Index: /brary/doc/images/xfig/RVs.fig.bak
===================================================================
--- /library/doc/images/xfig/RVs.fig.bak (revision 261)
+++  (revision )
@@ -1,67 +1,0 @@
-#FIG 3.2  Produced by xfig version 3.2.5
-Landscape
-Center
-Metric
-A4      
-100.00
-Single
--2
-1200 2
-6 2430 2790 3510 3060
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 3150 2790 3150 3060
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 2430 2790 3510 2790 3510 3060 2430 3060 2430 2790
-4 1 0 50 -1 0 10 0.0000 6 105 75 3375 2970 2\001
-4 1 0 50 -1 0 12 0.0000 6 135 240 2790 2970 "a"\001
--6
-6 2430 3060 3510 3330
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 3150 3060 3150 3330
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 2430 3060 3510 3060 3510 3330 2430 3330 2430 3060
-4 1 0 50 -1 0 10 0.0000 6 105 75 3375 3240 3\001
-4 1 0 50 -1 0 12 0.0000 6 135 255 2790 3240 "b"\001
--6
-6 2430 3330 3510 3600
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 3150 3330 3150 3600
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 2430 3330 3510 3330 3510 3600 2430 3600 2430 3330
-4 1 0 50 -1 0 10 0.0000 6 105 75 3375 3510 1\001
-4 1 0 50 -1 0 12 0.0000 6 135 240 2790 3510 "c"\001
--6
-6 4590 3780 7110 4365
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 4590 4095 7110 4095 7110 4365 4590 4365 4590 4095
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 4950 4095 4950 4365
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5310 4095 5310 4365
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5670 4095 5670 4365
-4 1 0 50 -1 0 12 0.0000 6 165 1050 5760 3915 RV_NAMES\001
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 3
-	1 1 1.00 60.00 120.00
-	 3510 3465 4770 3465 4770 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
-	1 1 1.00 60.00 120.00
-	 4770 3465 4770 4095
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 5
-	1 1 1.00 60.00 120.00
-	 3510 2925 4140 2925 4140 3330 5130 3330 5130 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
-	1 1 1.00 60.00 120.00
-	 5130 3330 5130 4095
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 4590 2745 7110 2745 7110 3015 4590 3015 4590 2745
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 4950 2745 4950 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5310 2745 5310 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5670 2745 5670 3015
-4 1 0 50 -1 0 12 0.0000 6 180 1650 2970 2655 std::map<string,int>\001
-4 1 0 50 -1 0 12 0.0000 6 165 885 5760 2565 RV_SIZES\001
-4 1 0 50 -1 0 12 0.0000 6 165 795 2970 2430 RV_MAP\001
Index: /brary/doc/images/xfig/datalinks.fig.bak
===================================================================
--- /library/doc/images/xfig/datalinks.fig.bak (revision 261)
+++  (revision )
@@ -1,136 +1,0 @@
-#FIG 3.2  Produced by xfig version 3.2.5
-Landscape
-Center
-Metric
-A4      
-100.00
-Single
--2
-1200 2
-6 4590 2430 6390 4365
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 4950 2745 4950 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5310 2745 5310 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5670 2745 5670 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
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-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5670 3825 5670 4095
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 4950 3825 6030 3825 6030 4095 4950 4095 4950 3825
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 6030 2745 6030 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 6390 2745 6390 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 4770 3015 5130 3825
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 5490 3015 5490 3825
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
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-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
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-4 1 0 50 -1 0 12 0.0000 6 165 930 5490 4320 Down_data\001
--6
-6 6930 2430 9270 4320
-6 6930 3825 8010 4320
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-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
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-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 6930 3825 8010 3825 8010 4095 6930 4095 6930 3825
-4 1 0 50 -1 0 12 0.0000 6 165 930 7470 4275 Down_data\001
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 7920 2745 7920 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
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-	1 1 1.00 60.00 120.00
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-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
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-	1 1 1.00 60.00 120.00
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-	 8730 3825 8730 4095
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-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 7740 3015 8550 3825
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
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-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 7560 2745 7560 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 8460 3015 8905 3826
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
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-4 1 0 50 -1 0 12 0.0000 6 180 690 8145 2565 Up_data\001
-4 1 0 50 -1 0 12 0.0000 6 165 1035 8730 4275 Down2_data\001
--6
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-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
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-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 6210 5940 6210 6210
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 5490 5940 6570 5940 6570 6210 5490 6210 5490 5940
-4 1 0 50 -1 0 12 0.0000 6 165 930 6030 6390 Down_data\001
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 7290 5940 7290 6210
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 6930 5940 7650 5940 7650 6210 6930 6210 6930 5940
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 7290 5130 7465 5941
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 7650 5130 6390 5940
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 6480 4860 6480 5130
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 5940 5130 5670 5940
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 6660 5130 6030 5940
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 6300 5130 7110 5940
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 6120 4860 6120 5130
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 5760 4860 6840 4860 6840 5130 5760 5130 5760 4860
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 7470 4860 7470 5130
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 7110 4860 7830 4860 7830 5130 7110 5130 7110 4860
-4 1 0 50 -1 0 12 0.0000 6 165 1035 7290 6390 Down2_data\001
-4 1 0 50 -1 0 12 0.0000 6 180 795 7470 4770 Up2_data\001
-4 1 0 50 -1 0 12 0.0000 6 180 690 6300 4770 Up_data\001
Index: /brary/doc/images/xfig/fig2png
===================================================================
--- /library/doc/images/xfig/fig2png (revision 261)
+++  (revision )
@@ -1,8 +1,0 @@
-#!/bin/sh
-
-export NAME=`basename $1 .fig`
-echo $NAME
-
-# produce  .pdftex_t, .pdf
-fig2dev -L png $NAME.fig > ../$NAME.png
-
Index: /brary/doc/images/xfig/RVs.fig
===================================================================
--- /library/doc/images/xfig/RVs.fig (revision 261)
+++  (revision )
@@ -1,64 +1,0 @@
-#FIG 3.2  Produced by xfig version 3.2.5
-Landscape
-Center
-Metric
-A4      
-100.00
-Single
--2
-1200 2
-6 4590 3780 7110 4365
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 4590 4095 7110 4095 7110 4365 4590 4365 4590 4095
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 4950 4095 4950 4365
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5310 4095 5310 4365
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5670 4095 5670 4365
-4 1 0 50 -1 0 12 0.0000 6 165 1050 5760 3915 RV_NAMES\001
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 3
-	1 1 1.00 60.00 120.00
-	 3510 3465 4770 3465 4770 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
-	1 1 1.00 60.00 120.00
-	 4770 3465 4770 4095
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-	1 1 1.00 60.00 120.00
-	 3510 2925 4140 2925 4140 3330 5130 3330 5130 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
-	1 1 1.00 60.00 120.00
-	 5130 3330 5130 4095
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 4590 2745 7110 2745 7110 3015 4590 3015 4590 2745
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 4950 2745 4950 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5310 2745 5310 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5670 2745 5670 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 3150 2790 3150 3060
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 2430 2790 3510 2790 3510 3060 2430 3060 2430 2790
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 3150 3060 3150 3330
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 2430 3060 3510 3060 3510 3330 2430 3330 2430 3060
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 3150 3330 3150 3600
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 2430 3330 3510 3330 3510 3600 2430 3600 2430 3330
-4 1 0 50 -1 0 12 0.0000 6 180 1650 2970 2655 std::map<string,int>\001
-4 1 0 50 -1 0 12 0.0000 6 165 885 5760 2565 RV_SIZES\001
-4 1 0 50 -1 0 12 0.0000 6 165 795 2970 2430 RV_MAP\001
-4 1 0 50 -1 0 10 0.0000 6 105 75 3375 2970 2\001
-4 1 0 50 -1 0 12 0.0000 6 135 240 2790 2970 "a"\001
-4 1 0 50 -1 0 10 0.0000 6 105 75 3375 3240 3\001
-4 1 0 50 -1 0 12 0.0000 6 135 255 2790 3240 "b"\001
-4 1 0 50 -1 0 10 0.0000 6 105 75 3375 3510 1\001
-4 1 0 50 -1 0 12 0.0000 6 135 240 2790 3510 "c"\001
-4 1 0 50 -1 0 12 0.0000 6 135 240 4770 4275 "c"\001
-4 1 0 50 -1 0 12 0.0000 6 135 240 5130 4275 "a"\001
-4 1 0 50 -1 0 12 0.0000 6 135 255 5490 4275 "b"\001
Index: /brary/doc/images/xfig/datalinks.fig
===================================================================
--- /library/doc/images/xfig/datalinks.fig (revision 261)
+++  (revision )
@@ -1,132 +1,0 @@
-#FIG 3.2  Produced by xfig version 3.2.5
-Landscape
-Center
-Metric
-A4      
-100.00
-Single
--2
-1200 2
-6 5490 5940 6570 6435
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5850 5940 5850 6210
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 6210 5940 6210 6210
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 5490 5940 6570 5940 6570 6210 5490 6210 5490 5940
-4 1 0 50 -1 0 12 0.0000 6 165 930 6030 6390 Down_data\001
--6
-6 6930 3825 8010 4320
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 7290 3825 7290 4095
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 7650 3825 7650 4095
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 6930 3825 8010 3825 8010 4095 6930 4095 6930 3825
-4 1 0 50 -1 0 12 0.0000 6 165 930 7470 4275 Down_data\001
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 7290 5940 7290 6210
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 6930 5940 7650 5940 7650 6210 6930 6210 6930 5940
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 7290 5130 7465 5941
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 7650 5130 6390 5940
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 6480 4860 6480 5130
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 5940 5130 5670 5940
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 6660 5130 6030 5940
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 6300 5130 7110 5940
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 6120 4860 6120 5130
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 5760 4860 6840 4860 6840 5130 5760 5130 5760 4860
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 7470 4860 7470 5130
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 7110 4860 7830 4860 7830 5130 7110 5130 7110 4860
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 7920 2745 7920 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 8280 2745 8280 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 8640 2745 8640 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 7380 3015 7110 3825
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
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-	 8100 3015 7470 3825
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-	 8370 3825 9090 3825 9090 4095 8370 4095 8370 3825
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 7740 3015 8550 3825
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 7200 2745 9000 2745 9000 3015 7200 3015 7200 2745
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 7560 2745 7560 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 8460 3015 8905 3826
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 8820 3015 7830 3825
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 4950 2745 4950 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5310 2745 5310 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5670 2745 5670 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5310 3825 5310 4095
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 5670 3825 5670 4095
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 4950 3825 6030 3825 6030 4095 4950 4095 4950 3825
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 6030 2745 6030 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-	 6390 2745 6390 3015
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 4770 3015 5130 3825
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 5490 3015 5490 3825
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
-	1 1 1.00 60.00 120.00
-	1 1 1.00 60.00 120.00
-	 6255 3015 5850 3825
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
-	 4590 2745 6390 2745 6390 3015 4590 3015 4590 2745
-4 1 0 50 -1 0 12 0.0000 6 165 1035 7290 6390 Down2_data\001
-4 1 0 50 -1 0 12 0.0000 6 180 795 7470 4770 Up2_data\001
-4 1 0 50 -1 0 12 0.0000 6 180 690 6300 4770 Up_data\001
-4 1 0 50 -1 0 12 0.0000 6 165 1035 8730 4275 Down2_data\001
-4 1 0 50 -1 0 12 0.0000 6 165 930 5490 4320 Down_data\001
-4 1 0 50 -1 0 12 0.0000 6 180 690 5490 2655 Up_data\001
-4 1 0 50 -1 0 12 0.0000 6 180 690 8145 2655 Up_data\001
Index: /applications/bdmtoolbox/doc/from_bdm/process_class.sh
===================================================================
--- /applications/bdmtoolbox/doc/from_bdm/process_class.sh (revision 1052)
+++ /applications/bdmtoolbox/doc/from_bdm/process_class.sh (revision 1054)
@@ -23,3 +23,5 @@
 
