Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/objscore.cpp b/website/archive/binaries/mac/src/muscle/objscore.cpp
deleted file mode 100644 (file)
index 6af91d9..0000000
--- a/website/archive/binaries/mac/src/muscle/objscore.cpp
+++ /dev/null
@@ -1,113 +0,0 @@
-#include "muscle.h"\r
-#include "msa.h"\r
-#include "objscore.h"\r
-#include "profile.h"\r
-#include "timing.h"\r
-\r
-#if    TIMING\r
-TICKS g_ticksObjScore = 0;\r
-#endif\r
-\r
-SCORE ObjScore(const MSA &msa, const unsigned SeqIndexes1[],\r
-  unsigned uSeqCount1, const unsigned SeqIndexes2[], unsigned uSeqCount2)\r
-       {\r
-#if    TIMING\r
-       TICKS t1 = GetClockTicks();\r
-#endif\r
-       const unsigned uSeqCount = msa.GetSeqCount();\r
-\r
-       OBJSCORE OS = g_ObjScore;\r
-       if (g_ObjScore == OBJSCORE_SPM)\r
-               {\r
-        if (uSeqCount <= 100)\r
-                       OS = OBJSCORE_XP;\r
-               else\r
-                       OS = OBJSCORE_SPF;\r
-               }\r
-\r
-       MSA msa1;\r
-       MSA msa2;\r
-\r
-       switch (OS)\r
-               {\r
-       case OBJSCORE_DP:\r
-       case OBJSCORE_XP:\r
-               MSAFromSeqSubset(msa, SeqIndexes1, uSeqCount1, msa1);\r
-               MSAFromSeqSubset(msa, SeqIndexes2, uSeqCount2, msa2);\r
-\r
-               SetMSAWeightsMuscle(msa1);\r
-               SetMSAWeightsMuscle(msa2);\r
-               break;\r
-\r
-       case OBJSCORE_SP:\r
-       case OBJSCORE_SPF:\r
-       case OBJSCORE_PS:\r
-       // Yuck -- casting away const (design flaw)\r
-               SetMSAWeightsMuscle((MSA &) msa);\r
-               break;\r
-               }\r
-\r
-       SCORE Score = 0;\r
-       switch (OS)\r
-               {\r
-       case OBJSCORE_SP:\r
-               Score = ObjScoreSP(msa);\r
-               break;\r
-\r
-       case OBJSCORE_DP:\r
-               Score = ObjScoreDP(msa1, msa2);\r
-               break;\r
-\r
-       case OBJSCORE_XP:\r
-               Score = ObjScoreXP(msa1, msa2);\r
-               break;\r
-\r
-       case OBJSCORE_PS:\r
-               Score = ObjScorePS(msa);\r
-               break;\r
-\r
-       case OBJSCORE_SPF:\r
-               Score = ObjScoreSPDimer(msa);\r
-               break;\r
-       \r
-       default:\r
-               Quit("Invalid g_ObjScore=%d", g_ObjScore);\r
-               }\r
-#if    TIMING\r
-       TICKS t2 = GetClockTicks();\r
-       g_ticksObjScore += (t2 - t1);\r
-#endif\r
-       return Score;\r
-       }\r
-\r
-SCORE ObjScoreIds(const MSA &msa, const unsigned Ids1[],\r
-  unsigned uCount1, const unsigned Ids2[], unsigned uCount2)\r
-       {\r
-#if    TIMING\r
-       TICKS t1 = GetClockTicks();\r
-#endif\r
-       unsigned *SeqIndexes1 = new unsigned[uCount1];\r
-       unsigned *SeqIndexes2 = new unsigned[uCount2];\r
-\r
-       for (unsigned n = 0; n < uCount1; ++n)\r
-               SeqIndexes1[n] = msa.GetSeqIndex(Ids1[n]);\r
-\r
-       for (unsigned n = 0; n < uCount2; ++n)\r
-               SeqIndexes2[n] = msa.GetSeqIndex(Ids2[n]);\r
-\r
-#if DOUBLE_AFFINE\r
-       extern SCORE ObjScoreDA(const MSA &msa, SCORE *ptrLetters, SCORE *ptrGaps);\r
-       SCORE Letters, Gaps;\r
-       SCORE dObjScore = ObjScoreDA(msa, &Letters, &Gaps);\r
-\r
-       delete[] SeqIndexes1;\r
-       delete[] SeqIndexes2;\r
-#else\r
-       SCORE dObjScore = ObjScore(msa, SeqIndexes1, uCount1, SeqIndexes2, uCount2);\r
-#endif\r
-#if    TIMING\r
-       TICKS t2 = GetClockTicks();\r
-       g_ticksObjScore += (t2 - t1);\r
-#endif\r
-       return dObjScore;\r
-       }\r