Bug fixes, code comments, and minor changes

25 files changed, 1508 insertions, 0 deletions

diff --git a/sourcecodes/data/old/example_sci_bk/Lluban.txt b/sourcecodes/data/old/example_sci_bk/Lluban.txt
new file mode 100644
index 00000000..38108f00
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Lluban.txt
@@ -0,0 +1,15 @@
+From	To
+Gene1	Genotype
+Gene2	Genotype
+Gene3	Genotype
+Phenotype	Genotype
+Gene1	Genotype
+Gene2	Genotype
+Gene3	Genotype
+Phenotype	Gene1
+Phenotype	Gene2
+Phenotype	Gene3
+Phenotype	Genotype
+Phenotype	Gene1
+Phenotype	Gene2
+Phenotype	Gene3
diff --git a/sourcecodes/data/old/example_sci_bk/Llucontinuous_input.txt b/sourcecodes/data/old/example_sci_bk/Llucontinuous_input.txt
new file mode 100644
index 00000000..79295d7e
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Llucontinuous_input.txt
@@ -0,0 +1,503 @@
+Genotype	Gene3	Gene2	Phenotype	Gene1
+2	1	1	1	1
+2	-1.0008	-0.44837	0.21808	-1.196
+1	-0.29368	-0.53043	-1.0893	-0.10136
+2	0.70835	0.72886	-0.18098	-0.42907
+1	0.63703	0.86428	1.7013	0.1425
+1	-1.2402	-0.69712	-1.7002	-0.71634
+1	-1.1952	0.27155	-0.79413	-1.0965
+2	0.62914	0.94265	1.8385	0.6135
+1	-1.91	-2.379	-3.1094	-1.0924
+2	-0.83436	-0.90968	-1.3598	1.335
+1	0.15685	0.4766	1.2891	-1.3309
+2	0.7047	1.0623	1.9811	1.2821
+1	0.59747	-0.023123	0.88555	-0.8844
+1	-1.0557	-1.5548	-1.3016	-0.77687
+2	1.5206	2.0289	0.90366	1.8089
+1	0.65525	-0.47226	-1.1824	0.41863
+2	-0.39262	0.382	-0.64829	0.40947
+2	0.14966	0.22972	0.33797	0.69647
+1	-1.8836	-0.68534	-0.99941	-0.78961
+1	0.48181	0.01241	1.2145	0.16835
+2	1.4673	2.0438	2.4674	2.5234
+1	-1.3242	-0.80218	-1.6446	-0.31044
+1	-1.2471	-2.0351	-1.0296	-1.937
+1	0.23695	-0.01724	-0.32851	-0.16484
+1	-0.13986	-0.6065	-0.8491	-0.95538
+2	0.90888	1.0365	2.7222	1.3507
+1	-0.30556	-1.1546	-0.86033	-2.2006
+2	0.5391	0.99532	0.96947	1.1575
+2	1.1235	0.37982	0.64439	0.94362
+2	1.7073	1.9303	2.8018	1.9158
+1	-0.20553	-0.074104	-0.50073	-1.0697
+1	-0.27415	0.23076	-0.27564	-0.11286
+1	-1.304	-1.1213	-0.71793	-1.3462
+2	0.54315	0.55846	0.87411	1.2432
+1	-1.0659	-0.38067	-1.4372	-2.0927
+1	0.21278	-1.0115	-1.0984	-0.72751
+1	-2.9061	-1.3118	-3.8372	-2.0448
+2	-0.69608	-0.61145	-1.0037	0.12181
+1	0.66835	0.018886	-1.0081	-1.4165
+1	0.32575	-0.51767	1.0187	-0.40914
+2	0.65837	1.2791	1.8388	2.2906
+2	0.37574	0.21618	-0.89435	1.2643
+1	0.13513	-0.31405	-0.16057	0.77712
+2	0.16054	0.40635	0.036165	1.6374
+1	1.9393	1.5717	2.6922	1.1933
+1	-0.59118	-0.47154	-0.20293	-1.5576
+1	-0.35938	-0.49565	-0.20837	0.61043
+2	-0.57133	0.15921	-0.44158	0.43312
+1	0.31835	0.49002	2.2029	0.17685
+1	-0.0093708	-0.85889	-1.0934	-1.6905
+1	-0.90501	-1.4637	-1.5526	-1.828
+2	0.11531	-0.022781	0.88843	0.8607
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+2	-0.22236	-0.13023	0.37608	0.18027
+1	-0.90103	-0.38393	-1.1513	-0.78153
+2	0.66848	0.81005	1.3945	3.3654
+2	0.10539	0.59781	0.77864	0.63865
+1	-1.15	-1.4531	-2.929	-1.6867
+1	0.20842	-0.0039076	-0.12879	-0.31459
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+2	0.041926	0.86223	1.2222	1.0289
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+1	-1.1701	-0.57889	-0.8843	-0.11873
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+2	0.92209	2.2111	1.208	2.7402
+2	-0.93755	-0.26009	0.54448	0.20265