 cat tmp__classes | xargs ./filter_annotated.pl
-cp ../html/bdm_doc/annotated.html ../html/bdm_doc/annotated_$CLASS.html
+
+CLS_DEF=`echo $CLASS | sed "s/::/_/g"`
+cp ../html/bdm_doc/annotated.html ../html/bdm_doc/annotated_$CLS_DEF.html
Index: /applications/bdmtoolbox/doc/from_bdm/make_all.sh
===================================================================
--- /applications/bdmtoolbox/doc/from_bdm/make_all.sh (revision 1053)
+++ /applications/bdmtoolbox/doc/from_bdm/make_all.sh (revision 1054)
@@ -6,4 +6,5 @@
 ./process_class.sh bdm::DS
 ./process_class.sh bdm::logger
+./process_class.sh bdm::Controller
 
 cp -u ../../../../library/doc/html/*.png ../html/bdm_doc
Index: /applications/bdmtoolbox/doc/local/000scenarios.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/000scenarios.dox (revision 1054)
+++ /applications/bdmtoolbox/doc/local/000scenarios.dox (revision 1054)
@@ -0,0 +1,48 @@
+/*!
+\page bdt_scenarios Use Case #1: Basic Scenarios of BDMToolbox
+
+A typical scenario may look like:
+\dot
+digraph estimation{
+	node [shape=box];
+	{rank="same"; "Data Source"; "Bayesian Model"}
+	"Data Source" -> "Bayesian Model" [label="data"];
+	"Bayesian Model" -> "Result Logger" [label="estimation\n result"];
+	"Data Source" -> "Result Logger" [label="Simulated\n data"];
+}
+\enddot
+Where active objects are:
+ -# Data Sources (bdm::DS), providing access to various form of recursive data
+ -# Bayesian estimators (bdm::BM), providing various exact and approximate algorithms for Bayesian inference
+ -# Controllers (bdm::Controller), generating control strategies, both feedback, or feedforward
+ -# Loggers (bdm::logger), for storing results of experiments
+
+These objects operate on data vectors, functions and probability densities:
+ -# random variable (bdm::RV) is a name of a variable, used as named connectors in the scenarios, 
+ -# probability density functions, (bdm::pdf), both conditional and unconditional,
+ -# functions, (bdm::fnc), of vector arguments,
+
+These classes act as "LEGO-like" bricks which can be composed a wide range of arrangements.
+
+Predefined scenarios implemented in mex are:
+ - Simulation, see \ref simulator.cpp
+ - Estimation, see \ref estimator.cpp
+ - Controll Loop, see \ref controlloop.cpp
+ - Multiple-Participant Decision-Making, see \ref arena.cpp
+
+Lists of available objects are:
+ - List of <a href="bdm_doc/annotated_bdm_DS.html" > Data Sources </a>
+ - List of <a href="bdm_doc/annotated_bdm_pdf.html" > Conditional pdfs</a>
+ - List of <a href="bdm_doc/annotated_bdm_epdf.html" > Non-conditional pdfs </a>
+ - List of <a href="bdm_doc/annotated_bdm_logger.html" > Loggers </a>
+ - List of <a href="bdm_doc/annotated_bdm_DS.html" > Bayesian Models</a>
+ - List of <a href="bdm_doc/annotated_bdm_Controllers.html" > Controllers</a>
+
+For details of their use, see tutorials:
+ - \ref userguide_pdf
+ - \ref userguide_sim
+ - \ref userguide_estim
+ - \ref userguide_ctrl
+ 
+
+ */
Index: /applications/bdmtoolbox/doc/local/01userguide_pdf.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/01userguide_pdf.dox (revision 1044)
+++ /applications/bdmtoolbox/doc/local/01userguide_pdf.dox (revision 1054)
@@ -41,5 +41,5 @@
 \endcode
 
-Other distributions are created analogously, see \ref bdm_doc/annotated_epdf.html
+Other distributions are created analogously, see <a href="annotated_bdm_epdf.html"> list </a>.
 
 \section ug_pdf_marg Marginalization and conditioning
@@ -104,5 +104,5 @@
 Compulsory fields \c g.dim and \c g.dimc are used to check correct dimension of inputs and outputs of the function. 
 
-List of functions is in \ref bdm_doc/annotated_fnc
+List of <a href="annotated_bdm_epdf.html"> functions </a>.
 
 \section ug_pdf_mex Using Matlab classes of pdfs
@@ -117,6 +117,6 @@
 See \ref mex_bdm, and files: mex/mex_classes/mexEpdf.m
 
-If you wish to write your own Matlab classes see \ref ug_dev_mat.
+If you wish to write your own Matlab classes see \ref devguide_mat.
 
-For list of all available pdf objects, see \ref annotated_epdf.html , \ref annotated_pdf.html and \ref annotated.html
+For list of all available pdf objects, see <a href="annotated_bdm_epdf.html"> BDM epdfs </a>, <a href="annotated_bdm_pdf.html"> BDM pdfs </a> and <a href="annotated.html"> Matlab classes </a>.
 */
Index: /applications/bdmtoolbox/doc/local/02userguide_sim.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/02userguide_sim.dox (revision 1044)
+++ /applications/bdmtoolbox/doc/local/02userguide_sim.dox (revision 1054)
@@ -2,5 +2,5 @@
 \page userguide_sim BDM Use - System, Data, Simulation
 
-This section serves as introduction to the scenario of data simulation. Since it is the simplest of all scenarios defined in \ref userguide0 it also serves as introduction to configuration of an experiment (see \ref ui) and basic decision making objects (bdm::RV and bdm::DS).
+This section serves as introduction to the scenario of data simulation. Since it is the simplest of all scenarios it also serves as introduction to configuration of an experiment (see \ref ui) and basic decision making objects (bdm::RV and bdm::DS).
 
 All experiments are demonstrated on mex file \c simulator, which is also available as a standalone application.
@@ -74,5 +74,5 @@
 
 No further specification, e.g. if the data are pre-recorded or computed on-the-fly, are given.
-For a list of available DataSources, see ...
+For a list of available DataSources, see <a href="annotated_bdm_DS.html"> list </a>.
 
