Bug fixes, code comments, and minor changes

3 files changed, 430 insertions, 409 deletions

diff --git a/sourcecodes/data/example_chl/bWRmap.txt b/sourcecodes/data/example_chl/bWRmap.txt
index b872d2f0..b24eae2f 100644
--- a/sourcecodes/data/example_chl/bWRmap.txt
+++ b/sourcecodes/data/example_chl/bWRmap.txt
@@ -1,5 +1,5 @@
-Ctrq3	2	0.487652	1.365854
-MAS	1	0.355012	0.479560
-Neutrophil	1	10.929756	15.048780
-Load	1	0.825354	4.077143
-Weight	1	0.088036	0.877077
+Ctrq3	0.487652	1.365854
+MAS	0.355012	0.479560
+Neutrophil	10.929756	15.048780
+Load	0.825354	4.077143
+Weight	0.088036	0.877077
diff --git a/sourcecodes/data/example_chl/bWRnet_figure.txt b/sourcecodes/data/example_chl/bWRnet_figure.txt
index 1798da4f..6a3a1dbc 100644
--- a/sourcecodes/data/example_chl/bWRnet_figure.txt
+++ b/sourcecodes/data/example_chl/bWRnet_figure.txt
@@ -15,419 +15,419 @@ MAS	1
 250	150
 1	1
 2	3	4
--2.2595	0.0292
--2.2129	0.0326
--2.1662	0.0362
--2.1196	0.0401
--2.0729	0.0443
--2.0263	0.0489
--1.9796	0.0539
--1.9330	0.0592
--1.8863	0.0648
--1.8397	0.0709
--1.7930	0.0774
--1.7464	0.0842
--1.6997	0.0915
--1.6531	0.0992
--1.6064	0.1072
--1.5598	0.1157
--1.5131	0.1246
--1.4665	0.1338
--1.4199	0.1434
--1.3732	0.1534
--1.3266	0.1636
--1.2799	0.1742
--1.2333	0.1850
--1.1866	0.1961
--1.1400	0.2074
--1.0933	0.2188
--1.0467	0.2303
--1.0000	0.2419
--0.9534	0.2535
--0.9067	0.2651
--0.8601	0.2766
--0.8134	0.2879
--0.7668	0.2991
--0.7201	0.3099
--0.6735	0.3205
--0.6268	0.3307
--0.5802	0.3404
--0.5335	0.3496
--0.4869	0.3583
--0.4402	0.3663
--0.3936	0.3737
--0.3470	0.3804
--0.3003	0.3864
--0.2537	0.3916
--0.2070	0.3959
--0.1604	0.3994
--0.1137	0.4021
--0.0671	0.4038
--0.0204	0.4047
-0.0262	0.4046
-0.0729	0.4037
-0.1195	0.4018
-0.1662	0.3991
-0.2128	0.3954
-0.2595	0.3910
-0.3061	0.3857
-0.3528	0.3797
-0.3994	0.3729
-0.4461	0.3654
-0.4927	0.3572
-0.5394	0.3485
-0.5860	0.3392
-0.6327	0.3294
-0.6793	0.3192
-0.7259	0.3086
-0.7726	0.2977
-0.8192	0.2865
-0.8659	0.2752
-0.9125	0.2637
-0.9592	0.2521
-1.0058	0.2405
-1.0525	0.2289
-1.0991	0.2173
-1.1458	0.2059
-1.1924	0.1947
-1.2391	0.1837
-1.2857	0.1729
-1.3324	0.1623
-1.3790	0.1521
-1.4257	0.1422
-1.4723	0.1326
-1.5190	0.1234
-1.5656	0.1146
-1.6123	0.1062
-1.6589	0.0982
-1.7056	0.0906
-1.7522	0.0834
-1.7989	0.0765
-1.8455	0.0701
-1.8921	0.0641
-1.9388	0.0585
-1.9854	0.0532
-2.0321	0.0483
-2.0787	0.0438
-2.1254	0.0396
-2.1720	0.0357
-2.2187	0.0321
-2.2653	0.0288
-2.3120	0.0258
-2.3586	0.0231
-2.4053	0.0206
+-0.3226	0.0292
+-0.3060	0.0326
+-0.2895	0.0362
+-0.2729	0.0401
+-0.2564	0.0443
