Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/local.cpp b/website/archive/binaries/mac/src/muscle/local.cpp
deleted file mode 100644 (file)
index c4d7a37..0000000
--- a/website/archive/binaries/mac/src/muscle/local.cpp
+++ /dev/null
@@ -1,100 +0,0 @@
-#include "muscle.h"\r
-#include "textfile.h"\r
-#include "msa.h"\r
-#include "profile.h"\r
-#include "pwpath.h"\r
-#include "tree.h"\r
-\r
-#define TRACE  0\r
-\r
-static void MSAFromFileName(const char *FileName, MSA &a)\r
-       {\r
-       TextFile File(FileName);\r
-       a.FromFile(File);\r
-       }\r
-\r
-static ProfPos *ProfileFromMSALocal(MSA &msa, Tree &tree)\r
-       {\r
-       const unsigned uSeqCount = msa.GetSeqCount();\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               msa.SetSeqId(uSeqIndex, uSeqIndex);\r
-\r
-       TreeFromMSA(msa, tree, g_Cluster1, g_Distance1, g_Root1);\r
-       SetMuscleTree(tree);\r
-       return ProfileFromMSA(msa);\r
-       }\r
-\r
-void Local()\r
-       {\r
-       if (0 == g_pstrFileName1 || 0 == g_pstrFileName2)\r
-               Quit("Must specify both -in1 and -in2 for -sw");\r
-\r
-       SetSeqWeightMethod(g_SeqWeight1);\r
-\r
-       MSA msa1;\r
-       MSA msa2;\r
-\r
-       MSAFromFileName(g_pstrFileName1, msa1);\r
-       MSAFromFileName(g_pstrFileName2, msa2);\r
-\r
-       ALPHA Alpha = ALPHA_Undefined;\r
-       switch (g_SeqType)\r
-               {\r
-       case SEQTYPE_Auto:\r
-               Alpha = msa1.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
-\r
-       msa1.FixAlpha();\r
-       msa2.FixAlpha();\r
-\r
-       if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)\r
-               SetPPScore(PPSCORE_SPN);\r
-\r
-       const unsigned uSeqCount1 = msa1.GetSeqCount();\r
-       const unsigned uSeqCount2 = msa2.GetSeqCount();\r
-       const unsigned uMaxSeqCount = (uSeqCount1 > uSeqCount2 ? uSeqCount1 : uSeqCount2);\r
-       MSA::SetIdCount(uMaxSeqCount);\r
-\r
-       unsigned uLength1 = msa1.GetColCount();\r
-       unsigned uLength2 = msa2.GetColCount();\r
-\r
-       Tree tree1;\r
-       Tree tree2;\r
-\r
-       ProfPos *Prof1 = ProfileFromMSALocal(msa1, tree1);\r
-       ProfPos *Prof2 = ProfileFromMSALocal(msa2, tree2);\r
-\r
-       PWPath Path;\r
-       SW(Prof1, uLength1, Prof2, uLength2, Path);\r
-\r
-#if    TRACE\r
-       Path.LogMe();\r
-#endif\r
-\r
-       MSA msaOut;\r
-       AlignTwoMSAsGivenPathSW(Path, msa1, msa2, msaOut);\r
-\r
-#if    TRACE\r
-       msaOut.LogMe();\r
-#endif\r
-\r
-       TextFile fileOut(g_pstrOutFileName, true);\r
-       msaOut.ToFile(fileOut);\r
-       }\r