Merge pull request opencobra#2376 from rmtfleming/develop

solver bugs with QP rcost

Author: rmtfleming

src/analysis/FBA/optimizeCbModel.m

@@ -607,7 +607,7 @@
         solution.slack  = [];
 
     elseif strcmp(minNorm, 'one')
-        % Optimize the absolute value of fluxes
+        % Minimise the absolute value of fluxes
         % Solve secondary LP to optimize weighted 1-norm of v
         % Weight provided by model.g1
         % Set up the optimization problem
@@ -637,6 +637,8 @@
         end
         optProblem2.b  = [optProblem.b;zeros(2*nRxns,1);objectiveLP];
 
+        optProblem2.b  = [optProblem.b;zeros(2*nRxns,1);objectiveLP];
+
         %csense for 3 & 4 above
         optProblem2.csense = [optProblem.csense; repmat('G',2*nRxns,1)];
         % constrain the optimal value according to the original problem
@@ -648,7 +650,7 @@
             %LPproblem2.csense(nTotalVars+1) = 'L';  %wrong
         end
 
-        optProblem2.osense = 1;
+        optProblem2.osense = 1;%minimise
         % Re-solve the problem
         if allowLoops
             solution = solveCobraLP(optProblem2, param);

src/base/solvers/solveCobraQP.m

@@ -442,8 +442,8 @@
         end
 
         %parse mosek result structure
-        [stat,origStat,x,y,yl,yu,z,zl,zu,k,basis,pobjval,dobjval] = parseMskResult(res);
-        w = -(zl - zu);
+        [stat,origStat,x,y,yl,yu,z,zl,zu,s,basis,pobjval,dobjval] = parseMskResult(res);
+        w = (zl - zu);
 
         %debugging
         if problemTypeParams.printLevel>2

test/verifiedTests/analysis/testPrint/surfNet.txt

@@ -0,0 +1,24 @@
+
+Met #1  13dpg[c]
+
+Consuming reactions: none
+Producing reactions:
+  #49  <a href="matlab: surfNet([], 'GAPD', 0, NaN, 0, 1, [], 0, 0.800000);">GAPD</a>
+<a href="matlab: surfNet([], 'g3p[c]', 0, NaN, 0, 1, [], 0, 0.800000);">g3p[c]</a> + <a href="matlab: surfNet([], 'nad[c]', 0, NaN, 0, 1, [], 0, 0.800000);">nad[c]</a> + <a href="matlab: surfNet([], 'pi[c]', 0, NaN, 0, 1, [], 0, 0.800000);">pi[c]</a>   <=>   <a href="matlab: surfNet([], '13dpg[c]', 0, NaN, 0, 1, [], 0, 0.800000);">13dpg[c]</a> + <a href="matlab: surfNet([], 'h[c]', 0, NaN, 0, 1, [], 0, 0.800000);">h[c]</a> + <a href="matlab: surfNet([], 'nadh[c]', 0, NaN, 0, 1, [], 0, 0.800000);">nadh[c]</a> 
+  #75  <a href="matlab: surfNet([], 'PGK', 0, NaN, 0, 1, [], 0, 0.800000);">PGK</a>
+<a href="matlab: surfNet([], '3pg[c]', 0, NaN, 0, 1, [], 0, 0.800000);">3pg[c]</a> + <a href="matlab: surfNet([], 'atp[c]', 0, NaN, 0, 1, [], 0, 0.800000);">atp[c]</a>   <=>   <a href="matlab: surfNet([], '13dpg[c]', 0, NaN, 0, 1, [], 0, 0.800000);">13dpg[c]</a> + <a href="matlab: surfNet([], 'adp[c]', 0, NaN, 0, 1, [], 0, 0.800000);">adp[c]</a> 
+
+<a href="matlab: surfNet([], [], 0, NaN, 0, 1, [], 0, 0.800000, struct('showPrev', true));">Show previous steps...</a>
+
+Met #1  13dpg[c]
+
+Consuming reactions: none
+Producing reactions:
+  #49  <a href="matlab: surfNet([], 'GAPD', 0, NaN, 0, 1, [], 0, 0.800000);">GAPD</a>
+<a href="matlab: surfNet([], 'g3p[c]', 0, NaN, 0, 1, [], 0, 0.800000);">g3p[c]</a> + <a href="matlab: surfNet([], 'nad[c]', 0, NaN, 0, 1, [], 0, 0.800000);">nad[c]</a> + <a href="matlab: surfNet([], 'pi[c]', 0, NaN, 0, 1, [], 0, 0.800000);">pi[c]</a>   <=>   <a href="matlab: surfNet([], '13dpg[c]', 0, NaN, 0, 1, [], 0, 0.800000);">13dpg[c]</a> + <a href="matlab: surfNet([], 'h[c]', 0, NaN, 0, 1, [], 0, 0.800000);">h[c]</a> + <a href="matlab: surfNet([], 'nadh[c]', 0, NaN, 0, 1, [], 0, 0.800000);">nadh[c]</a> 
+  #75  <a href="matlab: surfNet([], 'PGK', 0, NaN, 0, 1, [], 0, 0.800000);">PGK</a>
+<a href="matlab: surfNet([], '3pg[c]', 0, NaN, 0, 1, [], 0, 0.800000);">3pg[c]</a> + <a href="matlab: surfNet([], 'atp[c]', 0, NaN, 0, 1, [], 0, 0.800000);">atp[c]</a>   <=>   <a href="matlab: surfNet([], '13dpg[c]', 0, NaN, 0, 1, [], 0, 0.800000);">13dpg[c]</a> + <a href="matlab: surfNet([], 'adp[c]', 0, NaN, 0, 1, [], 0, 0.800000);">adp[c]</a> 
+
+<a href="matlab: surfNet([], [], 0, NaN, 0, 1, [], 0, 0.800000, struct('showPrev', true));">Show previous steps...</a>
+'NOTEXIST' is not a metabolite, reaction or gene of the model.
+Searching for related objects:

test/verifiedTests/analysis/testTopology/test.ext

@@ -0,0 +1,13 @@
+/home/rfleming/drive/sbgCloud/code/fork-cobratoolbox/test/verifiedTests/analysis/testTopology/test
+H-representation
+linearity 7 1 2 3 4 5 6 7
+begin
+7 10 integer
+0 -1 0 0 0 0 0 1 0 0
+0 1 -2 -2 0 0 0 0 0 0
+0 0 1 0 0 -1 -1 0 0 0
+0 0 0 1 -1 1 0 0 0 0
+0 0 0 0 1 0 1 0 -1 0
+0 0 1 1 0 0 0 0 0 -1
+0 0 0 -1 1 -1 0 0 0 0
+end

test/verifiedTests/analysis/testTopology/test.ine

@@ -0,0 +1,13 @@
+/home/rfleming/drive/sbgCloud/code/fork-cobratoolbox/test/verifiedTests/analysis/testTopology/test
+H-representation
+linearity 7 1 2 3 4 5 6 7
+begin
+7 10 integer
+0 -1 0 0 0 0 0 1 0 0
+0 1 -2 -2 0 0 0 0 0 0
+0 0 1 0 0 -1 -1 0 0 0
+0 0 0 1 -1 1 0 0 0 0
+0 0 0 0 1 0 1 0 -1 0
+0 0 1 1 0 0 0 0 0 -1
+0 0 0 -1 1 -1 0 0 0 0
+end