+-0.2398	0.0489
+-0.2232	0.0539
+-0.2067	0.0592
+-0.1901	0.0648
+-0.1735	0.0709
+-0.1570	0.0774
+-0.1404	0.0842
+-0.1239	0.0915
+-0.1073	0.0992
+-0.0907	0.1072
+-0.0742	0.1157
+-0.0576	0.1246
+-0.0411	0.1338
+-0.0245	0.1434
+-0.0079	0.1534
+0.0086	0.1636
+0.0252	0.1742
+0.0417	0.1850
+0.0583	0.1961
+0.0749	0.2074
+0.0914	0.2188
+0.1080	0.2303
+0.1245	0.2419
+0.1411	0.2535
+0.1577	0.2651
+0.1742	0.2766
+0.1908	0.2879
+0.2073	0.2991
+0.2239	0.3099
+0.2405	0.3205
+0.2570	0.3307
+0.2736	0.3404
+0.2901	0.3496
+0.3067	0.3583
+0.3233	0.3663
+0.3398	0.3737
+0.3564	0.3804
+0.3729	0.3864
+0.3895	0.3916
+0.4061	0.3959
+0.4226	0.3994
+0.4392	0.4021
+0.4558	0.4038
+0.4723	0.4047
+0.4889	0.4046
+0.5054	0.4037
+0.5220	0.4018
+0.5386	0.3991
+0.5551	0.3954
+0.5717	0.3910
+0.5882	0.3857
+0.6048	0.3797
+0.6214	0.3729
+0.6379	0.3654
+0.6545	0.3572
+0.6710	0.3485
+0.6876	0.3392
+0.7042	0.3294
+0.7207	0.3192
+0.7373	0.3086
+0.7538	0.2977
+0.7704	0.2865
+0.7870	0.2752
+0.8035	0.2637
+0.8201	0.2521
+0.8366	0.2405
+0.8532	0.2289
+0.8698	0.2173
+0.8863	0.2059
+0.9029	0.1947
+0.9194	0.1837
+0.9360	0.1729
+0.9526	0.1623
+0.9691	0.1521
+0.9857	0.1422
+1.0022	0.1326
+1.0188	0.1234
+1.0354	0.1146
+1.0519	0.1062
+1.0685	0.0982
+1.0851	0.0906
+1.1016	0.0834
+1.1182	0.0765
+1.1347	0.0701
+1.1513	0.0641
+1.1679	0.0585
+1.1844	0.0532
+1.2010	0.0483
+1.2175	0.0438
+1.2341	0.0396
+1.2507	0.0357
+1.2672	0.0321
+1.2838	0.0288
+1.3003	0.0258
+1.3169	0.0231
+1.3335	0.0206
 Load	1
 250	150
 2	1	2
 0
--3.0935	0.0030
--3.0388	0.0036
--2.9842	0.0043
--2.9295	0.0050
--2.8748	0.0059
--2.8202	0.0069
--2.7655	0.0081
--2.7108	0.0094
--2.6562	0.0110
--2.6015	0.0127
--2.5469	0.0147
--2.4922	0.0169
--2.4375	0.0194
--2.3829	0.0222
--2.3282	0.0253
--2.2735	0.0287
--2.2189	0.0326
--2.1642	0.0368
--2.1095	0.0415
--2.0549	0.0466
--2.0002	0.0522
--1.9456	0.0583
--1.8909	0.0649
--1.8362	0.0720
--1.7816	0.0797
--1.7269	0.0879
--1.6722	0.0966
--1.6176	0.1059
--1.5629	0.1158
--1.5083	0.1261
--1.4536	0.1370
--1.3989	0.1484
--1.3443	0.1602
--1.2896	0.1724
--1.2349	0.1850
--1.1803	0.1979
--1.1256	0.2111
--1.0709	0.2244
--1.0163	0.2379
--0.9616	0.2514
--0.9070	0.2649
--0.8523	0.2782
--0.7976	0.2914
--0.7430	0.3042
--0.6883	0.3166
--0.6336	0.3285
--0.5790	0.3398
--0.5243	0.3504
--0.4697	0.3603
--0.4150	0.3693
--0.3603	0.3774
--0.3057	0.3845
--0.2510	0.3905
--0.1963	0.3954
--0.1417	0.3992
--0.0870	0.4017
--0.0323	0.4031
-0.0223	0.4032
-0.0770	0.4021
-0.1316	0.3997
-0.1863	0.3962
-0.2410	0.3915
-0.2956	0.3857
-0.3503	0.3788
-0.4050	0.3709
-0.4596	0.3620
