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Delete unneeded directory
[jabaws.git] / website / archive / binaries / mac / src / muscle / aligngivenpathsw.cpp
diff --git a/website/archive/binaries/mac/src/muscle/aligngivenpathsw.cpp b/website/archive/binaries/mac/src/muscle/aligngivenpathsw.cpp
deleted file mode 100644 (file)
index d3e03c1..0000000
--- a/website/archive/binaries/mac/src/muscle/aligngivenpathsw.cpp
+++ /dev/null
@@ -1,237 +0,0 @@
-#include "muscle.h"\r
-#include "msa.h"\r
-#include "pwpath.h"\r
-#include "profile.h"\r
-\r
-#define        TRACE   0\r
-\r
-static void AppendDelete(const MSA &msaA, unsigned &uColIndexA,\r
-  unsigned uSeqCountA, unsigned uSeqCountB, MSA &msaCombined,\r
-  unsigned &uColIndexCombined)\r
-       {\r
-#if    TRACE\r
-       Log("AppendDelete ColIxA=%u ColIxCmb=%u\n",\r
-         uColIndexA, uColIndexCombined);\r
-#endif\r
-       for (unsigned uSeqIndexA = 0; uSeqIndexA < uSeqCountA; ++uSeqIndexA)\r
-               {\r
-               char c = msaA.GetChar(uSeqIndexA, uColIndexA);\r
-               msaCombined.SetChar(uSeqIndexA, uColIndexCombined, c);\r
-               }\r
-\r
-       for (unsigned uSeqIndexB = 0; uSeqIndexB < uSeqCountB; ++uSeqIndexB)\r
-               msaCombined.SetChar(uSeqCountA + uSeqIndexB, uColIndexCombined, '-');\r
-\r
-       ++uColIndexCombined;\r
-       ++uColIndexA;\r
-       }\r
-\r
-static void AppendInsert(const MSA &msaB, unsigned &uColIndexB,\r
-  unsigned uSeqCountA, unsigned uSeqCountB, MSA &msaCombined,\r
-  unsigned &uColIndexCombined)\r
-       {\r
-#if    TRACE\r
-       Log("AppendInsert ColIxB=%u ColIxCmb=%u\n",\r
-         uColIndexB, uColIndexCombined);\r
-#endif\r
-       for (unsigned uSeqIndexA = 0; uSeqIndexA < uSeqCountA; ++uSeqIndexA)\r
-               msaCombined.SetChar(uSeqIndexA, uColIndexCombined, '-');\r
-\r
-       for (unsigned uSeqIndexB = 0; uSeqIndexB < uSeqCountB; ++uSeqIndexB)\r
-               {\r
-               char c = msaB.GetChar(uSeqIndexB, uColIndexB);\r
-               msaCombined.SetChar(uSeqCountA + uSeqIndexB, uColIndexCombined, c);\r
-               }\r
-\r
-       ++uColIndexCombined;\r
-       ++uColIndexB;\r
-       }\r
-\r
-static void AppendUnalignedTerminals(const MSA &msaA, unsigned &uColIndexA, unsigned uColCountA,\r
-  const MSA &msaB, unsigned &uColIndexB, unsigned uColCountB, unsigned uSeqCountA,\r
-  unsigned uSeqCountB, MSA &msaCombined, unsigned &uColIndexCombined)\r
-       {\r
-#if    TRACE\r
-       Log("AppendUnalignedTerminals ColIxA=%u ColIxB=%u ColIxCmb=%u\n",\r
-         uColIndexA, uColIndexB, uColIndexCombined);\r
-#endif\r
-       const unsigned uLengthA = msaA.GetColCount();\r
-       const unsigned uLengthB = msaB.GetColCount();\r
-\r
-       unsigned uNewColCount = uColCountA;\r
-       if (uColCountB > uNewColCount)\r
-               uNewColCount = uColCountB;\r
-\r
-       for (unsigned n = 0; n < uColCountA; ++n)\r
-               {\r
-               for (unsigned uSeqIndexA = 0; uSeqIndexA < uSeqCountA; ++uSeqIndexA)\r
-                       {\r
-                       char c = msaA.GetChar(uSeqIndexA, uColIndexA + n);\r
-                       c = UnalignChar(c);\r
-                       msaCombined.SetChar(uSeqIndexA, uColIndexCombined + n, c);\r
-                       }\r
-               }\r
-       for (unsigned n = uColCountA; n < uNewColCount; ++n)\r
-               {\r
-               for (unsigned uSeqIndexA = 0; uSeqIndexA < uSeqCountA; ++uSeqIndexA)\r