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+2	0.84872	0.59768	1.9205	1.1233
+1	0.029696	-1.4186	-0.39548	-0.029631
+2	2.0013	1.9999	3.0139	1.6432
+2	1.1324	0.89689	-0.1229	0.15109
+2	0.93618	2.4521	1.7229	3.4367
+1	-1.0037	-1.435	-2.2126	-1.9473
+2	-2.2472	-1.296	-2.3762	-1.9611
+2	0.62477	1.5212	1.2814	1.4403
+2	0.17619	0.488	0.38575	0.19632
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+2	1.3618	1.6805	1.2152	2.1905
+2	-0.36075	1.0698	0.38569	2.5707
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+2	0.9795	1.3777	0.26495	0.23258
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+2	0.52259	0.76325	0.93484	0.060827
+1	0.89037	0.68007	0.50459	-0.88464
+2	1.0031	1.3853	1.7313	0.75303
+2	0.6954	1.3692	0.19298	1.6174
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+2	-1.7796	-1.2709	-2.5775	-0.36996
+2	0.41557	1.9905	1.839	1.1327
+1	0.53878	-0.71974	-0.65395	-0.62597
+2	0.22326	1.3888	0.17221	1.2265
+1	-0.12667	-1.1336	-0.67	-3.6161
+2	1.0183	1.5883	2.2784	1.7509
+1	-2.0415	-2.2483	-2.8307	-3.1148
+2	-1.1513	-0.08575	-0.62876	2.164
+1	0.1961	0.075096	1.9551	0.039445
+2	-0.96925	0.12921	-1.2741	1.8371
+1	0.34137	0.086468	1.4716	0.55236
+1	-0.20756	-0.74846	0.65256	-0.7032
+2	1.1736	1.0214	1.258	1.0002
+2	0.48081	1.3275	0.54443	1.2194
+2	-0.45146	0.38298	0.64902	0.90395
+1	0.75519	-1.0627	-0.35778	-1.7689
+1	-1.4308	-1.0998	-1.0094	-0.66361
+1	-0.097019	0.18029	-9.0423e-07	0.59444
+2	1.3769	2.4872	3.2855	0.98727
+2	0.79201	0.76361	0.88459	3.119
+2	2.5125	2.4776	4.6119	3.966
+1	0.57129	-0.93689	-0.20516	-0.42323
+1	-0.91517	-0.25445	-1.3515	-0.99354
+1	0.17456	-0.98904	-0.49643	-0.8997
+1	-2.2724	-1.6869	-3.8034	-2.0882
+2	-1.8188	-0.57721	-2.4386	0.058963
+2	-0.19227	0.038901	-0.85065	0.6644
+1	-1.5517	-0.57182	-0.9874	-1.4081
+2	-0.47999	0.49667	0.27351	0.6261
+2	0.45041	0.48469	0.55808	2.0659
+1	-1.1302	-1.255	-2.7206	-1.2712
+1	-0.60672	-1.1008	-2.6889	-1.0078
+1	-1.0508	-0.99612	-1.555	-1.0463
+2	0.14434	0.97791	1.2498	1.7391
+2	0.21333	1.6686	1.219	1.8919
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+1	-2.0611	-2.1245	-3.6067	-1.6584
+2	-0.3534	0.45962	-0.39991	0.45667
+1	-0.37564	-0.63085	-1.2641	-1.3292
+1	0.30023	-0.20283	0.041852	-0.17139
+2	0.25089	1.0204	1.8084	1.0493
+1	-0.44041	-1.1143	-0.59224	-0.84288
+2	-0.11392	0.5681	-0.054604	0.88897
+1	0.41829	-1.042	-0.0042274	-1.9512
+2	1.4863	2.9227	3.0012	3.1253
+1	-0.60588	-1.1196	-1.4647	-0.92268
+1	-0.10497	-0.74629	-1.8353	-0.35425
+1	-1.2499	-0.83335	-2.4047	-1.4657
+1	-0.51414	-1.4602	-0.54649	-1.0475
+1	0.56956	0.79545	0.86494	-0.59471
+1	-0.64964	-0.78543	-1.9412	-2.2114
+2	1.0044	0.56431	1.2968	1.3807
+1	-1.1924	-0.69401	-0.72828	-1.7252
+2	0.15739	1.0449	0.3742	1.4303
+2	0.49582	1.4353	1.1652	1.5814
+
diff --git a/sourcecodes/data/old/example_sci_bk/Llugraphviz.txt b/sourcecodes/data/old/example_sci_bk/Llugraphviz.txt
new file mode 100644
index 00000000..88bbd3ba
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Llugraphviz.txt
@@ -0,0 +1,10 @@
+digraph G {
+size="10,10";  ratio = fill;
+node [shape=square,width=1.5];
+Genotype -> Gene3;
+Genotype -> Gene1;
+Gene3 -> Phenotype;
+Gene2 -> Gene3;
+Gene2 -> Phenotype;
+Gene1 -> Gene2;
+}
\ No newline at end of file
diff --git a/sourcecodes/data/old/example_sci_bk/Lluk.txt b/sourcecodes/data/old/example_sci_bk/Lluk.txt