-0.5143	0.3523
-0.5689	0.3418
-0.6236	0.3306
-0.6783	0.3188
-0.7329	0.3065
-0.7876	0.2937
-0.8423	0.2807
-0.8969	0.2674
-0.9516	0.2539
-1.0063	0.2404
-1.0609	0.2269
-1.1156	0.2135
-1.1702	0.2003
-1.2249	0.1874
-1.2796	0.1747
-1.3342	0.1624
-1.3889	0.1505
-1.4436	0.1391
-1.4982	0.1281
-1.5529	0.1176
-1.6075	0.1077
-1.6622	0.0983
-1.7169	0.0894
-1.7715	0.0811
-1.8262	0.0734
-1.8809	0.0662
-1.9355	0.0595
-1.9902	0.0533
-2.0449	0.0476
-2.0995	0.0424
-2.1542	0.0377
-2.2088	0.0333
-2.2635	0.0294
-2.3182	0.0259
-2.3728	0.0227
+1.5239	0.0030
+1.5690	0.0036
+1.6142	0.0043
+1.6593	0.0050
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+3.1030	0.1979
+3.1481	0.2111
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+5.6295	0.0662
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+5.8551	0.0377
+5.9002	0.0333
+5.9453	0.0294
+5.9905	0.0259
+6.0356	0.0227
 Neutrophil	1
 250	150
 2	1	2
 1	5
--2.3403	0.0245
--2.2876	0.0277
--2.2349	0.0313
--2.1823	0.0353
--2.1296	0.0396
--2.0770	0.0444
--2.0243	0.0496
--1.9716	0.0552
--1.9190	0.0613
--1.8663	0.0679
--1.8136	0.0750
--1.7610	0.0825
--1.7083	0.0906
--1.6556	0.0992
--1.6030	0.1083
--1.5503	0.1180
--1.4977	0.1281
--1.4450	0.1386
--1.3923	0.1496
--1.3397	0.1611
--1.2870	0.1729
--1.2343	0.1851
--1.1817	0.1975
--1.1290	0.2102
--1.0764	0.2231
--1.0237	0.2361
--0.9710	0.2491
--0.9184	0.2621
--0.8657	0.2750
--0.8130	0.2878
--0.7604	0.3002
--0.7077	0.3124
--0.6550	0.3240
--0.6024	0.3352
--0.5497	0.3458
--0.4971	0.3557
--0.4444	0.3648
--0.3917	0.3731
--0.3391	0.3806
--0.2864	0.3870
--0.2337	0.3925
--0.1811	0.3969
--0.1284	0.4002
--0.0758	0.4025
--0.0231	0.4035
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-0.1349	0.3999
-0.1876	0.3964
-0.2402	0.3919
-0.2929	0.3863
-0.3456	0.3797
-0.3982	0.3722
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-0.7142	0.3109
-0.7669	0.2987
-0.8195	0.2862
-0.8722	0.2735
-0.9248	0.2605
-0.9775	0.2475
-1.0302	0.2345
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-1.1882	0.1960
-1.2408	0.1835
-1.2935	0.1714
-1.3462	0.1597
-1.3988	0.1483
-1.4515	0.1373
-1.5041	0.1268
-1.5568	0.1167
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-1.7148	0.0896
-1.7675	0.0816
-1.8201	0.0741
-1.8728	0.0670
-1.9254	0.0605
-1.9781	0.0545
-2.0308	0.0489
-2.0834	0.0438
-2.1361	0.0391
-2.1888	0.0348
-2.2414	0.0308
-2.2941	0.0273
-2.3468	0.0241
-2.3994	0.0212
-2.4521	0.0186
-2.5047	0.0163
-2.5574	0.0142
-2.6101	0.0123
-2.6627	0.0107
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-2.7681	0.0080
-2.8207	0.0069
-2.8734	0.0059
