Changeset 404 for experiments/frams/foraminifera/data/scripts/forams_repro.inc

Timestamp:

06/30/15 23:02:42 (9 years ago)

Author:

oriona

Message:

removed unused part of code, refactorization

File:

• experiments/frams/foraminifera/data/scripts/forams_repro.inc (modified) (11 diffs)

experiments/frams/foraminifera/data/scripts/forams_repro.inc

@@ -4 +4 @@
 // -------------------------------- step begin --------------------------------
 
-function reproduce_haploid(repro_list, number)
+function reproduce_haploid(repro_list)
 {
         var len = repro_list.size;
@@ -14 +14 @@
                 var parent2 = Populations[0].get(repro_list[i + 1]);
 
-                number = parent.user2["Va"] / ExpParams.ofnumd + parent2.user2["Va"] / ExpParams.ofnumd;
+                var number = parent.user2["Va"] / ExpParams.ofnumd + parent2.user2["Va"] / ExpParams.ofnumd;
+
                 for (var j = 0; j < number; j++)
                 {
-                        //size
-                        var rsize = (parent.user1["delta_d"] + ExpParams.diplo_rad);
-                        if (Math.rnd01 < 0.5)
-                        {
-                                rsize = parent2.user1["delta_d"] + ExpParams.diplo_rad;
-                        }
-
-                        var deltas = parent.user1["delta_d"];
-                        //mutation
-                        if (Math.rnd01 < ExpParams.mutationprob)
-                        {
-                                var diff = delta_change * deltas;
-                                if (Math.rnd01 < 0.5)
-                                {
-                                        deltas -= diff;
-                                }
-                                else
-                                {
-                                        deltas += diff;
-                                }
-                                rsize = ExpParams.diplo_rad + deltas;
-                        }
-
-                        var geno = "//0\np:sh=1,sx=" + rsize + ",sy=" + rsize + ",sz=" + rsize + ", rz=3.14159265358979";
-                        geno += "\nn:p=0,d=\"S\""; //TODO is this the only difference with haploid code? TODO why initial genotypes are not used as defined in ExpParams?
-                        var cr = Populations[0].add(geno);
-                        cr.energ0 = ExpParams.ofnumd;
-                        cr.energy = cr.energ0;
-                        var dsize =  ExpParams.diplo_rad * ExpParams.delta_rate + ExpParams.diplo_rad;
-                        cr.user1 = [ {"vamin" : (rsize / dsize) * ExpParams.v_min_d, "amin": parent.user1["amin"], "delta_h" : parent.user1["delta_h"], "delta_d" : deltas }, {"vamin" : (rsize / dsize) * ExpParams.v_min_d, "amin": parent2.user1["amin"], "delta_h" : parent2.user1["delta_h"], "delta_d" : deltas }];
-                        cr.user2 = { "Va" : cr.energ0, "gen" : 1 , "growth_step" : ExpParams.growth_step, "rsize": rsize, "vinit": cr.energ0};
-                        placeRandomlyNotColliding(cr);
-                }
-        }
-
-        for (var j = 0; j < repro_list.size; j++)
-        {
-                Populations[0].kill(repro_list[j]);
-        }
-}
-
-function reproduce_diploid(repro_list, number)
+                        createOffspring(ExpParams.gend, ExpParams.ofnumd, [parent.user1, parent2.user1], {"Va" : ExpParams.ofnumd, "gen" : 1 , "growth_step" : ExpParams.growth_step, "rsize": ExpParams.rads[1], "vinit": ExpParams.ofnumd}); //TODO genes from both generations in user1
+                }
+        }
+        killParents(repro_list);
+}
+
+function reproduce_diploid(repro_list)
 {
         for (var i = 0; i < repro_list.size; i++)
@@ -64 +30 @@
                 var parent = Populations[0].get(repro_list[i]);
 
