Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / muscle / nwrec.cpp

diff --git a/website/archive/binaries/mac/src/muscle/nwrec.cpp b/website/archive/binaries/mac/src/muscle/nwrec.cpp
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-/***\r
-Needleman-Wunch recursions\r
-\r
-Notation: i,j are prefix lengths so are in\r
-ranges i = [0,|A|] and j = [0,|B|].\r
-\r
-Profile positions are in ranges [0,|A|-1]\r
-and [0,|B|-1] so prefix length i corresponds\r
-to position (i-1) in the profile, and similarly\r
-for j.\r
-\r
-Terminal gap scoring\r
---------------------\r
-Terminal gaps are scored as with open [close]\r
-penalties only at the left [right] terminal,\r
-as follows:\r
-\r
-      0  i\r
-         |  |\r
-       A XXXXX...\r
-       B ---XX...\r
-\r
-          i |A|-1\r
-          |  |\r
-       A ...XXXXX\r
-       B ...XX---\r
-\r
-In these examples, open / close penalty at position\r
-i is  included, but close / open penalty at |A|-1 /\r
-0 is not included.\r
-\r
-This is implemented by setting the open [close] \r
-penalty to zero in the first [last] position of\r
-each profile.\r
-\r
-Consider adding a column to a sub-alignment. After the\r
-column is added, there are i letters from A and j letters\r
-from B.\r
-\r
-The column starts a left-terminal gap if:\r
-       Delete with i=1, j=0 or\r
-       Insert with i=0, j=1.\r
-\r
-The column ends a left-terminal gap if:\r
-       Match following Delete with j=1, or\r
-       Match following Insert with i=1.\r
-\r
-The column starts a right-terminal gap if:\r
-       Delete following a Match and i=|A|, or\r
-       Insert following a Match and j=|B|.\r
-\r
-The column ends a right-terminal gap if:\r
-       Match with i=|A|, j=|B| following Delete or Insert.\r
-       \r
-RECURSION RELATIONS\r
-===================\r
-\r
-         i-1\r
-          |\r
-DD     A ..X X\r
-       B ..- -\r
-\r
-MD     A ..X X\r
-       B ..X -\r
-\r
-D(i,j) = max\r
-                       D(i-1,j) + e\r
-                       M(i-1,j) + goA(i-1)\r
-Valid for:\r
-       i = [1,|A|-1]\r
-       j = [1,|B|]\r
-\r
-I(i,j) By symmetry with D(i,j).\r
-\r
-       i-2\r
-        | i-1\r
-               | |\r
-MM     A ..X X\r
-       B ..X X\r
-\r
-DM     A ..X X\r
-       B ..- X\r
-\r
-IM  A ..- X\r
-       B ..X X\r
-           | |\r
-               | j-1\r
-          j-2\r
-\r
-M(i,j) = L(i-1,j-1) + max\r
-                       M(i-1,j-1)\r
-                       D(i-1,j-1) + gcA(i-2)\r
-                       I(i-1,j-1) + gcB(j-2)\r
-Valid for:\r
-       i = [2,|A|]\r
-       j = [2,|B|]\r
-\r
-Equivalently:\r
-\r
-M(i+1,j+1) = L(i,j) + max\r
-                       M(i,j)\r
-                       D(i,j) + gcA(i-1)\r
-                       I(i,j) + gcB(j-1)\r
-\r
-Valid for:\r
-       i = [1,|A|-1]\r
-       j = [1,|B|-1]\r
-\r
-Boundary conditions\r
-===================\r
-\r
-A XXXX\r
-B ----\r
-       D(0,0) = -infinity\r
-\r
-       D(i,0) = ie\r
-               i = [1,|A|]\r
-\r
-       D(0,j) = -infinity\r
-               j = [0,|B|]\r
-\r
-I(0,0), I(0,j) and I(i,0) by symmetry with D.\r
-\r
-       M(0,0) = 0\r
-       M(i,0) = -infinity, i > 0\r
-       M(0,j) = -infinity, j > 0\r
-\r
-A X\r
-B -\r
-       D(1,0) = e\r
-       D(1,j) = -infinity, j = [1,|B|]\r
-               (assuming no I-D allowed).\r
-\r
-       D(0,1) = -infinity\r
-       D(1,1) = -infinity\r
-       D(i,1) = max.\r
-***/\r