Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/realigndiffse.cpp b/website/archive/binaries/mac/src/muscle/realigndiffse.cpp
deleted file mode 100644 (file)
index 559c333..0000000
--- a/website/archive/binaries/mac/src/muscle/realigndiffse.cpp
+++ /dev/null
@@ -1,142 +0,0 @@
-#include "muscle.h"\r
-#include "msa.h"\r
-#include "tree.h"\r
-#include "profile.h"\r
-#include "pwpath.h"\r
-#include "seqvect.h"\r
-#include "estring.h"\r
-\r
-#define TRACE          0\r
-\r
-void DeleteProgNode(ProgNode &Node)\r
-       {\r
-       delete[] Node.m_Prof;\r
-       delete[] Node.m_EstringL;\r
-       delete[] Node.m_EstringR;\r
-\r
-       Node.m_Prof = 0;\r
-       Node.m_EstringL = 0;\r
-       Node.m_EstringR = 0;\r
-       }\r
-\r
-static void MakeNode(ProgNode &OldNode, ProgNode &NewNode, bool bSwapLR)\r
-       {\r
-       if (bSwapLR)\r
-               {\r
-               NewNode.m_EstringL = OldNode.m_EstringR;\r
-               NewNode.m_EstringR = OldNode.m_EstringL;\r
-               }\r
-       else\r
-               {\r
-               NewNode.m_EstringL = OldNode.m_EstringL;\r
-               NewNode.m_EstringR = OldNode.m_EstringR;\r
-               }\r
-       NewNode.m_Prof = OldNode.m_Prof;\r
-       NewNode.m_uLength = OldNode.m_uLength;\r
-       NewNode.m_Weight = OldNode.m_Weight;\r
-\r
-       OldNode.m_Prof = 0;\r
-       OldNode.m_EstringL = 0;\r
-       OldNode.m_EstringR = 0;\r
-       }\r
-\r
-void RealignDiffsE(const MSA &msaIn, const SeqVect &v,\r
-  const Tree &NewTree, const Tree &OldTree, \r
-  const unsigned uNewNodeIndexToOldNodeIndex[],\r
-  MSA &msaOut, ProgNode *OldProgNodes)\r
-       {\r
-       assert(OldProgNodes != 0);\r
-\r
-       const unsigned uNodeCount = NewTree.GetNodeCount();\r
-       if (uNodeCount%2 == 0)\r
-               Quit("RealignDiffs: Expected odd number of nodes");\r
-\r
-       const unsigned uMergeCount = (uNodeCount - 1)/2;\r
-       ProgNode *NewProgNodes = new ProgNode[uNodeCount];\r
-\r
-       for (unsigned uNewNodeIndex = 0; uNewNodeIndex < uNodeCount; ++uNewNodeIndex)\r
-               {\r
-               if (NODE_CHANGED == uNewNodeIndexToOldNodeIndex[uNewNodeIndex])\r
-                       continue;\r
-\r
-               unsigned uOldNodeIndex = uNewNodeIndexToOldNodeIndex[uNewNodeIndex];\r
-               assert(uNewNodeIndex < uNodeCount);\r
-               assert(uOldNodeIndex < uNodeCount);\r
-\r
-               ProgNode &NewNode = NewProgNodes[uNewNodeIndex];\r
-               ProgNode &OldNode = OldProgNodes[uOldNodeIndex];\r
-               bool bSwapLR = false;\r
-               if (!NewTree.IsLeaf(uNewNodeIndex))\r
-                       {\r
-                       unsigned uNewLeft = NewTree.GetLeft(uNewNodeIndex);\r
-                       unsigned uNewRight = NewTree.GetRight(uNewNodeIndex);\r
-                       unsigned uOld = uNewNodeIndexToOldNodeIndex[uNewNodeIndex];\r
-                       unsigned uOldLeft = OldTree.GetLeft(uOld);\r
-                       unsigned uOldRight = OldTree.GetRight(uOld);\r
-                       assert(uOldLeft < uNodeCount && uOldRight < uNodeCount);\r
-                       if (uOldLeft != uNewNodeIndexToOldNodeIndex[uNewLeft])\r
-                               {\r
-                               assert(uOldLeft == uNewNodeIndexToOldNodeIndex[uNewRight]);\r
-                               bSwapLR = true;\r
-                               }\r
-                       }\r
-               MakeNode(OldNode, NewNode, bSwapLR);\r
-#if    TRACE\r
-               Log("MakeNode old=%u new=%u swap=%d length=%u weight=%.3g\n",\r
-                 uOldNodeIndex, uNewNodeIndex, bSwapLR, NewNode.m_uLength, NewNode.m_Weight);\r
-#endif\r
-               }\r
-\r
-       unsigned uJoin = 0;\r
-       SetProgressDesc("Refine tree");\r
-       for (unsigned uNewNodeIndex = NewTree.FirstDepthFirstNode();\r
-         NULL_NEIGHBOR != uNewNodeIndex;\r
-         uNewNodeIndex = NewTree.NextDepthFirstNode(uNewNodeIndex))\r
-               {\r
-               if (NODE_CHANGED != uNewNodeIndexToOldNodeIndex[uNewNodeIndex])\r
-                       continue;\r
-\r
-               Progress(uJoin, uMergeCount - 1);\r
-               ++uJoin;\r
-\r
-               const unsigned uMergeNodeIndex = uNewNodeIndex;\r
-               ProgNode &Parent = NewProgNodes[uMergeNodeIndex];\r
-\r
-               const unsigned uLeft = NewTree.GetLeft(uNewNodeIndex);\r
-               const unsigned uRight = NewTree.GetRight(uNewNodeIndex);\r
-\r
-               ProgNode &Node1 = NewProgNodes[uLeft];\r
-               ProgNode &Node2 = NewProgNodes[uRight];\r
-\r
-               AlignTwoProfs(\r
-                       Node1.m_Prof, Node1.m_uLength, Node1.m_Weight,\r
-                       Node2.m_Prof, Node2.m_uLength, Node2.m_Weight,\r
-                       Parent.m_Path,\r
-                       &Parent.m_Prof, &Parent.m_uLength);\r
-               PathToEstrings(Parent.m_Path, &Parent.m_EstringL, &Parent.m_EstringR);\r
-\r
-               Parent.m_Weight = Node1.m_Weight + Node2.m_Weight;\r
-\r
-               delete[] Node1.m_Prof;\r
-               delete[] Node2.m_Prof;\r
-\r
-               Node1.m_Prof = 0;\r
-               Node2.m_Prof = 0;\r
-               }\r
-\r
-       ProgressStepsDone();\r
-\r
-       if (g_bBrenner)\r
-               MakeRootMSABrenner((SeqVect &) v, NewTree, NewProgNodes, msaOut);\r
-       else\r
-               MakeRootMSA(v, NewTree, NewProgNodes, msaOut);\r
-\r
-#if    DEBUG\r
-       AssertMSAEqIgnoreCaseAndGaps(msaIn, msaOut);\r
-#endif\r
-\r
-       for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)\r
-               DeleteProgNode(NewProgNodes[uNodeIndex]);\r
-\r
-       delete[] NewProgNodes;\r
-       }\r