Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/diffobjscore.cpp b/website/archive/binaries/mac/src/muscle/diffobjscore.cpp
deleted file mode 100644 (file)
index 5b064fe..0000000
--- a/website/archive/binaries/mac/src/muscle/diffobjscore.cpp
+++ /dev/null
@@ -1,162 +0,0 @@
-#include "muscle.h"\r
-#include "msa.h"\r
-#include "objscore.h"\r
-#include "profile.h"\r
-\r
-#define TRACE                          0\r
-#define COMPARE_3_52           0\r
-#define BRUTE_LETTERS          0\r
-\r
-static SCORE ScoreColLetters(const MSA &msa, unsigned uColIndex)\r
-       {\r
-       SCOREMATRIX &Mx = *g_ptrScoreMatrix;\r
-       const unsigned uSeqCount = msa.GetSeqCount();\r
-\r
-#if    BRUTE_LETTERS\r
-       SCORE BruteScore = 0;\r
-       for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount; ++uSeqIndex1)\r
-               {\r
-               unsigned uLetter1 = msa.GetLetterEx(uSeqIndex1, uColIndex);\r
-               if (uLetter1 >= g_AlphaSize)\r
-                       continue;\r
-               WEIGHT w1 = msa.GetSeqWeight(uSeqIndex1);\r
-               for (unsigned uSeqIndex2 = uSeqIndex1 + 1; uSeqIndex2 < uSeqCount; ++uSeqIndex2)\r
-                       {\r
-                       unsigned uLetter2 = msa.GetLetterEx(uSeqIndex2, uColIndex);\r
-                       if (uLetter2 >= g_AlphaSize)\r
-                               continue;\r
-                       WEIGHT w2 = msa.GetSeqWeight(uSeqIndex2);\r
-                       BruteScore += w1*w2*Mx[uLetter1][uLetter2];\r
-                       }\r
-               }\r
-#endif\r
-       \r
-       double N = 0;\r
-       for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount; ++uSeqIndex1)\r
-               {\r
-               WEIGHT w = msa.GetSeqWeight(uSeqIndex1);\r
-               N += w;\r
-               }\r
-       if (N <= 0)\r
-               return 0;\r
-\r
-       FCOUNT Freqs[20];\r
-       memset(Freqs, 0, sizeof(Freqs));\r
-       SCORE Score = 0;\r
-       for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount; ++uSeqIndex1)\r
-               {\r
-               unsigned uLetter = msa.GetLetterEx(uSeqIndex1, uColIndex);\r
-               if (uLetter >= g_AlphaSize)\r
-                       continue;\r
-               WEIGHT w = msa.GetSeqWeight(uSeqIndex1);\r
-               Freqs[uLetter] += w;\r
-               Score -= w*w*Mx[uLetter][uLetter];\r
-               }\r
-\r
-       for (unsigned uLetter1 = 0; uLetter1 < g_AlphaSize; ++uLetter1)\r
-               {\r
-               const FCOUNT f1 = Freqs[uLetter1];\r
-               Score += f1*f1*Mx[uLetter1][uLetter1];\r
-               for (unsigned uLetter2 = uLetter1 + 1; uLetter2 < g_AlphaSize; ++uLetter2)\r
-                       {\r
-                       const FCOUNT f2 = Freqs[uLetter2];\r
-                       Score += 2*f1*f2*Mx[uLetter1][uLetter2];\r
-                       }\r
-               }\r
-       Score /= 2;\r
-#if    BRUTE_LETTERS\r
-       assert(BTEq(BruteScore, Score));\r
-#endif\r
-       return Score;\r
-       }\r
-\r
-static SCORE ScoreLetters(const MSA &msa, const unsigned Edges[],\r