 
@@ -131,4 +131,6 @@
 A standard Data source has two levels, \c logdt and \c logut which means "log all outputs, dt" and "log all inputs, ut".
 Readers familiar with Simulink environment may look at the RV as being unique identifiers of inputs and outputs of simulation blocks. The inputs are connected automatically with the outputs with matching RV. This view is however, very incomplete, RV have more roles than this.
+
+List is available <a href="annotated_bdm_logger.html"> loggers </a>.
 
 \section ug_pdfds How to create a simulator from pdfs 
@@ -250,4 +252,4 @@
 \endcode
 
-For list of all DataSources and loggers, see \ref app_base
+List of all <a href="annotated_bdm_DS.html"> DataSources </a> and <a href="annotated_bdm_logger.html">loggers </a>.
 */
Index: /applications/bdmtoolbox/doc/local/002mex_classes.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/002mex_classes.dox (revision 1054)
+++ /applications/bdmtoolbox/doc/local/002mex_classes.dox (revision 1054)
@@ -0,0 +1,39 @@
+/*!
+\page mex_bdm  Use Case #3: combining Matlab classes and BDM classes
+
+The classes written in Matlab can be combined with standard BDM classes via corresponding C++ classes with equal names, i.e. mexBM.m is accepted by C++ class mexBM
+
+The class bdm::mexEpdf has the following Matlab structure:
+\code
+class = 'mexEpdf';
+object = any_mexEpdf_object;
+\endcode
+
+This clas acts as an interface between BDM objects of type bdm::epdf and Matlab objects of type mexEpdf.
+
+Example:
+\code
+clear all
+
+f.class = 'mexEpdf';
+f.object = mexLaplace;
+f.object.mu =12;
+f.object.b = 1;
+f.object.rv = RV('b',1);
+
+
+DS.class='EpdfDS';
+DS.epdf =f; %U
+
+experiment.ndat=10;
+
+M=simulator(DS,experiment);
+
+M.DS_dt_b
+\endcode
+
+Here, Matlab class mexLaplace is created and plugged in as attribute \c object of bdm class 'mexEpdf'.
+Class bdm::EpdfDS accepts this kind of object and perfroms its task, i.e. it generates samples from the density.
+
+
+*/
Index: /applications/bdmtoolbox/doc/local/20devguide_matlab.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/20devguide_matlab.dox (revision 1044)
+++ /applications/bdmtoolbox/doc/local/20devguide_matlab.dox (revision 1054)
@@ -19,5 +19,5 @@
 See relevant documentation in Matlab.
 
-For list of existing mex* classes see \ref annotated.html
+For list of existing mex* classes see <a href="annotated.html"> list </a>.
 
 \section dev_mat_pdf Creating your own probability density
Index: /applications/bdmtoolbox/doc/local/03userguide_estim.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/03userguide_estim.dox (revision 1044)
+++ /applications/bdmtoolbox/doc/local/03userguide_estim.dox (revision 1054)
@@ -43,4 +43,6 @@
 Implementation of these operations is heavily dependent on the specific class of prior pdf, or its approximations. We can identify only a few principal approaches to this problem. For example, analytical estimation which is possible within sufficient the Exponential Family, or estimation when both prior and posterior are approximated by empirical densities. 
 These approaches are first level of descendants of class \c BM, classes bdm::BMEF and bdm::PF, respectively.
+
+List of all available <a href="annotated_bdm_BM.html"> Bayesian Models </a>.
 
 \section ug2_arx_basic Estimation of ARX models
@@ -185,4 +187,5 @@
 In order to create a new extension of an estimator, copy file with class mexLaplaceBM.m and redefine the methods therein. If needed create new classes for pdfs by inheriting from mexEpdf, it the same way as in the mexLaplace.m example class.
 
