solver ' is:'],f, ...
-                    'while the value constructed from c''*x + 0.5*x''*F*x:', solution.obj,...
-                    'while the value constructed from osense*(c''*x + x''*F*x) :', osense*(c'*solution.full + solution.full'*F*solution.full))
+            %expect some variability if the norm of the optimal flux vector is large
+            %TODO how to scale this
+            if norm(solution.obj - f) > getCobraSolverParams('LP', 'feasTol')*100 && norm(solution.full)<1e2
+                warning('solveCobraQP: Objectives do not match. Rescale problem if you rely on the exact value of the optimal objective.')
+                fprintf('%s%g\n','The difference between the optimal value of the solver objective and objective from c''*x + 0.5*x''*F*x is: ' ,f - solution.obj)
             end
         else
             solution.obj = NaN;

src/dataIntegration/transcriptomics/preprocessing/selectGeneFromGPR.m

@@ -25,7 +25,7 @@
 % OUTPUTS:
 %   expressionCol:  reaction expression, corresponding to model.rxns.
 %                   No gene-expression data and orphan reactions will
-%                   be given a value of -1.
+%                   be given a value of NaN.
 %   gene_used:      gene identifier, corresponding to model.rxns, from GPRs
 %                   whose value (expression and/or significance) was chosen for that
 %                   reaction