-                       msaCombined.SetChar(uSeqIndexA, uColIndexCombined + n, '.');\r
-               }\r
-\r
-       for (unsigned n = 0; n < uColCountB; ++n)\r
-               {\r
-               for (unsigned uSeqIndexB = 0; uSeqIndexB < uSeqCountB; ++uSeqIndexB)\r
-                       {\r
-                       char c = msaB.GetChar(uSeqIndexB, uColIndexB + n);\r
-                       c = UnalignChar(c);\r
-                       msaCombined.SetChar(uSeqCountA + uSeqIndexB, uColIndexCombined + n, c);\r
-                       }\r
-               }\r
-       for (unsigned n = uColCountB; n < uNewColCount; ++n)\r
-               {\r
-               for (unsigned uSeqIndexB = 0; uSeqIndexB < uSeqCountB; ++uSeqIndexB)\r
-                       msaCombined.SetChar(uSeqCountA + uSeqIndexB, uColIndexCombined + n, '.');\r
-               }\r
-\r
-       uColIndexCombined += uNewColCount;\r
-       uColIndexA += uColCountA;\r
-       uColIndexB += uColCountB;\r
-       }\r
-\r
-static void AppendMatch(const MSA &msaA, unsigned &uColIndexA, const MSA &msaB,\r
-  unsigned &uColIndexB, unsigned uSeqCountA, unsigned uSeqCountB,\r
-  MSA &msaCombined, unsigned &uColIndexCombined)\r
-       {\r
-#if    TRACE\r
-       Log("AppendMatch ColIxA=%u ColIxB=%u ColIxCmb=%u\n",\r
-         uColIndexA, uColIndexB, uColIndexCombined);\r
-#endif\r
-\r
-       for (unsigned uSeqIndexA = 0; uSeqIndexA < uSeqCountA; ++uSeqIndexA)\r
-               {\r
-               char c = msaA.GetChar(uSeqIndexA, uColIndexA);\r
-               msaCombined.SetChar(uSeqIndexA, uColIndexCombined, c);\r
-               }\r
-\r
-       for (unsigned uSeqIndexB = 0; uSeqIndexB < uSeqCountB; ++uSeqIndexB)\r
-               {\r
-               char c = msaB.GetChar(uSeqIndexB, uColIndexB);\r
-               msaCombined.SetChar(uSeqCountA + uSeqIndexB, uColIndexCombined, c);\r
-               }\r
-\r
-       ++uColIndexA;\r
-       ++uColIndexB;\r
-       ++uColIndexCombined;\r
-       }\r
-\r
-void AlignTwoMSAsGivenPathSW(const PWPath &Path, const MSA &msaA, const MSA &msaB,\r
-  MSA &msaCombined)\r
-       {\r
-       msaCombined.Clear();\r
-\r
-#if    TRACE\r
-       Log("AlignTwoMSAsGivenPathSW\n");\r
-       Log("Template A:\n");\r
-       msaA.LogMe();\r
-       Log("Template B:\n");\r
-       msaB.LogMe();\r
-#endif\r
-\r
-       const unsigned uColCountA = msaA.GetColCount();\r
-       const unsigned uColCountB = msaB.GetColCount();\r
-\r
-       const unsigned uSeqCountA = msaA.GetSeqCount();\r
-       const unsigned uSeqCountB = msaB.GetSeqCount();\r
-\r
-       msaCombined.SetSeqCount(uSeqCountA + uSeqCountB);\r
-\r
-// Copy sequence names into combined MSA\r
-       for (unsigned uSeqIndexA = 0; uSeqIndexA < uSeqCountA; ++uSeqIndexA)\r
-               {\r
-               msaCombined.SetSeqName(uSeqIndexA, msaA.GetSeqName(uSeqIndexA));\r
-               msaCombined.SetSeqId(uSeqIndexA, msaA.GetSeqId(uSeqIndexA));\r
-               }\r
-\r
-       for (unsigned uSeqIndexB = 0; uSeqIndexB < uSeqCountB; ++uSeqIndexB)\r
-               {\r
-               msaCombined.SetSeqName(uSeqCountA + uSeqIndexB, msaB.GetSeqName(uSeqIndexB));\r
-               msaCombined.SetSeqId(uSeqCountA + uSeqIndexB, msaB.GetSeqId(uSeqIndexB));\r
-               }\r
-\r
-       unsigned uColIndexA = 0;\r
-       unsigned uColIndexB = 0;\r
-       unsigned uColIndexCombined = 0;\r
-       const unsigned uEdgeCount = Path.GetEdgeCount();\r
-       for (unsigned uEdgeIndex = 0; uEdgeIndex < uEdgeCount; ++uEdgeIndex)\r