-For list of all estimators, see \ref app_base.
+For list of all Matlab estimators, see <a href="annotated.html"> list </a>.
+
 */
Index: /applications/bdmtoolbox/doc/local/001wrappers.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/001wrappers.dox (revision 1054)
+++ /applications/bdmtoolbox/doc/local/001wrappers.dox (revision 1054)
@@ -0,0 +1,130 @@
+/*!
+\page bdt_wrappers Use Case #2: Matlab wrappers for BDM functions
+
+A wrapper is a mex file that does the following:
+ -# reads its arguments from Matlab structures and translates them into C++ structures
+ -# calls the corresponding function in C++,
+ -# converts the results into Matlab structures and passes them to the output
+ 
+The use of these functions is inefficient, however, it is very usefull for:
+ - operations on parts of the experiment configurations for scenarios, see ...
+ - insight into the results, e.g. mean values of non-standard densities 
+ - algorithms written in Matlab using these functions can be trivially re-written into C++
+ 
+General notation of wrappers is: <b> \<class\>_\<function\>.m </b>
+
+For example, function \b epdf_mean.m  represents function \b mean  of class \b epdf  and any it its offsprings.
+
+For full list of available wrappers see content of directory /bdmtoolbox/mex
+
+\section bdt_wr_conv Convenience wrappers
+
+A useful wrapper is called \b class_defaults which takes the input matlab structure tries to copy it into BDM class and returns a structure how BDM interprets it.
+
+This is useful for:
+ - checking if the fields are correctly named: fields of input structure that are not in the output are not understood
+ - seeing what defaults the BDM assigns to fields that are optional
+ 
+Example:
+\code
+>> CLS.class='RV'
+
+CLS = 
+
+    class: 'RV'
+
+>> CLSout=class_defaults(CLS)
+
+CLSout = 
+
+    class: 'RV'
+    names: {1x0 cell}
+    sizes: [1x0 double]
+    times: [1x0 double]
+\endcode
+
+The fields that are understood and accepted were filled.
+
+\code
+>> CLS.class='egauss'
+
+CLS = 
+
+    class: 'egauss'
+
+>> CLSout=class_defaults(CLS)
+??? Unexpected Standard exception from MEX file.
+What() is:UIException: the compulsory Setting named
+"mu" is missing. Check path "".
+\endcode
+
+In this case, empty class of type 'egauss' is not allowed, the fields named "mu" is compulsory. The next step would be to add define CLS.mu.
+
+
+\section bdt_wrp_epdf Wrappers for pdfs
+
+The follwing wrappers are provided:
+ - \b epdf_mean returning mean value of any epdf function in <a href="annotated_bdm_epdf.html"> list </a>.
+ \code 
+ >> G.class='egamma';
+ >> G.alpha = 3;
+ >> G.beta = 4;
+ >> epdf_mean(G) 
+
+ ans =
+
+    0.7500 
+ \endcode
+ - \b epdf_variance returning variance of any epdf function in <a href="annotated_bdm_epdf.html"> list </a>..
+ \code
+ >> epdf_variance(G)
+
+ ans =
+
+    0.1875
+ \endcode
+ - \b epdf_evallog_mat returns logarithm of the values in argument,
+ - \b epdf_sample_mat sample given number of independent samples for this density,
+ - \b epdf_marginal sample given number of independent samples for this density,
+ - \b epdf_condition sample given number of independent samples for this density,
+ - \b epdf_sample_mat sample given number of independent samples for this density,
+
+List of arguments of each function can be obtained by running the function with no argument:
+\code
+>> epdf_mean
+??? Error using ==> epdf_mean
+Usage:
+vec=pdf_mean(pdf_struct)
+  pdf_struct = struct('class','pdf_offspring',...);  %
+  description of pdf
+output:
+  vec mean value of given pdf.
+\endcode
+
+For up-to-date list of wrappers see files in <a href="files.html"> files.html</a>
+ 
+ \section bdt_wrp_off Wrappers of offsprings
+ 
+ When a new class defines its private function, its wrapper starts with the name of the class that defines it.
+ An example is function \b enorm_bhattacharyya.m  which id defined only for normal distributed densities (enorm\<sqmat\>)
+
+\section bdt_wrp_bm Wrappers for Bayesian Models (BMs)
+
+Wrappers for BM correspond to the main functions of BM, that is:
+ - \b bayes recursive update of posterior statistics by currently observed data and data in conditions, function \b bm_bayes
+ - \b bayesweighted recursive update of posterior statistics by currently observed data and data in conditions, when data are generated from this class only with probability w, function \b bm_bayesweighted
+ - \b epredictor returns unconditional predictor of the next data observation (if such density is available) \b bm_epredictor
+
+Example:
+\code
+>> CLS.class='multiBM'                % Estimator of multinomial density
+>> CLS.prior.beta = [1,2];            % Prior is Dirichlet with statistics beta
+
+>> CLSapost=bm_bayes(CLS, [0.5 0.5])  % update posterior, using data [0.5, 0.5]
+>> CLSapost.prior.beta
+
+ans =
+
+    1.5000    2.5000
+\endcode 
+ */
Index: /applications/bdmtoolbox/doc/local/04userguide_ctrl.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/04userguide_ctrl.dox (revision 1044)
+++ /applications/bdmtoolbox/doc/local/04userguide_ctrl.dox (revision 1054)
@@ -42,4 +42,5 @@
 variants and approximations of dynamic programming (or optimal control), see [].
 
+List of available <a href="annotated_bdm_Controller.html"> Controllers</a>.
 TODO...
 
