Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/realigndiffs.cpp b/website/archive/binaries/mac/src/muscle/realigndiffs.cpp
deleted file mode 100644 (file)
index d0bac98..0000000
--- a/website/archive/binaries/mac/src/muscle/realigndiffs.cpp
+++ /dev/null
@@ -1,115 +0,0 @@
-#include "muscle.h"\r
-#include "msa.h"\r
-#include "tree.h"\r
-#include "profile.h"\r
-#include "pwpath.h"\r
-\r
-#define TRACE  0\r
-\r
-// Progressive alignment according to a diffs tree.\r
-\r
-static void MakeNode(const MSA &msaIn, const Tree &Diffs, unsigned uDiffsNodeIndex,\r
-   const unsigned IdToDiffsTreeNodeIndex[], ProgNode &Node)\r
-       {\r
-       const unsigned uSeqCount = msaIn.GetSeqCount();\r
-\r
-       unsigned *Ids = new unsigned[uSeqCount];\r
-\r
-       unsigned uSeqsInDiffCount = 0;\r
-       for (unsigned uId = 0; uId < uSeqCount; ++uId)\r
-               {\r
-               if (IdToDiffsTreeNodeIndex[uId] == uDiffsNodeIndex)\r
-                       {\r
-                       Ids[uSeqsInDiffCount] = uId;\r
-                       ++uSeqsInDiffCount;\r
-                       }\r
-               }\r
-       if (0 == uSeqsInDiffCount)\r
-               Quit("MakeNode: no seqs in diff");\r
-\r
-       MSASubsetByIds(msaIn, Ids, uSeqsInDiffCount, Node.m_MSA);\r
-\r
-#if    DEBUG\r
-       ValidateMuscleIds(Node.m_MSA);\r
-#endif\r
-\r
-       DeleteGappedCols(Node.m_MSA);\r
-       delete[] Ids;\r
-       }\r
-\r
-void RealignDiffs(const MSA &msaIn, const Tree &Diffs,\r
-  const unsigned IdToDiffsTreeNodeIndex[], MSA &msaOut)\r
-       {\r
-       assert(Diffs.IsRooted());\r
-\r
-#if    TRACE\r
-       Log("RealignDiffs\n");\r
-       Log("Diff tree:\n");\r
-       Diffs.LogMe();\r
-#endif\r
-\r
-       const unsigned uNodeCount = Diffs.GetNodeCount();\r
-       if (uNodeCount%2 == 0)\r
-               Quit("RealignDiffs: Expected odd number of nodes");\r
-\r
-       const unsigned uMergeCount = (uNodeCount - 1)/2;\r
-\r
-       ProgNode *ProgNodes = new ProgNode[uNodeCount];\r
-\r
-       unsigned uJoin = 0;\r
-       SetProgressDesc("Refine tree");\r
-       for (unsigned uDiffsNodeIndex = Diffs.FirstDepthFirstNode();\r
-         NULL_NEIGHBOR != uDiffsNodeIndex;\r
-         uDiffsNodeIndex = Diffs.NextDepthFirstNode(uDiffsNodeIndex))\r
-               {\r
-               if (Diffs.IsLeaf(uDiffsNodeIndex))\r
-                       {\r
-                       assert(uDiffsNodeIndex < uNodeCount);\r
-                       if (uDiffsNodeIndex >= uNodeCount)\r
-                               Quit("TreeNodeIndex=%u NodeCount=%u\n", uDiffsNodeIndex, uNodeCount);\r
-\r
-                       ProgNode &Node = ProgNodes[uDiffsNodeIndex];\r
-                       MakeNode(msaIn, Diffs, uDiffsNodeIndex, IdToDiffsTreeNodeIndex, Node);\r
-\r
-                       Node.m_uLength = Node.m_MSA.GetColCount();\r
-                       }\r
-               else\r
-                       {\r
-                       Progress(uJoin, uMergeCount);\r
-                       ++uJoin;\r
-                       const unsigned uMergeNodeIndex = uDiffsNodeIndex;\r
-                       ProgNode &Parent = ProgNodes[uMergeNodeIndex];\r
-\r
-                       const unsigned uLeft = Diffs.GetLeft(uDiffsNodeIndex);\r
-                       const unsigned uRight = Diffs.GetRight(uDiffsNodeIndex);\r
-\r
-                       ProgNode &Node1 = ProgNodes[uLeft];\r
-                       ProgNode &Node2 = ProgNodes[uRight];\r
-\r
-                       PWPath Path;\r
-                       AlignTwoMSAs(Node1.m_MSA, Node2.m_MSA, Parent.m_MSA, Path);\r
-\r
-#if    TRACE\r
-                       {\r
-                       Log("Combined:\n");\r
-                       Parent.m_MSA.LogMe();\r
-                       }\r
-#endif\r
-\r
-                       Node1.m_MSA.Clear();\r
-                       Node2.m_MSA.Clear();\r
-                       }\r
-               }\r
-       ProgressStepsDone();\r
-\r
-       unsigned uRootNodeIndex = Diffs.GetRootNodeIndex();\r
-       const ProgNode &RootProgNode = ProgNodes[uRootNodeIndex];\r
-       msaOut.Copy(RootProgNode.m_MSA);\r
-\r
-#if    DEBUG\r
-       AssertMSAEqIgnoreCaseAndGaps(msaIn, msaOut);\r
-#endif\r
-\r
-       delete[] ProgNodes;\r
-       ProgNodes = 0;\r
-       }\r