Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/refine.cpp b/website/archive/binaries/mac/src/muscle/refine.cpp
deleted file mode 100644 (file)
index 94f0046..0000000
--- a/website/archive/binaries/mac/src/muscle/refine.cpp
+++ /dev/null
@@ -1,80 +0,0 @@
-#include "muscle.h"\r
-#include "textfile.h"\r
-#include "seqvect.h"\r
-#include "distfunc.h"\r
-#include "msa.h"\r
-#include "tree.h"\r
-#include "clust.h"\r
-#include "profile.h"\r
-#include "clustsetmsa.h"\r
-\r
-void Refine()\r
-       {\r
-       SetOutputFileName(g_pstrOutFileName);\r
-       SetInputFileName(g_pstrInFileName);\r
-       SetStartTime();\r
-\r
-       SetMaxIters(g_uMaxIters);\r
-       SetSeqWeightMethod(g_SeqWeight1);\r
-\r
-       TextFile fileIn(g_pstrInFileName);\r
-       MSA msa;\r
-       msa.FromFile(fileIn);\r
-\r
-       const unsigned uSeqCount = msa.GetSeqCount();\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 = msa.GuessAlpha();\r
-               break;\r
-\r
-       case SEQTYPE_Protein:\r
-               Alpha = ALPHA_Amino;\r
-               break;\r
-\r
-       case SEQTYPE_DNA:\r
-               Alpha = ALPHA_DNA;\r
-               break;\r
-\r
-       case SEQTYPE_RNA:\r
-               Alpha = ALPHA_RNA;\r
-               break;\r
-\r
-       default:\r
-               Quit("Invalid SeqType");\r
-               }\r
-       SetAlpha(Alpha);\r
-       msa.FixAlpha();\r
-\r
-       SetPPScore();\r
-       if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)\r
-               SetPPScore(PPSCORE_SPN);\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
-               msa.SetSeqId(uSeqIndex, uSeqIndex);\r
-       SetMuscleInputMSA(msa);\r
-\r
-       Tree GuideTree;\r
-       TreeFromMSA(msa, GuideTree, g_Cluster2, g_Distance2, g_Root2);\r
-       SetMuscleTree(GuideTree);\r
-\r
-       if (g_bAnchors)\r
-               RefineVert(msa, GuideTree, g_uMaxIters);\r
-       else\r
-               RefineHoriz(msa, GuideTree, g_uMaxIters, false, false);\r
-\r
-       ValidateMuscleIds(msa);\r
-       ValidateMuscleIds(GuideTree);\r
-\r
-//     TextFile fileOut(g_pstrOutFileName, true);\r
-//     msa.ToFile(fileOut);\r
-       MuscleOutput(msa);\r
-       }\r