+                if (parent.user2["gen"] != 1)
+                {
+                        Simulator.print("gen: " + parent.user2["gen"]);
+                }
+
                 if (parent.user2["gen"] == 1)
                 {
-
                         var number = parent.user2["Va"] / ExpParams.ofnumh;
-
-
                         for (var j = 0; j < number / 2; j++)
                         {
@@ -76 +44 @@
                                 if (Math.rnd01 < ExpParams.crossprob)
                                 {
-                                        var tmp = parent.user1[0]["vamin"];
-                                        parent.user1[0]["vamin"] = parent.user1[1]["vamin"];
-                                        parent.user1[1]["vamin"] = tmp;
+                                        crossover(parent, "vamin");
                                         crossed = 1;
                                 }
@@ -84 +50 @@
                                 for (var k = 0; k < 2; k++)
                                 {
-                                        var rsize = parent.user1[k]["delta_h"]  + ExpParams.haplo_rad;
-                                        var vamin = parent.user1[k]["vamin"];
-                                        var deltas =  parent.user1[k]["delta_h"];
-
-
-                                        if (Math.rnd01 < ExpParams.mutationprob)
-                                        {
-                                                var diff = delta_change * deltas;
-                                                if (Math.rnd01 < 0.5)
-                                                {
-                                                        deltas -= diff;
-                                                }
-                                                else
-                                                {
-                                                        deltas += diff;
-                                                }
-                                                rsize = ExpParams.diplo_rad + deltas;
-                                        }
-
-                                        var geno = "//0\np:sh=1,sx=" + rsize + ",sy=" + rsize + ",sz=" + rsize + ", rz=3.14159265358979";
-                                        var cr = Populations[0].add(geno);
-                                        cr.energ0 = ExpParams.ofnumh;
-                                        cr.energy = cr.energ0;
-                                        //vamin depends on rsize
-                                        var hsize = ExpParams.haplo_rad * ExpParams.delta_rate + ExpParams.haplo_rad;
-                                        cr.user1 = {"vamin" : (rsize / hsize) * ExpParams.v_min_h, "amin": ExpParams.age_min_d, "delta_h" : deltas, "delta_d" : parent.user1[0]["delta_d"]};
-                                        cr.user2 = { "Va" : cr.energ0, "gen" : 0 , "growth_step" : ExpParams.growth_step, "rsize" : rsize, "vinit": cr.energ0};
-                                        placeRandomlyNotColliding(cr);
+                                        createOffspring(ExpParams.genh, ExpParams.ofnumh, {"vamin" : ExpParams.v_min_h, "amin": ExpParams.age_min_h}, {"Va" : ExpParams.ofnumh, "gen" : 0 , "growth_step" : ExpParams.growth_step, "rsize" : ExpParams.rads[0], "vinit": ExpParams.ofnumh});
                                 }
 
@@ -117 +56 @@
                                 if (crossed == 1)
                                 {
-                                        var tmp = parent.user1[0]["vamin"];
-                                        parent.user1[0]["vamin"] = parent.user1[1]["vamin"];
-                                        parent.user1[1]["vamin"] = tmp;
+                                        crossover(parent, "vamin");
                                         crossed = 0;
                                 }
-
                         }
                 }
         }
+        killParents(repro_list);
+}
+
+function crossover(parent, gene)
+{
+        var tmp = parent.user1[0][gene];
+        parent.user1[0][gene] = parent.user1[1][gene];
+        parent.user1[1][gene] = tmp;
+}
+
+function killParents(repro_list)
+{
         for (var j = 0; j < repro_list.size; j++)
         {
@@ -132 +80 @@
 }
 
+function createOffspring(geno, energy, new_user1, new_user2)
+{
+        var cr = Populations[0].add(geno);
+        cr.energ0 = energy;
+        cr.energy = cr.energ0;
+        setGenotype(cr, new_user1, new_user2);
+        placeRandomlyNotColliding(cr);
+}
 
 function onStep()
@@ -152 +108 @@
                         haploids += 1;
                         e_inc_h += cr.energy;
-                        size_h += cr.user1["delta_h"] + ExpParams.haplo_rad;
+                        size_h += ExpParams.rads[0]; //TODO change of size dependant on gene
                         vmin_h += cr.user1["vamin"];
                 }
@@ -159 +115 @@
                         diploids += 1;
                         e_inc_d += cr.energy;
-                        size_d += cr.user1[0]["delta_d"] + ExpParams.diplo_rad;
+                        size_d += ExpParams.rads[1]; //TODO change of size dependant on gene
                         vmin_d += cr.user1[0]["vamin"];
                 }
@@ -219 +175 @@
                                         to_repro_h.add(i);
                                 }
-                                else if (cr.user2["gen"] == 1)
+                                if (cr.user2["gen"] == 1)
                                 {
                                         to_repro_d.add(i);
@@ -227 +183 @@
                 if (to_repro_h.size > 1)
                 {
-                        reproduce_haploid(to_repro_h, ExpParams.ofnumh);
+                        reproduce_haploid(to_repro_h);
                 }
                 if (to_repro_d.size > 0)
                 {
-                        reproduce_diploid(to_repro_d, ExpParams.ofnumd);
+                        reproduce_diploid(to_repro_d);
                 }
         }