Index: /plications/bdmtoolbox/doc/local/00scenarios.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/00scenarios.dox (revision 1044)
+++  (revision )
@@ -1,29 +1,0 @@
-/*!
-\page bdt_scenarios Basic Scenarios of BDMToolbox
-
-The basic elements of BDM are:
- -# probability density functions, (bdm::pdf), both conditional and unconditional 
- -# functions, (bdm::fnc), of vector arguments
- -# Bayesian estimators (bdm::BM), providing variaous exact and approximate algorithms for Bayesian inference
- -# Data Sources (bdm::DS), providing access to various form of recursive data
- -# Controllers (bdm::Controller), generating control strategies, both feedback, or feedforward
- -# Loggers (bdm::logger), for storing results of experiments
-
-The objects are designed to allow mutual combination of these. Distinction of what needs to be connected where is provided by class RV which stands for random variable.
-
-Predefined scenarios implemented in mex are:
-
- - Simulation, see \ref simulator.cpp
- - Estimation, see \ref estimator.cpp
- - Controll Loop, see \ref controlloop.cpp
- - Multiple-Participant Decision-Making, see \ref arena.cpp
-
-For details of their use, see tutorials:
- - \ref userguide_pdf
- - \ref userguide_sim
- - \ref userguide_estim
- - \ref userguide_ctrl
- 
- 
-
- */
Index: /plications/bdmtoolbox/doc/local/21mex_bdm.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/21mex_bdm.dox (revision 1044)
+++  (revision )
@@ -1,39 +1,0 @@
-/*!
-\page mex_bdm  BDMToolbox Development - combining Matlab classes and BDM classes
-
-The classes written in Matlab can be combined with standard BDM classes via corresponding C++ classes with equal names, i.e. mexBM.m is accepted by C++ class mexBM
-
-The class bdm::mexEpdf has the following Matlab structure:
-\code
-class = 'mexEpdf';
-object = any_mexEpdf_object;
-\endcode
-
-This clas acts as an interface between BDM objects of type bdm::epdf and Matlab objects of type mexEpdf.
-
-Example:
-\code
-clear all
-
-f.class = 'mexEpdf';
-f.object = mexLaplace;
-f.object.mu =12;
-f.object.b = 1;
-f.object.rv = RV('b',1);
-
-
-DS.class='EpdfDS';
-DS.epdf =f; %U
-
-experiment.ndat=10;
-
-M=simulator(DS,experiment);
-
-M.DS_dt_b
-\endcode
-
-Here, Matlab class mexLaplace is created and plugged in as attribute \c object of bdm class 'mexEpdf'.
-Class bdm::EpdfDS accepts this kind of object and perfroms its task, i.e. it generates samples from the density.
-
-
-*/
Index: /plications/bdmtoolbox/doc/local/10wrappers.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/10wrappers.dox (revision 1044)
+++  (revision )
@@ -1,131 +1,0 @@
-/*!
-\page bdt_wrappers Elementary functions operating on descriptive matlab structures
-
-A wrapper is a mex file that does the following:
- -# reads its arguments from Matlab structures and translates them into C++ structures
- -# calls the corresponding function in C++,
- -# converts the results into Matlab structures and passes them to the output
- 
-The use of these functions is inefficient, however, it is very usefull for:
- - operations on parts of the experiment configurations for scenarios, see example in \ref some_ref
- - insight into the results, e.g. mean values of non-standard densities 
- - algorithms written in Matlab using these functions can be trivially re-written into C++
- 
- 
-General notation of wrappers is: <b> \<class\>_\<function\>.m </b>
-
-For example, function \b epdf_mean.m  represents function \b mean  of class \b epdf  and any it its offsprings.
-
-For full list of available wrappers see content of directory /bdmtoolbox/mex
-
-\section bdt_wr_conv Convenience wrappers
-
-A useful wrapper is called \b class_defaults which takes the input matlab structure tries to copy it into BDM class and returns a structure how BDM interprets it.
-
-This is useful for:
- - checking if the fields are correctly named: fields of input structure that are not in the output are not understood
- - seeing what defaults the BDM assigns to fields that are optional
- 
-Example:
-\code
->> CLS.class='RV'
-
-CLS = 
-
-    class: 'RV'
-
->> CLSout=class_defaults(CLS)
-
-CLSout = 
-
-    class: 'RV'
-    names: {1x0 cell}
-    sizes: [1x0 double]
-    times: [1x0 double]
-\endcode
-
-The fields that are understood and accepted were filled.
-
-\code
->> CLS.class='egauss'
-
-CLS = 
-
-    class: 'egauss'
-
->> CLSout=class_defaults(CLS)
-??? Unexpected Standard exception from MEX file.
-What() is:UIException: the compulsory Setting named
-"mu" is missing. Check path "".
-\endcode
-
-In this case, empty class of type 'egauss' is not allowed, the fields named "mu" is compulsory. The next step would be to add define CLS.mu.
-
-
-\section bdt_wrp_epdf Wrappers for pdfs
-
-The follwing wrappers are provided:
- - \b epdf_mean returning mean value of any epdf function in \ref annotated_epdf.
- \code 
- >> G.class='egamma';
- >> G.alpha = 3;
- >> G.beta = 4;
- >> epdf_mean(G) 
-
- ans =
-
-    0.7500 
- \endcode
- - \b epdf_variance returning variance of any epdf function in \ref annotated_epdf.
- \code
- >> epdf_variance(G)
-
- ans =
-
-    0.1875
- \endcode
- - \b epdf_evallog_mat returns logarithm of the values in argument,
- - \b epdf_sample_mat sample given number of independent samples for this density,
- - \b epdf_marginal sample given number of independent samples for this density,
- - \b epdf_condition sample given number of independent samples for this density,
- - \b epdf_sample_mat sample given number of independent samples for this density,
-
-List of arguments of each function can be obtained by running the function with no argument:
-\code
->> epdf_mean
-??? Error using ==> epdf_mean
-Usage:
-vec=pdf_mean(pdf_struct)
-  pdf_struct = struct('class','pdf_offspring',...);  %
-  description of pdf
-output:
-  vec mean value of given pdf.
-\endcode
-
-For up-to-date list of wrappers see files in \ref files.html
- 
- \section bdt_wrp_off Wrappers of offsprings
- 
- When a new class defines its private function, its wrapper starts with the name of the class that defines it.
- An example is function \b enorm_bhattacharyya.m  which id defined only for normal distributed densities (enorm\<sqmat\>)
-
-\section bdt_wrp_bm Wrappers for Bayesian Models (BMs)
-
-Wrappers for BM correspond to the main functions of BM, that is:
- - \b bayes recursive update of posterior statistics by currently observed data and data in conditions, function \b bm_bayes
- - \b bayesweighted recursive update of posterior statistics by currently observed data and data in conditions, when data are generated from this class only with probability w, function \b bm_bayesweighted