new file mode 100644
index 00000000..83b33d23
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Lluk.txt
@@ -0,0 +1 @@
+1000
diff --git a/sourcecodes/data/old/example_sci_bk/Llumap.txt b/sourcecodes/data/old/example_sci_bk/Llumap.txt
new file mode 100644
index 00000000..958281d5
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Llumap.txt
@@ -0,0 +1,5 @@
+Genotype	2	0.500305	1.514000
+Gene3	1	1.027261	-0.015284
+Gene2	1	1.160583	0.138097
+Phenotype	1	1.554104	0.069005
+Gene1	1	1.515414	0.174451
diff --git a/sourcecodes/data/old/example_sci_bk/Llumapdata.txt b/sourcecodes/data/old/example_sci_bk/Llumapdata.txt
new file mode 100644
index 00000000..d684ea06
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Llumapdata.txt
@@ -0,0 +1 @@
+Genotype	Gene1	Gene2	Gene3	Phenotype
diff --git a/sourcecodes/data/old/example_sci_bk/Lluname.txt b/sourcecodes/data/old/example_sci_bk/Lluname.txt
new file mode 100644
index 00000000..f3a1f5bf
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Lluname.txt
@@ -0,0 +1 @@
+Genotype	Gene3	Gene2	Phenotype	Gene1
diff --git a/sourcecodes/data/old/example_sci_bk/Llunet_figure.txt b/sourcecodes/data/old/example_sci_bk/Llunet_figure.txt
new file mode 100644
index 00000000..bdc07cbd
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Llunet_figure.txt
@@ -0,0 +1,433 @@
+5
+1200	1200	
+Genotype	0	0
+Gene1	120	200
+Gene2	0	400
+Gene3	120	600
+Phenotype	0	800
+Genotype	2
+250	150
+0
+2	2	4
+1	0.4860
+2	0.5140
+Gene1	1
+250	150
+1	1
+1	3
+-3.5013	0.0009
+-3.4313	0.0012
+-3.3613	0.0015
+-3.2912	0.0019
+-3.2212	0.0024
+-3.1512	0.0030
+-3.0811	0.0037
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+-2.8010	0.0083
+-2.7310	0.0101
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+-2.1007	0.0451
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+1.6111	0.1103
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+1.8212	0.0774
+1.8912	0.0681
+1.9613	0.0596
+2.0313	0.0520
+2.1013	0.0451
+2.1714	0.0389
+2.2414	0.0334
+2.3114	0.0286
+2.3815	0.0243
+2.4515	0.0206
+2.5215	0.0173
+2.5916	0.0145
+2.6616	0.0121
+2.7316	0.0101
+2.8017	0.0083
+2.8717	0.0068
+2.9417	0.0056
+3.0118	0.0046
+3.0818	0.0037
+3.1518	0.0030
+3.2219	0.0024
+3.2919	0.0019
+3.3619	0.0015
+3.4320	0.0012
+3.5020	0.0009
+Gene2	1
+250	150
+1	2
+2	4	5
+-3.5862	0.0008
+-3.5124	0.0010
+-3.4385	0.0013
+-3.3647	0.0016
+-3.2909	0.0020
+-3.2171	0.0026
+-3.1432	0.0032
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+-2.9956	0.0050
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diff --git a/sourcecodes/data/old/example_sci_bk/Llunet_figure_new.txt b/sourcecodes/data/old/example_sci_bk/Llunet_figure_new.txt
new file mode 100644
index 00000000..7e6f0d97
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Llunet_figure_new.txt
@@ -0,0 +1,433 @@
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diff --git a/sourcecodes/data/old/example_sci_bk/Llunlevels.txt b/sourcecodes/data/old/example_sci_bk/Llunlevels.txt
new file mode 100644
index 00000000..714e56bd
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Llunlevels.txt
@@ -0,0 +1,2 @@
+Genotype	1	2
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diff --git a/sourcecodes/data/old/example_sci_bk/Llunnode.txt b/sourcecodes/data/old/example_sci_bk/Llunnode.txt