-  unsigned uEdgeCount)\r
-       {\r
-       const unsigned uSeqCount = msa.GetSeqCount();\r
-       const unsigned uColCount = msa.GetColCount();\r
-\r
-// Letters\r
-       SCORE Score = 0;\r
-       for (unsigned uEdgeIndex = 0; uEdgeIndex < uEdgeCount; ++uEdgeIndex)\r
-               {\r
-               const unsigned uColIndex = Edges[uEdgeIndex];\r
-               assert(uColIndex < uColCount);\r
-               Score += ScoreColLetters(msa, uColIndex);\r
-               }\r
-       return Score;\r
-       }\r
-\r
-void GetLetterScores(const MSA &msa, SCORE Scores[])\r
-       {\r
-       const unsigned uColCount = msa.GetColCount();\r
-       for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)\r
-               Scores[uColIndex] = ScoreColLetters(msa, uColIndex);\r
-       }\r
-\r
-SCORE DiffObjScore(\r
-  const MSA &msa1, const PWPath &Path1, const unsigned Edges1[], unsigned uEdgeCount1, \r
-  const MSA &msa2, const PWPath &Path2, const unsigned Edges2[], unsigned uEdgeCount2)\r
-       {\r
-#if    TRACE\r
-       {\r
-       Log("============DiffObjScore===========\n");\r
-       Log("msa1:\n");\r
-       msa1.LogMe();\r
-       Log("\n");\r
-       Log("Cols1: ");\r
-       for (unsigned i = 0; i < uEdgeCount1; ++i)\r
-               Log(" %u", Edges1[i]);\r
-       Log("\n\n");\r
-       Log("msa2:\n");\r
-       msa2.LogMe();\r
-       Log("Cols2: ");\r
-       for (unsigned i = 0; i < uEdgeCount2; ++i)\r
-               Log(" %u", Edges2[i]);\r
-       Log("\n\n");\r
-       }\r
-#endif\r
-\r
-#if    COMPARE_3_52\r
-       extern SCORE g_SPScoreLetters;\r
-       extern SCORE g_SPScoreGaps;\r
-       SCORE SP1 = ObjScoreSP(msa1);\r
-       SCORE SPLetters1 = g_SPScoreLetters;\r
-       SCORE SPGaps1 = g_SPScoreGaps;\r
-\r
-       SCORE SP2 = ObjScoreSP(msa2);\r
-       SCORE SPLetters2 = g_SPScoreLetters;\r
-       SCORE SPGaps2 = g_SPScoreGaps;\r
-       SCORE SPDiffLetters = SPLetters2 - SPLetters1;\r
-       SCORE SPDiffGaps = SPGaps2 - SPGaps1;\r
-       SCORE SPDiff = SPDiffLetters + SPDiffGaps;\r
-#endif\r
-\r
-       SCORE Letters1 = ScoreLetters(msa1, Edges1, uEdgeCount1);\r
-       SCORE Letters2 = ScoreLetters(msa2, Edges2, uEdgeCount2);\r
-\r
-       SCORE Gaps1 = ScoreGaps(msa1, Edges1, uEdgeCount1);\r
-       SCORE Gaps2 = ScoreGaps(msa2, Edges2, uEdgeCount2);\r
-\r
-       SCORE DiffLetters = Letters2 - Letters1;\r
-       SCORE DiffGaps = Gaps2 - Gaps1;\r
-       SCORE Diff = DiffLetters + DiffGaps;\r
-\r
-#if    COMPARE_3_52\r
-       Log("ObjScoreSP    Letters1=%.4g  Letters2=%.4g  DiffLetters=%.4g\n",\r
-         SPLetters1, SPLetters2, SPDiffLetters);\r
-\r
-       Log("DiffObjScore  Letters1=%.4g  Letters2=%.4g  DiffLetters=%.4g\n",\r
-         Letters1, Letters2, DiffLetters);\r
-\r
-       Log("ObjScoreSP    Gaps1=%.4g  Gaps2=%.4g  DiffGaps=%.4g\n",\r
-         SPGaps1, SPGaps2, SPDiffGaps);\r
-\r
-       Log("DiffObjScore  Gaps1=%.4g  Gaps2=%.4g  DiffGaps=%.4g\n",\r
-         Gaps1, Gaps2, DiffGaps);\r
-\r
-       Log("SP diff=%.4g DiffObjScore Diff=%.4g\n", SPDiff, Diff);\r
-#endif\r
-\r
-       return Diff;\r
-       }\r