-2.9260	0.0050
+-10.5298	0.0245
+-9.9542	0.0277
+-9.3786	0.0313
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+-7.6518	0.0444
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+-6.5006	0.0552
+-5.9250	0.0613
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+7.8893	0.3240
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+10.1917	0.3648
+10.7673	0.3731
+11.3429	0.3806
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+12.4940	0.3925
+13.0696	0.3969
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+15.3720	0.4035
+15.9476	0.4022
+16.5232	0.3999
+17.0988	0.3964
+17.6744	0.3919
+18.2500	0.3863
+18.8256	0.3797
+19.4012	0.3722
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+20.5524	0.3545
+21.1280	0.3445
+21.7036	0.3339
+22.2792	0.3226
+22.8548	0.3109
+23.4304	0.2987
+24.0060	0.2862
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+26.3083	0.2345
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+27.4595	0.2086
+28.0351	0.1960
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+30.9131	0.1373
+31.4887	0.1268
+32.0643	0.1167
+32.6399	0.1072
+33.2155	0.0981
+33.7911	0.0896
+34.3667	0.0816
+34.9423	0.0741
+35.5179	0.0670
+36.0934	0.0605
+36.6690	0.0545
+37.2446	0.0489
+37.8202	0.0438
+38.3958	0.0391
+38.9714	0.0348
+39.5470	0.0308
+40.1226	0.0273
+40.6982	0.0241
+41.2738	0.0212
+41.8494	0.0186
+42.4250	0.0163
+43.0006	0.0142
+43.5762	0.0123
+44.1518	0.0107
+44.7274	0.0093
+45.3030	0.0080
+45.8786	0.0069
+46.4542	0.0059
+47.0298	0.0050
 Weight	1
 250	150
 2	1	4
 0
--2.7996	0.0076
--2.7425	0.0089
--2.6853	0.0105
--2.6281	0.0122
--2.5709	0.0142
--2.5137	0.0164
--2.4565	0.0190
--2.3993	0.0218
--2.3421	0.0250
--2.2850	0.0286
--2.2278	0.0326
--2.1706	0.0370
--2.1134	0.0419
--2.0562	0.0473
--1.9990	0.0531
--1.9418	0.0596
--1.8846	0.0665
--1.8275	0.0741
--1.7703	0.0822
--1.7131	0.0909
--1.6559	0.1002
--1.5987	0.1101
--1.5415	0.1206
--1.4843	0.1316
--1.4271	0.1432
--1.3700	0.1553
--1.3128	0.1678
--1.2556	0.1808
--1.1984	0.1941
--1.1412	0.2076
--1.0840	0.2215
--1.0268	0.2354
--0.9696	0.2494
--0.9125	0.2633
--0.8553	0.2772
--0.7981	0.2907
--0.7409	0.3040
--0.6837	0.3168
--0.6265	0.3290
--0.5693	0.3406
--0.5121	0.3514
--0.4550	0.3614
--0.3978	0.3704
--0.3406	0.3784
--0.2834	0.3853
--0.2262	0.3910
--0.1690	0.3955
--0.1118	0.3988
--0.0546	0.4007
-0.0025	0.4013
-0.0597	0.4006
-0.1169	0.3985
-0.1741	0.3952
-0.2313	0.3906
-0.2885	0.3847
-0.3457	0.3778
-0.4029	0.3697
-0.4600	0.3605
-0.5172	0.3505
-0.5744	0.3396
-0.6316	0.3280
-0.6888	0.3157
-0.7460	0.3028
-0.8032	0.2896
