feat: functions run from matlab path

Author: edkerk

code/otherChanges/fitGAM.m

@@ -4,8 +4,11 @@
 
 function model = fitGAM(model)
 
+funcDir = dbstack('-completenames');
+funcDir = regexprep(funcDir(1).file,[funcDir(1).name '\.m'],'')
+
 %Load chemostat data:
-fid = fopen('../../data/physiology/chemostatData_VanHoek1998.tsv','r');
+fid = fopen(fullfile(funcDir,'../../data/physiology/chemostatData_VanHoek1998.tsv','r'));
 exp_data = textscan(fid,'%f32 %f32 %f32 %f32','Delimiter','\t','HeaderLines',1);
 exp_data = [exp_data{1} exp_data{2} exp_data{3} exp_data{4}];
 fclose(fid);

code/otherChanges/sumBioMass.m

@@ -23,16 +23,19 @@
     dispOutput = true;
 end
 
+funcDir = dbstack('-completenames');
+funcDir = regexprep(funcDir(1).file,[funcDir(1).name '\.m'],'')
+
 %Load original biomass component MWs:
 %TODO: compute MW automatically from chemical formulas (check that all components have them first)
-fid = fopen('../../data/physiology/biomassComposition_Forster2003.tsv');
+fid = fopen(fullfile(funcDir,'../../data/physiology/biomassComposition_Forster2003.tsv'));
 Forster2003 = textscan(fid,'%s %s %f32 %f32 %s','Delimiter','\t','HeaderLines',1);
 data.mets   = Forster2003{1};
 data.MWs    = double(Forster2003{4});
 fclose(fid);
 
 %load additional cofactor/ion MWs:
-fid = fopen('../../data/physiology/biomassComposition_Cofactor_Ion.tsv');
+fid = fopen(fullfile(funcDir,'../../data/physiology/biomassComposition_Cofactor_Ion.tsv'));
 CofactorsIons = textscan(fid,'%s %s %f32 %f32 %s %s','Delimiter','\t','HeaderLines',1);
 data_new.mets = CofactorsIons{1};
 data_new.MWs  = double(CofactorsIons{4});