- - \b epredictor returns unconditional predictor of the next data observation (if such density is available) \b bm_epredictor
-
-Example:
-\code
->> CLS.class='multiBM'                % Estimator of multinomial density
->> CLS.prior.beta = [1,2];            % Prior is Dirichlet with statistics beta
-
->> CLSapost=bm_bayes(CLS, [0.5 0.5])  % update posterior, using data [0.5, 0.5]
->> CLSapost.prior.beta
-
-ans =
-
-    1.5000    2.5000
-\endcode 
- */
Index: /applications/bdmtoolbox/doc/xfig/RVs.fig.bak
===================================================================
--- /applications/bdmtoolbox/doc/xfig/RVs.fig.bak (revision 1054)
+++ /applications/bdmtoolbox/doc/xfig/RVs.fig.bak (revision 1054)
@@ -0,0 +1,67 @@
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+4 1 0 50 -1 0 12 0.0000 6 180 1650 2970 2655 std::map<string,int>\001
+4 1 0 50 -1 0 12 0.0000 6 165 885 5760 2565 RV_SIZES\001
+4 1 0 50 -1 0 12 0.0000 6 165 795 2970 2430 RV_MAP\001
Index: /applications/bdmtoolbox/doc/xfig/datalinks.fig.bak
===================================================================
--- /applications/bdmtoolbox/doc/xfig/datalinks.fig.bak (revision 1054)
+++ /applications/bdmtoolbox/doc/xfig/datalinks.fig.bak (revision 1054)
@@ -0,0 +1,136 @@
+#FIG 3.2  Produced by xfig version 3.2.5
+Landscape
+Center
+Metric
+A4      
+100.00
+Single
+-2
+1200 2
+6 4590 2430 6390 4365
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 4950 2745 4950 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 5310 2745 5310 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 5670 2745 5670 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 5310 3825 5310 4095
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 5670 3825 5670 4095
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 4950 3825 6030 3825 6030 4095 4950 4095 4950 3825
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 6030 2745 6030 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 6390 2745 6390 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
+	 4770 3015 5130 3825
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
+	 5490 3015 5490 3825
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
+	 6255 3015 5850 3825
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 4590 2745 6390 2745 6390 3015 4590 3015 4590 2745
+4 1 0 50 -1 0 12 0.0000 6 180 690 5490 2565 Up_data\001
+4 1 0 50 -1 0 12 0.0000 6 165 930 5490 4320 Down_data\001
+-6
+6 6930 2430 9270 4320
+6 6930 3825 8010 4320
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 7290 3825 7290 4095
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 7650 3825 7650 4095
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 6930 3825 8010 3825 8010 4095 6930 4095 6930 3825
+4 1 0 50 -1 0 12 0.0000 6 165 930 7470 4275 Down_data\001
+-6
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 7920 2745 7920 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 8730 3825 8730 4095
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 8370 3825 9090 3825 9090 4095 8370 4095 8370 3825
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
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+	1 1 1.00 60.00 120.00
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+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 7560 2745 7560 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
+	 8460 3015 8905 3826
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
+	 8820 3015 7830 3825
+4 1 0 50 -1 0 12 0.0000 6 180 690 8145 2565 Up_data\001
+4 1 0 50 -1 0 12 0.0000 6 165 1035 8730 4275 Down2_data\001
+-6
+6 5490 5940 6570 6435
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 6210 5940 6210 6210
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 5490 5940 6570 5940 6570 6210 5490 6210 5490 5940
+4 1 0 50 -1 0 12 0.0000 6 165 930 6030 6390 Down_data\001
+-6
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 7290 5940 7290 6210
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 6930 5940 7650 5940 7650 6210 6930 6210 6930 5940
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
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+	1 1 1.00 60.00 120.00
+	 7290 5130 7465 5941
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
+	 7650 5130 6390 5940
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 6480 4860 6480 5130
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
+	 5940 5130 5670 5940
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
+	 6660 5130 6030 5940
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
+	 6300 5130 7110 5940
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 6120 4860 6120 5130
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 5760 4860 6840 4860 6840 5130 5760 5130 5760 4860
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 7470 4860 7470 5130
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 7110 4860 7830 4860 7830 5130 7110 5130 7110 4860
+4 1 0 50 -1 0 12 0.0000 6 165 1035 7290 6390 Down2_data\001
+4 1 0 50 -1 0 12 0.0000 6 180 795 7470 4770 Up2_data\001
+4 1 0 50 -1 0 12 0.0000 6 180 690 6300 4770 Up_data\001
Index: /applications/bdmtoolbox/doc/xfig/fig2png
===================================================================
--- /applications/bdmtoolbox/doc/xfig/fig2png (revision 1054)
+++ /applications/bdmtoolbox/doc/xfig/fig2png (revision 1054)
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+export NAME=`basename $1 .fig`
+echo $NAME
+
+# produce  .pdftex_t, .pdf
+fig2dev -L png $NAME.fig > ../$NAME.png
+
Index: /applications/bdmtoolbox/doc/xfig/RVs.fig
===================================================================
--- /applications/bdmtoolbox/doc/xfig/RVs.fig (revision 1054)
+++ /applications/bdmtoolbox/doc/xfig/RVs.fig (revision 1054)
@@ -0,0 +1,64 @@
+#FIG 3.2  Produced by xfig version 3.2.5
+Landscape
+Center
+Metric
+A4      
+100.00
+Single
+-2
+1200 2
+6 4590 3780 7110 4365
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 4590 4095 7110 4095 7110 4365 4590 4365 4590 4095
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 4950 4095 4950 4365
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 5310 4095 5310 4365
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 5670 4095 5670 4365
+4 1 0 50 -1 0 12 0.0000 6 165 1050 5760 3915 RV_NAMES\001
+-6
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 3
+	1 1 1.00 60.00 120.00
+	 3510 3465 4770 3465 4770 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
+	1 1 1.00 60.00 120.00
+	 4770 3465 4770 4095
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 5
+	1 1 1.00 60.00 120.00
+	 3510 2925 4140 2925 4140 3330 5130 3330 5130 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
+	1 1 1.00 60.00 120.00
+	 5130 3330 5130 4095
