Changeset 418 for experiments/frams/foraminifera/data/scripts/foraminifera.inc

Timestamp:

08/01/15 16:32:10 (9 years ago)

Author:

oriona

Message:

invalid index error fixed

File:

• experiments/frams/foraminifera/data/scripts/foraminifera.inc (modified) (3 diffs)

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

@@ -4 +4 @@
 // -------------------------------- step begin --------------------------------
 
-function reproduce_haploid(repro_list)
+function reproduce_haploid(parent, parent2)
 {
-        var len = repro_list.size;
-        if (len % 2 != 0) len = repro_list.size - 1;
+        var number = parent.user2["Va"] / ExpParams.ofnumd + parent2.user2["Va"] / ExpParams.ofnumd;
 
-        for (var i = 0; i < len - 2 ; i = i + 2)
+        for (var j = 0; j < number; j++)
         {
-                var parent = Populations[0].get(repro_list[i]);
-                var parent2 = Populations[0].get(repro_list[i + 1]);
-
-                var number = parent.user2["Va"] / ExpParams.ofnumd + parent2.user2["Va"] / ExpParams.ofnumd;
-
-                for (var j = 0; j < number; j++)
-                {
-                        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
-                }
+                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)
+function reproduce_diploid(parent)
 {
-        for (var i = 0; i < repro_list.size; i++)
+        var number = parent.user2["Va"] / ExpParams.ofnumh;
+        for (var j = 0; j < number / 2; j++)
         {
-                var parent = Populations[0].get(repro_list[i]);
-
-                if (parent.user2["gen"] != 1)
+                var crossed = 0;
+                //crossover
+                if (Math.rnd01 < ExpParams.crossprob)
                 {
-                        Simulator.print("gen: " + parent.user2["gen"]);
+                        crossover(parent, "vamin");
+                        crossed = 1;
                 }
 
-                if (parent.user2["gen"] == 1)
+                for (var k = 0; k < 2; k++)
                 {
-                        var number = parent.user2["Va"] / ExpParams.ofnumh;
-                        for (var j = 0; j < number / 2; j++)
-                        {
-                                var crossed = 0;
-                                //crossover
-                                if (Math.rnd01 < ExpParams.crossprob)
-                                {
-                                        crossover(parent, "vamin");
-                                        crossed = 1;
-                                }
+                        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});
+                }
 
-                                for (var k = 0; k < 2; k++)
-                                {
-                                        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});
-                                }
-
-                                //reverse of crossover for fossilization
-                                if (crossed == 1)
-                                {
-                                        crossover(parent, "vamin");
-                                        crossed = 0;
-                                }
-                        }
+                //reverse of crossover for fossilization
+                if (crossed == 1)
+                {
+                        crossover(parent, "vamin");
+                        crossed = 0;
                 }
+                        
         }
-        killParents(repro_list);
 }
 
@@ -72 +49 @@
 }
 
-function killParents(repro_list)
-{
-        for (var j = 0; j < repro_list.size; j++)
-        {
-                Populations[0].kill(repro_list[j]);
-        }
-}
 
 function createOffspring(geno, energy, new_user1, new_user2)
@@ -164 +134 @@
         {
                 reprocounter = 0;
-                var to_repro_h = [];
-                var to_repro_d = [];
-                for (var i = 0; i < Populations[0].size; i++)
+                var parent1 = null;
+                var parent2 = null;
+                var pop = Populations[0];
+                for (var i = pop.size-1; i >= 0; i--)
                 {
-                        var cr = Populations[0].get(i);
-                        if (cr.signals.size > 0)
-                        {
-                                if (cr.user2["gen"] == 0)
+                        if (pop[i].signals.size > 0) 
+                        { 
+                                if (pop[i].user2["gen"]==1)
                                 {
-                                        to_repro_h.add(i);
+                                        reproduce_diploid(pop[i]);
+                                        pop.kill(i);
                                 }
-                                if (cr.user2["gen"] == 1)
+                                else if (parent1 == null)
                                 {
-                                        to_repro_d.add(i);
+                                        parent1 = pop[i];
                                 }
-                        }
-                }
-                if (to_repro_h.size > 1)
-                {
-                        reproduce_haploid(to_repro_h);
-                }
-                if (to_repro_d.size > 0)
-                {
-                        reproduce_diploid(to_repro_d);
+                                else if (parent2 == null)
+                                {
+                                        parent2 = pop[i];
+                                }  
+                                else
+                                {
+                                        reproduce_haploid(parent1, parent2);
+                                        pop.kill(parent1);
+                                        pop.kill(parent2);
+                                        parent1 = null;
+                                        parent2 = null;
+                                }
+                
+                        } 
                 }
         }