new file mode 100644
index 00000000..7ed6ff82
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Llunnode.txt
@@ -0,0 +1 @@
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diff --git a/sourcecodes/data/old/example_sci_bk/Llunrows.txt b/sourcecodes/data/old/example_sci_bk/Llunrows.txt
new file mode 100644
index 00000000..c15fb720
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Llunrows.txt
@@ -0,0 +1 @@
+501
diff --git a/sourcecodes/data/old/example_sci_bk/Lluparent.txt b/sourcecodes/data/old/example_sci_bk/Lluparent.txt
new file mode 100644
index 00000000..b8626c4c
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Lluparent.txt
@@ -0,0 +1 @@
+4
diff --git a/sourcecodes/data/old/example_sci_bk/Llustructure_input.txt b/sourcecodes/data/old/example_sci_bk/Llustructure_input.txt
new file mode 100644
index 00000000..bcf72d97
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Llustructure_input.txt
@@ -0,0 +1,6 @@
+Genotype	Gene3	Gene2	Phenotype	Gene1	
+0	1	0	0	1	
+0	0	0	1	0	
+0	1	0	1	0	
+0	0	0	0	0	
+0	0	1	0	0	
diff --git a/sourcecodes/data/old/example_sci_bk/Llustructure_input_temp.txt b/sourcecodes/data/old/example_sci_bk/Llustructure_input_temp.txt
new file mode 100644
index 00000000..95aa7a5d
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Llustructure_input_temp.txt
@@ -0,0 +1,6 @@
+Genotype	Gene3	Gene2	Phenotype	Gene1	
+0.000000	0.999929	0.183248	0.000431	1.000000	
+0.000000	0.000000	0.000000	1.000000	0.000000	
+0.000000	0.935752	0.000000	1.000000	0.000000	
+0.000000	0.000000	0.000000	0.000000	0.000000	
+0.000000	0.053385	0.881001	0.156255	0.000000	
diff --git a/sourcecodes/data/old/example_sci_bk/Llustructure_old.txt b/sourcecodes/data/old/example_sci_bk/Llustructure_old.txt
new file mode 100644
index 00000000..5b464577
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Llustructure_old.txt
@@ -0,0 +1,5 @@
+Genotype	0.4860	0.5140
+Gene3	0.0001	0.0001	0.0001	0.0001	0.0002	0.0002	0.0003	0.0004	0.0006	0.0008	0.0010	0.0013	0.0018	0.0023	0.0029	0.0037	0.0047	0.0059	0.0074	0.0092	0.0113	0.0139	0.0170	0.0206	0.0248	0.0297	0.0354	0.0419	0.0493	0.0576	0.0669	0.0773	0.0887	0.1012	0.1147	0.1292	0.1447	0.1610	0.1781	0.1958	0.2139	0.2323	0.2507	0.2688	0.2866	0.3036	0.3197	0.3345	0.3479	0.3597	0.3695	0.3773	0.3828	0.3861	0.3870	0.3855	0.3817	0.3756	0.3673	0.3570	0.3449	0.3311	0.3160	0.2996	0.2824	0.2645	0.2463	0.2279	0.2095	0.1915	0.1740	0.1570	0.1409	0.1256	0.1114	0.0981	0.0859	0.0747	0.0646	0.0555	0.0474	0.0402	0.0340	0.0285	0.0237	0.0197	0.0162	0.0132	0.0108	0.0087	0.0070	0.0056	0.0044	0.0035	0.0027	0.0021	0.0016	0.0013	0.0010	0.0007	0.0006
+Gene1	0.0009	0.0012	0.0015	0.0019	0.0024	0.0030	0.0037	0.0046	0.0056	0.0069	0.0083	0.0101	0.0121	0.0145	0.0174	0.0206	0.0243	0.0286	0.0335	0.0389	0.0451	0.0520	0.0597	0.0682	0.0775	0.0876	0.0986	0.1105	0.1231	0.1366	0.1508	0.1657	0.1811	0.1971	0.2134	0.2300	0.2467	0.2633	0.2797	0.2956	0.3110	0.3256	0.3392	0.3517	0.3629	0.3726	0.3808	0.3873	0.3920	0.3948	0.3958	0.3948	0.3920	0.3872	0.3807	0.3726	0.3628	0.3516	0.3391	0.3254	0.3108	0.2955	0.2795	0.2631	0.2465	0.2299	0.2133	0.1969	0.1810	0.1655	0.1507	0.1365	0.1230	0.1103	0.0985	0.0875	0.0774	0.0681	0.0596	0.0520	0.0451	0.0389	0.0334	0.0286	0.0243	0.0206	0.0173	0.0145	0.0121	0.0101	0.0083	0.0068	0.0056	0.0046	0.0037	0.0030	0.0024	0.0019	0.0015	0.0012	0.0009