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 4590 2745 7110 2745 7110 3015 4590 3015 4590 2745
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 4950 2745 4950 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 5310 2745 5310 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 5670 2745 5670 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 3150 2790 3150 3060
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 2430 2790 3510 2790 3510 3060 2430 3060 2430 2790
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 3150 3060 3150 3330
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 2430 3060 3510 3060 3510 3330 2430 3330 2430 3060
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 3150 3330 3150 3600
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 2430 3330 3510 3330 3510 3600 2430 3600 2430 3330
+4 1 0 50 -1 0 12 0.0000 6 180 1650 2970 2655 std::map<string,int>\001
+4 1 0 50 -1 0 12 0.0000 6 165 885 5760 2565 RV_SIZES\001
+4 1 0 50 -1 0 12 0.0000 6 165 795 2970 2430 RV_MAP\001
+4 1 0 50 -1 0 10 0.0000 6 105 75 3375 2970 2\001
+4 1 0 50 -1 0 12 0.0000 6 135 240 2790 2970 "a"\001
+4 1 0 50 -1 0 10 0.0000 6 105 75 3375 3240 3\001
+4 1 0 50 -1 0 12 0.0000 6 135 255 2790 3240 "b"\001
+4 1 0 50 -1 0 10 0.0000 6 105 75 3375 3510 1\001
+4 1 0 50 -1 0 12 0.0000 6 135 240 2790 3510 "c"\001
+4 1 0 50 -1 0 12 0.0000 6 135 240 4770 4275 "c"\001
+4 1 0 50 -1 0 12 0.0000 6 135 240 5130 4275 "a"\001
+4 1 0 50 -1 0 12 0.0000 6 135 255 5490 4275 "b"\001
Index: /applications/bdmtoolbox/doc/xfig/datalinks.fig
===================================================================
--- /applications/bdmtoolbox/doc/xfig/datalinks.fig (revision 1054)
+++ /applications/bdmtoolbox/doc/xfig/datalinks.fig (revision 1054)
@@ -0,0 +1,132 @@
+#FIG 3.2  Produced by xfig version 3.2.5
+Landscape
+Center
+Metric
+A4      
+100.00
+Single
+-2
+1200 2
+6 5490 5940 6570 6435
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 5850 5940 5850 6210
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 6210 5940 6210 6210
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 5490 5940 6570 5940 6570 6210 5490 6210 5490 5940
+4 1 0 50 -1 0 12 0.0000 6 165 930 6030 6390 Down_data\001
+-6
+6 6930 3825 8010 4320
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 7290 3825 7290 4095
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 7650 3825 7650 4095
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 6930 3825 8010 3825 8010 4095 6930 4095 6930 3825
+4 1 0 50 -1 0 12 0.0000 6 165 930 7470 4275 Down_data\001
+-6
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 7290 5940 7290 6210
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 6930 5940 7650 5940 7650 6210 6930 6210 6930 5940
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
+	 7290 5130 7465 5941
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
+	 7650 5130 6390 5940
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 6480 4860 6480 5130
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
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+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 5760 4860 6840 4860 6840 5130 5760 5130 5760 4860
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
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+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
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+	1 1 1.00 60.00 120.00
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
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+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
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+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 7560 2745 7560 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
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+	1 1 1.00 60.00 120.00
+	 8460 3015 8905 3826
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
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+	 8820 3015 7830 3825
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 4950 2745 4950 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 5310 2745 5310 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 5670 2745 5670 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 5310 3825 5310 4095
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 5670 3825 5670 4095
+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
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+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 6030 2745 6030 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+	 6390 2745 6390 3015
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
+	 4770 3015 5130 3825
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
+	 5490 3015 5490 3825
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 1 2
+	1 1 1.00 60.00 120.00
+	1 1 1.00 60.00 120.00
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+2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
+	 4590 2745 6390 2745 6390 3015 4590 3015 4590 2745
+4 1 0 50 -1 0 12 0.0000 6 165 1035 7290 6390 Down2_data\001
+4 1 0 50 -1 0 12 0.0000 6 180 795 7470 4770 Up2_data\001
+4 1 0 50 -1 0 12 0.0000 6 180 690 6300 4770 Up_data\001
+4 1 0 50 -1 0 12 0.0000 6 165 1035 8730 4275 Down2_data\001
+4 1 0 50 -1 0 12 0.0000 6 165 930 5490 4320 Down_data\001
+4 1 0 50 -1 0 12 0.0000 6 180 690 5490 2655 Up_data\001
+4 1 0 50 -1 0 12 0.0000 6 180 690 8145 2655 Up_data\001
Index: /applications/bdmtoolbox/mex/mex_classes/mexBM.m
===================================================================
--- /applications/bdmtoolbox/mex/mex_classes/mexBM.m (revision 944)
+++ /applications/bdmtoolbox/mex/mex_classes/mexBM.m (revision 1054)
@@ -1,12 +1,21 @@
+%> @file mexEpdf.m
+%> @brief File mapping root class of BM from BDM
+% ======================================================================
+%> @brief Abstract class of Bayesian Model (estimator), bdm::BM
+%
+%> This class provides a bridge between bdm::BM and Matlab
+% ======================================================================
 classdef mexBM
     properties
-        % description of internal variables
+        %> description of internal variables of parameters
         rv=RV
+        %> description of internal variables of data in condition
         rvc=RV
+        %> description of internal variables of observed data
         rvy=RV
-        % log of evidence (marginal likelihood) potentially computed by the
+        %> log of evidence (marginal likelihood) potentially computed by the
         % bayes rule for one step
         log_evidence
-        % posterior density - offspring of mexEpdf!
+        %> posterior density - offspring of mexEpdf!
         apost_pdf
         %
@@ -14,7 +23,9 @@
 
