Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/distcalc.cpp b/website/archive/binaries/mac/src/muscle/distcalc.cpp
deleted file mode 100644 (file)
index 80058f5..0000000
--- a/website/archive/binaries/mac/src/muscle/distcalc.cpp
+++ /dev/null
@@ -1,89 +0,0 @@
-#include "muscle.h"\r
-#include "distfunc.h"\r
-#include "distcalc.h"\r
-#include "msa.h"\r
-\r
-void DistCalcDF::Init(const DistFunc &DF)\r
-       {\r
-       m_ptrDF = &DF;\r
-       }\r
-\r
-void DistCalcDF::CalcDistRange(unsigned i, dist_t Dist[]) const\r
-       {\r
-       for (unsigned j = 0; j < i; ++j)\r
-               Dist[j] = m_ptrDF->GetDist(i, j);\r
-       }\r
-\r
-unsigned DistCalcDF::GetCount() const\r
-       {\r
-       return m_ptrDF->GetCount();\r
-       }\r
-\r
-unsigned DistCalcDF::GetId(unsigned i) const\r
-       {\r
-       return m_ptrDF->GetId(i);\r
-       }\r
-\r
-const char *DistCalcDF::GetName(unsigned i) const\r
-       {\r
-       return m_ptrDF->GetName(i);\r
-       }\r
-\r
-void DistCalcMSA::Init(const MSA &msa, DISTANCE Distance)\r
-       {\r
-       m_ptrMSA = &msa;\r
-       m_Distance = Distance;\r
-       }\r
-\r
-void DistCalcMSA::CalcDistRange(unsigned i, dist_t Dist[]) const\r
-       {\r
-       for (unsigned j = 0; j < i; ++j)\r
-               {\r
-               switch (m_Distance)\r
-                       {\r
-               case DISTANCE_PctIdKimura:\r
-                       {\r
-                       const float PctId = (float) m_ptrMSA->GetPctIdentityPair(i, j);\r
-                       Dist[j] = (float) KimuraDist(PctId);\r
-                       break;\r
-                       }\r
-               case DISTANCE_PctIdLog:\r
-                       {\r
-                       const float PctId = (float) m_ptrMSA->GetPctIdentityPair(i, j);\r
-                       Dist[j] = (float) PctIdToMAFFTDist(PctId);\r
-                       break;\r
-                       }\r
-               case DISTANCE_ScoreDist:\r
-                       {\r
-                       double GetScoreDist(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2);\r
-                       Dist[j] = (float) GetScoreDist(*m_ptrMSA, i, j);\r
-                       continue;\r
-                       }\r
-               case DISTANCE_Edit:\r
-                       {\r
-                       const float PctId = (float) m_ptrMSA->GetPctIdentityPair(i, j);\r
-                       if (PctId > 1.0)\r
-                               Quit("Internal error, DISTANCE_Edit, pct id=%.3g", PctId);\r
-                       Dist[j] = (float) 1.0 - PctId;\r
-                       break;\r
-                       }\r
-               default:\r
-                       Quit("DistCalcMSA: Invalid DISTANCE_%u", m_Distance);\r
-                       }\r
-               }\r
-       }\r
-\r
-unsigned DistCalcMSA::GetCount() const\r
-       {\r
-       return m_ptrMSA->GetSeqCount();\r
-       }\r
-\r
-unsigned DistCalcMSA::GetId(unsigned i) const\r
-       {\r
-       return m_ptrMSA->GetSeqId(i);\r
-       }\r
-\r
-const char *DistCalcMSA::GetName(unsigned i) const\r
-       {\r
-       return m_ptrMSA->GetSeqName(i);\r
-       }\r