Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/progressivealign.cpp b/website/archive/binaries/mac/src/muscle/progressivealign.cpp
deleted file mode 100644 (file)
index c2feb3b..0000000
--- a/website/archive/binaries/mac/src/muscle/progressivealign.cpp
+++ /dev/null
@@ -1,76 +0,0 @@
-#include "muscle.h"\r
-#include <math.h>\r
-#include "tree.h"\r
-#include "seqvect.h"\r
-#include "profile.h"\r
-#include "msa.h"\r
-#include "pwpath.h"\r
-#include "distfunc.h"\r
-\r
-#define TRACE 0\r
-\r
-void ProgressiveAlign(const SeqVect &v, const Tree &GuideTree, MSA &a)\r
-       {\r
-       assert(GuideTree.IsRooted());\r
-\r
-#if    TRACE\r
-       Log("GuideTree:\n");\r
-       GuideTree.LogMe();\r
-#endif\r
-\r
-       const unsigned uSeqCount = v.Length();\r
-       const unsigned uNodeCount = 2*uSeqCount - 1;\r
-\r
-       ProgNode *ProgNodes = new ProgNode[uNodeCount];\r
-\r
-       unsigned uJoin = 0;\r
-       unsigned uTreeNodeIndex = GuideTree.FirstDepthFirstNode();\r
-       SetProgressDesc("Align node");\r
-       do\r
-               {\r
-               if (GuideTree.IsLeaf(uTreeNodeIndex))\r
-                       {\r
-                       if (uTreeNodeIndex >= uNodeCount)\r
-                               Quit("TreeNodeIndex=%u NodeCount=%u\n", uTreeNodeIndex, uNodeCount);\r
-                       ProgNode &Node = ProgNodes[uTreeNodeIndex];\r
-                       unsigned uId = GuideTree.GetLeafId(uTreeNodeIndex);\r
-                       if (uId >= uSeqCount)\r
-                               Quit("Seq index out of range");\r
-                       const Seq &s = *(v[uId]);\r
-                       Node.m_MSA.FromSeq(s);\r
-                       Node.m_MSA.SetSeqId(0, uId);\r
-                       Node.m_uLength = Node.m_MSA.GetColCount();\r
-                       }\r
-               else\r
-                       {\r
-                       Progress(uJoin, uSeqCount - 1);\r
-                       ++uJoin;\r
-\r
-                       const unsigned uMergeNodeIndex = uTreeNodeIndex;\r
-                       ProgNode &Parent = ProgNodes[uMergeNodeIndex];\r
-\r
-                       const unsigned uLeft = GuideTree.GetLeft(uTreeNodeIndex);\r
-                       const unsigned uRight = GuideTree.GetRight(uTreeNodeIndex);\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
-                       Parent.m_uLength = Parent.m_MSA.GetColCount();\r
-\r
-                       Node1.m_MSA.Clear();\r
-                       Node2.m_MSA.Clear();\r
-                       }\r
-               uTreeNodeIndex = GuideTree.NextDepthFirstNode(uTreeNodeIndex);\r
-               }\r
-       while (NULL_NEIGHBOR != uTreeNodeIndex);\r
-       ProgressStepsDone();\r
-\r
-       unsigned uRootNodeIndex = GuideTree.GetRootNodeIndex();\r
-       const ProgNode &RootProgNode = ProgNodes[uRootNodeIndex];\r
-       a.Copy(RootProgNode.m_MSA);\r
-\r
-       delete[] ProgNodes;\r
-       ProgNodes = 0;\r
-       }\r