+Phenotype	0.0010	0.0013	0.0016	0.0021	0.0026	0.0033	0.0042	0.0052	0.0065	0.0080	0.0098	0.0120	0.0146	0.0176	0.0212	0.0253	0.0300	0.0354	0.0416	0.0486	0.0564	0.0651	0.0748	0.0854	0.0970	0.1096	0.1230	0.1374	0.1526	0.1685	0.1850	0.2021	0.2195	0.2370	0.2545	0.2718	0.2887	0.3049	0.3202	0.3344	0.3473	0.3587	0.3684	0.3763	0.3822	0.3860	0.3877	0.3872	0.3846	0.3798	0.3731	0.3644	0.3539	0.3418	0.3283	0.3136	0.2979	0.2813	0.2643	0.2468	0.2293	0.2118	0.1945	0.1777	0.1614	0.1458	0.1310	0.1170	0.1039	0.0918	0.0806	0.0704	0.0612	0.0529	0.0454	0.0388	0.0329	0.0278	0.0234	0.0195	0.0162	0.0134	0.0110	0.0090	0.0073	0.0059	0.0047	0.0038	0.0030	0.0024	0.0019	0.0015	0.0011	0.0009	0.0007	0.0005	0.0004	0.0003	0.0002	0.0002	0.0001
+Gene2	0.0008	0.0010	0.0013	0.0016	0.0020	0.0026	0.0032	0.0041	0.0050	0.0062	0.0077	0.0094	0.0114	0.0138	0.0166	0.0199	0.0237	0.0281	0.0331	0.0388	0.0453	0.0526	0.0607	0.0696	0.0795	0.0903	0.1021	0.1147	0.1282	0.1426	0.1578	0.1736	0.1900	0.2069	0.2241	0.2414	0.2587	0.2758	0.2924	0.3084	0.3236	0.3377	0.3506	0.3621	0.3719	0.3800	0.3863	0.3905	0.3927	0.3929	0.3910	0.3870	0.3811	0.3732	0.3636	0.3524	0.3397	0.3258	0.3108	0.2949	0.2783	0.2613	0.2440	0.2267	0.2095	0.1925	0.1760	0.1601	0.1449	0.1304	0.1167	0.1039	0.0920	0.0811	0.0711	0.0620	0.0537	0.0464	0.0398	0.0340	0.0288	0.0243	0.0205	0.0171	0.0142	0.0117	0.0097	0.0079	0.0064	0.0052	0.0042	0.0034	0.0027	0.0021	0.0017	0.0013	0.0010	0.0008	0.0006	0.0005	0.0004
diff --git a/sourcecodes/data/old/example_sci_bk/Lluthr.txt b/sourcecodes/data/old/example_sci_bk/Lluthr.txt
new file mode 100644
index 00000000..2eb3c4fe
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Lluthr.txt
@@ -0,0 +1 @@
+0.5
diff --git a/sourcecodes/data/old/example_sci_bk/Llutier.txt b/sourcecodes/data/old/example_sci_bk/Llutier.txt
new file mode 100644
index 00000000..da7084fb
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Llutier.txt
@@ -0,0 +1 @@
+3,Tier1,1,Genotype,Tier2,3,Gene1,Gene2,Gene3,Tier3,1,Phenotype,
\ No newline at end of file
diff --git a/sourcecodes/data/old/example_sci_bk/Llutype.txt b/sourcecodes/data/old/example_sci_bk/Llutype.txt
new file mode 100644
index 00000000..9ea66ce4
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Llutype.txt
@@ -0,0 +1,2 @@
+Genotype	Gene3	Gene2	Phenotype	Gene1
+2	1	1	1	1	
diff --git a/sourcecodes/data/old/example_sci_bk/Lluvar.txt b/sourcecodes/data/old/example_sci_bk/Lluvar.txt
new file mode 100644
index 00000000..56a6051c
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Lluvar.txt
@@ -0,0 +1 @@
+1
\ No newline at end of file
diff --git a/sourcecodes/data/old/example_sci_bk/Lluvardata.txt b/sourcecodes/data/old/example_sci_bk/Lluvardata.txt
new file mode 100644
index 00000000..56a6051c
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Lluvardata.txt
@@ -0,0 +1 @@
+1
\ No newline at end of file
diff --git a/sourcecodes/data/old/example_sci_bk/Lluvarname.txt b/sourcecodes/data/old/example_sci_bk/Lluvarname.txt
new file mode 100644
index 00000000..3fe283bd
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Lluvarname.txt
@@ -0,0 +1 @@
+Genotype
\ No newline at end of file
diff --git a/sourcecodes/data/old/example_sci_bk/Lluwhite.txt b/sourcecodes/data/old/example_sci_bk/Lluwhite.txt
