Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/muscle.cpp b/website/archive/binaries/mac/src/muscle/muscle.cpp
deleted file mode 100644 (file)
index 2a118bf..0000000
--- a/website/archive/binaries/mac/src/muscle/muscle.cpp
+++ /dev/null
@@ -1,130 +0,0 @@
-#include "muscle.h"\r
-#include "msa.h"\r
-#include "seqvect.h"\r
-#include "msa.h"\r
-#include "tree.h"\r
-#include "profile.h"\r
-\r
-void MUSCLE(SeqVect &v, MSA &msaOut)\r
-       {\r
-       const unsigned uSeqCount = v.Length();\r
-\r
-       if (0 == uSeqCount)\r
-               Quit("No sequences in input file");\r
-\r
-       ALPHA Alpha = ALPHA_Undefined;\r
-       switch (g_SeqType)\r
-               {\r
-       case SEQTYPE_Auto:\r
-               Alpha = v.GuessAlpha();\r
-               break;\r
-\r
-       case SEQTYPE_Protein:\r
-               Alpha = ALPHA_Amino;\r
-               break;\r
-\r
-       case SEQTYPE_RNA:\r
-               Alpha = ALPHA_RNA;\r
-               break;\r
-\r
-       case SEQTYPE_DNA:\r
-               Alpha = ALPHA_DNA;\r
-               break;\r
-\r
-       default:\r
-               Quit("Invalid seq type");\r
-               }\r
-       SetAlpha(Alpha);\r
-       v.FixAlpha();\r
-\r
-       if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)\r
-               {\r
-               SetPPScore(PPSCORE_SPN);\r
-               g_Distance1 = DISTANCE_Kmer4_6;\r
-               }\r
-\r
-       unsigned uMaxL = 0;\r
-       unsigned uTotL = 0;\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               unsigned L = v.GetSeq(uSeqIndex).Length();\r
-               uTotL += L;\r
-               if (L > uMaxL)\r
-                       uMaxL = L;\r
-               }\r
-\r
-       SetIter(1);\r
-       g_bDiags = g_bDiags1;\r
-       SetSeqStats(uSeqCount, uMaxL, uTotL/uSeqCount);\r
-\r
-       MSA::SetIdCount(uSeqCount);\r
-\r
-//// Initialize sequence ids.\r
-//// From this point on, ids must somehow propogate from here.\r
-//     for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-//             v.SetSeqId(uSeqIndex, uSeqIndex);\r
-\r
-       if (uSeqCount > 1)\r
-               MHackStart(v);\r
-\r
-       if (0 == uSeqCount)\r
-               {\r
-               msaOut.Clear();\r
-               return;\r
-               }\r
-\r
-       if (1 == uSeqCount && ALPHA_Amino == Alpha)\r
-               {\r
-               const Seq &s = v.GetSeq(0);\r
-               msaOut.FromSeq(s);\r
-               return;\r
-               }\r
-\r
-// First iteration\r
-       Tree GuideTree;\r
-       TreeFromSeqVect(v, GuideTree, g_Cluster1, g_Distance1, g_Root1);\r
-\r
-       SetMuscleTree(GuideTree);\r
-\r
-       ProgNode *ProgNodes = 0;\r
-       if (g_bLow)\r
-               ProgNodes = ProgressiveAlignE(v, GuideTree, msaOut);\r
-       else\r
-               ProgressiveAlign(v, GuideTree, msaOut);\r
-       SetCurrentAlignment(msaOut);\r
-\r
-       if (1 == g_uMaxIters || 2 == uSeqCount)\r
-               {\r
-               MHackEnd(msaOut);\r
-               return;\r
-               }\r
-\r
-       g_bDiags = g_bDiags2;\r
-       SetIter(2);\r
-\r
-       if (g_bLow)\r
-               {\r
-               if (0 != g_uMaxTreeRefineIters)\r
-                       RefineTreeE(msaOut, v, GuideTree, ProgNodes);\r
-               }\r
-       else\r
-               RefineTree(msaOut, GuideTree);\r
-\r
-       extern void DeleteProgNode(ProgNode &Node);\r
-       const unsigned uNodeCount = GuideTree.GetNodeCount();\r
-       for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)\r
-               DeleteProgNode(ProgNodes[uNodeIndex]);\r
-\r
-       delete[] ProgNodes;\r
-       ProgNodes = 0;\r
-\r
-       SetSeqWeightMethod(g_SeqWeight2);\r
-       SetMuscleTree(GuideTree);\r
-\r
-       if (g_bAnchors)\r
-               RefineVert(msaOut, GuideTree, g_uMaxIters - 2);\r
-       else\r
-               RefineHoriz(msaOut, GuideTree, g_uMaxIters - 2, false, false);\r
-\r
-       MHackEnd(msaOut);\r
-       }\r