Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/refinevert.cpp b/website/archive/binaries/mac/src/muscle/refinevert.cpp
deleted file mode 100644 (file)
index 0655651..0000000
--- a/website/archive/binaries/mac/src/muscle/refinevert.cpp
+++ /dev/null
@@ -1,159 +0,0 @@
-#include "muscle.h"\r
-#include "profile.h"\r
-#include "msa.h"\r
-#include "pwpath.h"\r
-#include "seqvect.h"\r
-#include "clust.h"\r
-#include "tree.h"\r
-\r
-#define TRACE 0\r
-\r
-struct Range\r
-       {\r
-       unsigned m_uBestColLeft;\r
-       unsigned m_uBestColRight;\r
-       };\r
-\r
-static void ListVertSavings(unsigned uColCount, unsigned uAnchorColCount,\r
-  const Range *Ranges, unsigned uRangeCount)\r
-       {\r
-       if (!g_bVerbose || !g_bAnchors)\r
-               return;\r
-       double dTotalArea = uColCount*uColCount;\r
-       double dArea = 0.0;\r
-       for (unsigned i = 0; i < uRangeCount; ++i)\r
-               {\r
-               unsigned uLength = Ranges[i].m_uBestColRight - Ranges[i].m_uBestColLeft;\r
-               dArea += uLength*uLength;\r
-               }\r
-       double dPct = (dTotalArea - dArea)*100.0/dTotalArea;\r
-       Log("Anchor columns found       %u\n", uAnchorColCount);\r
-       Log("DP area saved by anchors   %-4.1f%%\n", dPct);\r
-       }\r
-\r
-static void ColsToRanges(const unsigned BestCols[], unsigned uBestColCount,\r
-  unsigned uColCount, Range Ranges[])\r
-       {\r
-// N best columns produces N+1 vertical blocks.\r
-       const unsigned uRangeCount = uBestColCount + 1;\r
-       for (unsigned uIndex = 0; uIndex < uRangeCount ; ++uIndex)\r
-               {\r
-               unsigned uBestColLeft = 0;\r
-               if (uIndex > 0)\r
-                       uBestColLeft = BestCols[uIndex-1];\r
-               \r
-               unsigned uBestColRight = uColCount;\r
-               if (uIndex < uBestColCount)\r
-                       uBestColRight = BestCols[uIndex];\r
-\r
-               Ranges[uIndex].m_uBestColLeft = uBestColLeft;\r
-               Ranges[uIndex].m_uBestColRight = uBestColRight;\r
-               }\r
-       }\r
-\r
-// Return true if any changes made\r
-bool RefineVert(MSA &msaIn, const Tree &tree, unsigned uIters)\r
-       {\r
-       bool bAnyChanges = false;\r
-\r
-       const unsigned uColCountIn = msaIn.GetColCount();\r
-       const unsigned uSeqCountIn = msaIn.GetSeqCount();\r
-\r
-       if (uColCountIn < 3 || uSeqCountIn < 3)\r
-               return false;\r
-\r
-       unsigned *AnchorCols = new unsigned[uColCountIn];\r
-       unsigned uAnchorColCount;\r
-       SetMSAWeightsMuscle(msaIn);\r
-       FindAnchorCols(msaIn, AnchorCols, &uAnchorColCount);\r
-\r
-       const unsigned uRangeCount = uAnchorColCount + 1;\r
-       Range *Ranges = new Range[uRangeCount];\r
-\r
-#if    TRACE\r
-       Log("%u ranges\n", uRangeCount);\r
-#endif\r
-\r
-       ColsToRanges(AnchorCols, uAnchorColCount, uColCountIn, Ranges);\r
-       ListVertSavings(uColCountIn, uAnchorColCount, Ranges, uRangeCount);\r
-\r
-#if    TRACE\r
-       {\r
-       Log("Anchor cols: ");\r
-       for (unsigned i = 0; i < uAnchorColCount; ++i)\r
-               Log(" %u", AnchorCols[i]);\r
-       Log("\n");\r
-\r
-       Log("Ranges:\n");\r
-       for (unsigned i = 0; i < uRangeCount; ++i)\r
-               Log("%4u - %4u\n", Ranges[i].m_uBestColLeft, Ranges[i].m_uBestColRight);\r
-       }\r
-#endif\r
-\r
-       delete[] AnchorCols;\r
-\r
-       MSA msaOut;\r
-       msaOut.SetSize(uSeqCountIn, 0);\r
-\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCountIn; ++uSeqIndex)\r
-               {\r
-               const char *ptrName = msaIn.GetSeqName(uSeqIndex);\r
-               unsigned uId = msaIn.GetSeqId(uSeqIndex);\r
-               msaOut.SetSeqName(uSeqIndex, ptrName);\r
-               msaOut.SetSeqId(uSeqIndex, uId);\r
-               }\r
-\r
-       for (unsigned uRangeIndex = 0; uRangeIndex < uRangeCount; ++uRangeIndex)\r
-               {\r
-               MSA msaRange;\r
-\r
-               const Range &r = Ranges[uRangeIndex];\r
-\r
-               const unsigned uFromColIndex = r.m_uBestColLeft;\r
-               const unsigned uRangeColCount = r.m_uBestColRight - uFromColIndex;\r
-\r
-               if (0 == uRangeColCount)\r
-                       continue;\r
-               else if (1 == uRangeColCount)\r
-                       {\r
-                       MSAFromColRange(msaIn, uFromColIndex, 1, msaRange);\r
-                       MSAAppend(msaOut, msaRange);\r
-                       continue;\r
-                       }\r
-               MSAFromColRange(msaIn, uFromColIndex, uRangeColCount, msaRange);\r
-\r
-#if    TRACE\r
-               Log("\n-------------\n");\r
-               Log("Range %u - %u count=%u\n", r.m_uBestColLeft, r.m_uBestColRight, uRangeColCount);\r
-               Log("Before:\n");\r
-               msaRange.LogMe();\r
-#endif\r
-\r
-               bool bLockLeft = (0 != uRangeIndex);\r
-               bool bLockRight = (uRangeCount - 1 != uRangeIndex);\r
-               bool bAnyChangesThisBlock = RefineHoriz(msaRange, tree, uIters, bLockLeft, bLockRight);\r
-               bAnyChanges = (bAnyChanges || bAnyChangesThisBlock);\r
-\r
-#if    TRACE\r
-               Log("After:\n");\r
-               msaRange.LogMe();\r
-#endif\r
-\r
-               MSAAppend(msaOut, msaRange);\r
-\r
-#if    TRACE\r
-               Log("msaOut after Cat:\n");\r
-               msaOut.LogMe();\r
-#endif\r
-               }\r
-\r
-#if    DEBUG\r
-// Sanity check\r
-       AssertMSAEqIgnoreCaseAndGaps(msaIn, msaOut);\r
-#endif\r
-\r
-       delete[] Ranges;\r
-       if (bAnyChanges)\r
-               msaIn.Copy(msaOut);\r
-       return bAnyChanges;\r
-       }\r