new file mode 100644
index 00000000..83e81b8b
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/Lluwhite.txt
@@ -0,0 +1 @@
+From	To
diff --git a/sourcecodes/data/old/example_sci_bk/old/Llurun_evidencemodified.sh b/sourcecodes/data/old/example_sci_bk/old/Llurun_evidencemodified.sh
new file mode 100644
index 00000000..ee0dde13
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/old/Llurun_evidencemodified.sh
@@ -0,0 +1,38 @@
+#!/bin/sh
+# script for execution of deployed applications
+#
+# Sets up the MCR environment for the current $ARCH and executes 
+# the specified command.
+#
+exe_name=$0
+exe_dir=`dirname "$0"`
+echo "------------------------------------------"
+if [ "x$1" = "x" ]; then
+  echo Usage:
+  echo    $0 \<deployedMCRroot\> args
+else
+  echo Setting up environment variables
+  MCRROOT="$1"
+  echo ---
+  LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
+  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
+  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
+	MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ;
+	LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; 
+	LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
+	LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
+	LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;  
+  XAPPLRESDIR=${MCRROOT}/X11/app-defaults ;
+  export LD_LIBRARY_PATH;
+  export XAPPLRESDIR;
+  echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
+  shift 1
+  args=
+  while [ $# -gt 0 ]; do
+      token=`echo "$1" | sed 's/ /\\\\ /g'`   # Add blackslash before each blank
+      args="${args} ${token}" 
+      shift
+  done
+  "${exe_dir}"/evidencemodified Llu
+fi
+exit
diff --git a/sourcecodes/data/old/example_sci_bk/old/Llurun_initialstructure.sh b/sourcecodes/data/old/example_sci_bk/old/Llurun_initialstructure.sh
new file mode 100644
index 00000000..adde14dd
--- /dev/null
+++ b/sourcecodes/data/old/example_sci_bk/old/Llurun_initialstructure.sh
@@ -0,0 +1,38 @@
+#!/bin/sh
+# script for execution of deployed applications
+#
+# Sets up the MCR environment for the current $ARCH and executes 
+# the specified command.
+#
+exe_name=$0
+exe_dir=`dirname "$0"`
+echo "------------------------------------------"
+if [ "x$1" = "x" ]; then
+  echo Usage:
+  echo    $0 \<deployedMCRroot\> args
+else
+  echo Setting up environment variables
+  MCRROOT="$1"
+  echo ---
+  LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
+  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
+  LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
+	MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ;
+	LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; 
+	LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ;
+	LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ;
+	LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ;  
+  XAPPLRESDIR=${MCRROOT}/X11/app-defaults ;
+  export LD_LIBRARY_PATH;
+  export XAPPLRESDIR;
+  echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
+  shift 1
+  args=
+  while [ $# -gt 0 ]; do
+      token=`echo "$1" | sed 's/ /\\\\ /g'`   # Add blackslash before each blank
+      args="${args} ${token}" 
+      shift
+  done
+  "${exe_dir}"/initialstructure Llu
+fi
+exit