Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/sptest.cpp b/website/archive/binaries/mac/src/muscle/sptest.cpp
deleted file mode 100644 (file)
index ba06ecf..0000000
--- a/website/archive/binaries/mac/src/muscle/sptest.cpp
+++ /dev/null
@@ -1,176 +0,0 @@
-#include "muscle.h"\r
-#include "objscore.h"\r
-#include "msa.h"\r
-#include "textfile.h"\r
-#include "pwpath.h"\r
-\r
-const unsigned INDELS = 1;\r
-\r
-static void GetPos(const char Str[], unsigned L, int *pi1, int *pi2)\r
-       {\r
-       int i1;\r
-       for (;;)\r
-               {\r
-               i1 = rand()%(L-2) + 1;\r
-               if (Str[i1] == 'M')\r
-                       break;\r
-               }\r
-       int i2;\r
-       for (;;)\r
-               {\r
-               i2 = rand()%(L-2) + 1;\r
-               if (i1 != i2 && Str[i2] == 'M')\r
-                       break;\r
-               }\r
-       *pi1 = i1;\r
-       *pi2 = i2;\r
-       }\r
-\r
-static void MakePath(unsigned uSeqLength, unsigned uIndelCount, char Str[])\r
-       {\r
-       unsigned uPathLength = uSeqLength + uIndelCount;\r
-       for (unsigned i = 0; i < uPathLength; ++i)\r
-               Str[i] = 'M';\r
-\r
-       for (unsigned i = 0; i < uIndelCount; ++i)\r
-               {\r
-               int i1, i2;\r
-               GetPos(Str, uPathLength, &i1, &i2);\r
-               Str[i1] = 'D';\r
-               Str[i2] = 'I';\r
-               }\r
-\r
-       Str[uPathLength] = 0;\r
-       Log("MakePath=%s\n", Str);\r
-       }\r
-\r
-void SPTest()\r
-       {\r
-       SetPPScore(PPSCORE_SV);\r
-\r
-       SetListFileName("c:\\tmp\\muscle.log", false);\r
-\r
-       TextFile file1("c:\\tmp\\msa1.afa");\r
-       TextFile file2("c:\\tmp\\msa2.afa");\r
-\r
-       MSA msa1;\r
-       MSA msa2;\r
-\r
-       msa1.FromFile(file1);\r
-       msa2.FromFile(file2);\r
-\r
-       Log("msa1=\n");\r
-       msa1.LogMe();\r
-       Log("msa2=\n");\r
-       msa2.LogMe();\r
-\r
-       const unsigned uColCount = msa1.GetColCount();\r
-       if (msa2.GetColCount() != uColCount)\r
-               Quit("Different lengths");\r
-\r
-       const unsigned uSeqCount1 = msa1.GetSeqCount();\r
-       const unsigned uSeqCount2 = msa2.GetSeqCount();\r
-       const unsigned uSeqCount = uSeqCount1 + uSeqCount2;\r
-\r
-       MSA::SetIdCount(uSeqCount);\r
-\r
-       for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount1; ++uSeqIndex1)\r
-               {\r
-               msa1.SetSeqWeight(uSeqIndex1, 1.0);\r
-               msa1.SetSeqId(uSeqIndex1, uSeqIndex1);\r
-               }\r
-\r
-       for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqCount2; ++uSeqIndex2)\r
-               {\r
-               msa2.SetSeqWeight(uSeqIndex2, 1.0);\r
-               msa2.SetSeqId(uSeqIndex2, uSeqCount1 + uSeqIndex2);\r
-               }\r
-\r
-       MSA alnA;\r
-       MSA alnB;\r
-\r
-       char strPathA[1024];\r
-       char strPathB[1024];\r
-       MakePath(uColCount, INDELS, strPathA);\r
-       MakePath(uColCount, INDELS, strPathB);\r
-\r
-       PWPath PathA;\r
-       PWPath PathB;\r
-       PathA.FromStr(strPathA);\r
-       PathB.FromStr(strPathB);\r
-\r
-       Log("PathA=\n");\r
-       PathA.LogMe();\r
-       Log("PathB=\n");\r
-       PathB.LogMe();\r
-\r
-       AlignTwoMSAsGivenPath(PathA, msa1, msa2, alnA);\r
-       AlignTwoMSAsGivenPath(PathB, msa1, msa2, alnB);\r
-\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               alnA.SetSeqWeight(uSeqIndex, 1.0);\r
-               alnB.SetSeqWeight(uSeqIndex, 1.0);\r
-               }\r
-\r
-       unsigned Seqs1[1024];\r
-       unsigned Seqs2[1024];\r
-\r
-       for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount1; ++uSeqIndex1)\r
-               Seqs1[uSeqIndex1] = uSeqIndex1;\r
-\r
-       for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqCount2; ++uSeqIndex2)\r
-               Seqs2[uSeqIndex2] = uSeqCount1 + uSeqIndex2;\r
-\r
-       MSA msaA1;\r
-       MSA msaA2;\r
-       MSA msaB1;\r
-       MSA msaB2;\r
-       MSAFromSeqSubset(alnA, Seqs1, uSeqCount1, msaA1);\r
-       MSAFromSeqSubset(alnB, Seqs1, uSeqCount1, msaB1);\r
-       MSAFromSeqSubset(alnA, Seqs2, uSeqCount2, msaA2);\r
-       MSAFromSeqSubset(alnB, Seqs2, uSeqCount2, msaB2);\r
-\r
-       for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount1; ++uSeqIndex1)\r
-               {\r
-               msaA1.SetSeqWeight(uSeqIndex1, 1.0);\r
-               msaB1.SetSeqWeight(uSeqIndex1, 1.0);\r
-               }\r
-\r
-       for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqCount2; ++uSeqIndex2)\r
-               {\r
-               msaA2.SetSeqWeight(uSeqIndex2, 1.0);\r
-               msaB2.SetSeqWeight(uSeqIndex2, 1.0);\r
-               }\r
-\r
-       Log("msaA1=\n");\r
-       msaA1.LogMe();\r
-\r
-       Log("msaB1=\n");\r
-       msaB1.LogMe();\r
-\r
-       Log("msaA2=\n");\r
-       msaA2.LogMe();\r
-\r
-       Log("msaB2=\n");\r
-       msaB2.LogMe();\r
-\r
-       Log("alnA=\n");\r
-       alnA.LogMe();\r
-\r
-       Log("AlnB=\n");\r
-       alnB.LogMe();\r
-\r
-       Log("\nSPA\n---\n");\r
-       SCORE SPA = ObjScoreSP(alnA);\r
-       Log("\nSPB\n---\n");\r
-       SCORE SPB = ObjScoreSP(alnB);\r
-\r
-       Log("\nXPA\n---\n");\r
-       SCORE XPA = ObjScoreXP(msaA1, msaA2);\r
-       Log("\nXPB\n---\n");\r
-       SCORE XPB = ObjScoreXP(msaB1, msaB2);\r
-\r
-       Log("SPA=%.4g SPB=%.4g Diff=%.4g\n", SPA, SPB, SPA - SPB);\r
-       Log("XPA=%.4g XPB=%.4g Diff=%.4g\n", XPA, XPB, XPA - XPB);\r
-       }\r