-               {\r
-               const PWEdge &Edge = Path.GetEdge(uEdgeIndex);\r
-#if    TRACE\r
-               Log("\nEdge %u %c%u.%u\n",\r
-                 uEdgeIndex,\r
-                 Edge.cType,\r
-                 Edge.uPrefixLengthA,\r
-                 Edge.uPrefixLengthB);\r
-#endif\r
-               const char cType = Edge.cType;\r
-               const unsigned uPrefixLengthA = Edge.uPrefixLengthA;\r
-               unsigned uColCountA = 0;\r
-               if (uPrefixLengthA > 0)\r
-                       {\r
-                       const unsigned uNodeIndexA = uPrefixLengthA - 1;\r
-                       const unsigned uTplColIndexA = uNodeIndexA;\r
-                       if (uTplColIndexA > uColIndexA)\r
-                               uColCountA = uTplColIndexA - uColIndexA;\r
-                       }\r
-\r
-               const unsigned uPrefixLengthB = Edge.uPrefixLengthB;\r
-               unsigned uColCountB = 0;\r
-               if (uPrefixLengthB > 0)\r
-                       {\r
-                       const unsigned uNodeIndexB = uPrefixLengthB - 1;\r
-                       const unsigned uTplColIndexB = uNodeIndexB;\r
-                       if (uTplColIndexB > uColIndexB)\r
-                               uColCountB = uTplColIndexB - uColIndexB;\r
-                       }\r
-\r
-               AppendUnalignedTerminals(msaA, uColIndexA, uColCountA, msaB, uColIndexB, uColCountB,\r
-                 uSeqCountA, uSeqCountB, msaCombined, uColIndexCombined);\r
-\r
-               switch (cType)\r
-                       {\r
-               case 'M':\r
-                       {\r
-                       assert(uPrefixLengthA > 0);\r
-                       assert(uPrefixLengthB > 0);\r
-                       const unsigned uColA = uPrefixLengthA - 1;\r
-                       const unsigned uColB = uPrefixLengthB - 1;\r
-                       assert(uColIndexA == uColA);\r
-                       assert(uColIndexB == uColB);\r
-                       AppendMatch(msaA, uColIndexA, msaB, uColIndexB, uSeqCountA, uSeqCountB,\r
-                         msaCombined, uColIndexCombined);\r
-                       break;\r
-                       }\r
-               case 'D':\r
-                       {\r
-                       assert(uPrefixLengthA > 0);\r
-                       const unsigned uColA = uPrefixLengthA - 1;\r
-                       assert(uColIndexA == uColA);\r
-                       AppendDelete(msaA, uColIndexA, uSeqCountA, uSeqCountB, msaCombined, uColIndexCombined);\r
-                       break;\r
-                       }\r
-               case 'I':\r
-                       {\r
-                       assert(uPrefixLengthB > 0);\r
-                       const unsigned uColB = uPrefixLengthB - 1;\r
-                       assert(uColIndexB == uColB);\r
-                       AppendInsert(msaB, uColIndexB, uSeqCountA, uSeqCountB, msaCombined, uColIndexCombined);\r
-                       break;\r
-                       }\r
-               default:\r
-                       assert(false);\r
-                       }\r
-               }\r
-       unsigned uInsertColCountA = uColCountA - uColIndexA;\r
-       unsigned uInsertColCountB = uColCountB - uColIndexB;\r
-\r
-       AppendUnalignedTerminals(msaA, uColIndexA, uInsertColCountA, msaB, uColIndexB,\r
-         uInsertColCountB, uSeqCountA, uSeqCountB, msaCombined, uColIndexCombined);\r
-       }\r