Mac binaries

[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
new file mode 100644 (file)
index 0000000..d0bac98
--- /dev/null
+++ b/website/archive/binaries/mac/src/muscle/realigndiffs.cpp
@@ -0,0 +1,115 @@
+#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