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[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
new file mode 100644 (file)
index 0000000..d3e03c1
--- /dev/null
+++ b/website/archive/binaries/mac/src/muscle/aligngivenpathsw.cpp
@@ -0,0 +1,237 @@
+#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