Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/ppscore.cpp b/website/archive/binaries/mac/src/muscle/ppscore.cpp
deleted file mode 100644 (file)
index 813b8a2..0000000
--- a/website/archive/binaries/mac/src/muscle/ppscore.cpp
+++ /dev/null
@@ -1,93 +0,0 @@
-#include "muscle.h"\r
-#include "textfile.h"\r
-#include "msa.h"\r
-#include "tree.h"\r
-#include "profile.h"\r
-#include "objscore.h"\r
-\r
-bool g_bTracePPScore = false;\r
-MSA *g_ptrPPScoreMSA1 = 0;\r
-MSA *g_ptrPPScoreMSA2 = 0;\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_Cluster2, g_Distance2, g_Root1);\r
-       SetMuscleTree(tree);\r
-       return ProfileFromMSA(msa);\r
-       }\r
-\r
-void PPScore()\r
-       {\r
-       if (0 == g_pstrFileName1 || 0 == g_pstrFileName2)\r
-               Quit("-ppscore needs -in1 and -in2");\r
-\r
-       SetSeqWeightMethod(g_SeqWeight1);\r
-\r
-       TextFile file1(g_pstrFileName1);\r
-       TextFile file2(g_pstrFileName2);\r
-\r
-       MSA msa1;\r
-       MSA msa2;\r
-\r
-       msa1.FromFile(file1);\r
-       msa2.FromFile(file2);\r
-\r
-       const unsigned uLength1 = msa1.GetColCount();\r
-       const unsigned uLength2 = msa2.GetColCount();\r
-\r
-       if (uLength1 != uLength2)\r
-               Quit("Profiles must have the same length");\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
-       Tree tree1;\r
-       Tree tree2;\r
-       ProfPos *Prof1 = ProfileFromMSALocal(msa1, tree1);\r
-       ProfPos *Prof2 = ProfileFromMSALocal(msa2, tree2);\r
-\r
-       g_bTracePPScore = true;\r
-       g_ptrPPScoreMSA1 = &msa1;\r
-       g_ptrPPScoreMSA2 = &msa2;\r
-\r
-       SCORE Score = ObjScoreDP_Profs(Prof1, Prof2, uLength1);\r
-\r
-       Log("Score=%.4g\n", Score);\r
-       printf("Score=%.4g\n", Score);\r
-       }\r