-0.8603	0.2759
-0.9175	0.2621
-0.9747	0.2481
-1.0319	0.2342
-1.0891	0.2202
-1.1463	0.2064
-1.2035	0.1929
-1.2607	0.1796
-1.3178	0.1667
-1.3750	0.1542
-1.4322	0.1422
-1.4894	0.1306
-1.5466	0.1197
-1.6038	0.1092
-1.6610	0.0994
-1.7182	0.0901
-1.7753	0.0815
-1.8325	0.0734
-1.8897	0.0659
-1.9469	0.0590
-2.0041	0.0526
-2.0613	0.0468
-2.1185	0.0414
-2.1757	0.0366
-2.2328	0.0322
-2.2900	0.0283
-2.3472	0.0247
-2.4044	0.0215
-2.4616	0.0187
-2.5188	0.0162
-2.5760	0.0140
-2.6332	0.0120
-2.6903	0.0103
-2.7475	0.0088
-2.8047	0.0075
-2.8619	0.0064
-2.9191	0.0054
+0.6306	0.0076
+0.6356	0.0089
+0.6407	0.0105
+0.6457	0.0122
+0.6507	0.0142
+0.6558	0.0164
+0.6608	0.0190
+0.6659	0.0218
+0.6709	0.0250
+0.6759	0.0286
+0.6810	0.0326
+0.6860	0.0370
+0.6910	0.0419
+0.6961	0.0473
+0.7011	0.0531
+0.7061	0.0596
+0.7112	0.0665
+0.7162	0.0741
+0.7212	0.0822
+0.7263	0.0909
+0.7313	0.1002
+0.7363	0.1101
+0.7414	0.1206
+0.7464	0.1316
+0.7514	0.1432
+0.7565	0.1553
+0.7615	0.1678
+0.7665	0.1808
+0.7716	0.1941
+0.7766	0.2076
+0.7816	0.2215
+0.7867	0.2354
+0.7917	0.2494
+0.7967	0.2633
+0.8018	0.2772
+0.8068	0.2907
+0.8119	0.3040
+0.8169	0.3168
+0.8219	0.3290
+0.8270	0.3406
+0.8320	0.3514
+0.8370	0.3614
+0.8421	0.3704
+0.8471	0.3784
+0.8521	0.3853
+0.8572	0.3910
+0.8622	0.3955
+0.8672	0.3988
+0.8723	0.4007
+0.8773	0.4013
+0.8823	0.4006
+0.8874	0.3985
+0.8924	0.3952
+0.8974	0.3906
+0.9025	0.3847
+0.9075	0.3778
+0.9125	0.3697
+0.9176	0.3605
+0.9226	0.3505
+0.9276	0.3396
+0.9327	0.3280
+0.9377	0.3157
+0.9427	0.3028
+0.9478	0.2896
+0.9528	0.2759
+0.9579	0.2621
+0.9629	0.2481
+0.9679	0.2342
+0.9730	0.2202
+0.9780	0.2064
+0.9830	0.1929
+0.9881	0.1796
+0.9931	0.1667
+0.9981	0.1542
+1.0032	0.1422
+1.0082	0.1306
+1.0132	0.1197
+1.0183	0.1092
+1.0233	0.0994
+1.0283	0.0901
+1.0334	0.0815
+1.0384	0.0734
+1.0434	0.0659
+1.0485	0.0590
+1.0535	0.0526
+1.0585	0.0468
+1.0636	0.0414
+1.0686	0.0366
+1.0736	0.0322
+1.0787	0.0283
+1.0837	0.0247
+1.0888	0.0215
+1.0938	0.0187
+1.0988	0.0162
+1.1039	0.0140
+1.1089	0.0120
+1.1139	0.0103
+1.1190	0.0088
+1.1240	0.0075
+1.1290	0.0064
+1.1341	0.0054
diff --git a/sourcecodes/data/example_chl/bWRparameters.txt b/sourcecodes/data/example_chl/bWRparameters.txt
new file mode 100644
index 00000000..6d6eabf6
--- /dev/null
+++ b/sourcecodes/data/example_chl/bWRparameters.txt
@@ -0,0 +1,21 @@
+Ctrq3
+Discrete node with 2 states
+1	0.6341
+2	0.3659
+
+MAS
+Continuous node
+0.4796	0.3499
+
+Neutrophil
+Continuous node
+15.0488	10.8026
+
+Load
+Continuous node
+4.0771	0.8165
+
+Weight
+Continuous node
+0.8771	0.0875
+