     methods
+        %> check consistency of the object and fill defaults
         function p=validate(p)
             % checks if all paramateres match
         end
+        %> dimensionality of the class: dims = [size_of_posterior size_of_data size_of_condition]
         function dims=dimensions(p)
             %please fill
@@ -22,7 +33,9 @@
             dims = [0,0,0] %
         end
+        %> Performs Bayesian update of the internal posterior using data \a dt and condition \a cond.
         function obj=bayes(obj,dt,cond)
             % transform old estimate into new estimate
         end
+        %> Computes predictor of the observed data in the next step
         function p=epredictor(obj,cond)
             % return posterior density
@@ -39,7 +52,9 @@
             r=obj.rvy;
         end
+        %> Evidence of the last data, \f[f(y_t|y_0\ldots y_t-1, cond_0\ldots cond_t\f]
         function ev = logevidence(obj)
             ev = obj.log_evidence;
         end
+        %> Posterior pdf
         function post=posterior(obj);
             post = obj.apost_pdf;
Index: /applications/bdmtoolbox/mex/mex_classes/mexLaplace.m
===================================================================
--- /applications/bdmtoolbox/mex/mex_classes/mexLaplace.m (revision 944)
+++ /applications/bdmtoolbox/mex/mex_classes/mexLaplace.m (revision 1054)
@@ -1,2 +1,9 @@
+%> @file mexLaplace.m
+%> @brief Matrlab implemnetation of Laplace density
+% ======================================================================
+%> @brief Unconditional Laplace density
+%
+%> \f[ f(x|\mu,b) \propto \exp(-|x-\mu|/b)\f]
+% ======================================================================
 classdef mexLaplace < mexEpdf
     properties
Index: /applications/bdmtoolbox/mex/mex_classes/mexDirac.m
===================================================================
--- /applications/bdmtoolbox/mex/mex_classes/mexDirac.m (revision 983)
+++ /applications/bdmtoolbox/mex/mex_classes/mexDirac.m (revision 1054)
@@ -1,2 +1,9 @@
+%> @file mexDirec.m
+%> @brief Matlab implementation of Dirac density 
+% ======================================================================
+%> @brief Unconditional Dirac density
+%
+%> \f[ f(x| x_i) = \delta(x-x_i)\f]
+% ======================================================================
 classdef mexDirac < mexEpdf
     % Dirac delta probability distribution
Index: /applications/bdmtoolbox/build_doc.sh
===================================================================
--- /applications/bdmtoolbox/build_doc.sh (revision 1049)
+++ /applications/bdmtoolbox/build_doc.sh (revision 1054)
@@ -5,5 +5,5 @@
 this_dir=`pwd`
 cd doc/from_bdm
-./make_all
+./make_all.sh
 
 cd $this_dir
