Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / muscle / diaglist.h

diff --git a/website/archive/binaries/mac/src/muscle/diaglist.h b/website/archive/binaries/mac/src/muscle/diaglist.h
deleted file mode 100644 (file)
index a4464d5..0000000
--- a/website/archive/binaries/mac/src/muscle/diaglist.h
+++ /dev/null
@@ -1,89 +0,0 @@
-#ifndef diaglist_h\r
-#define diaglist_h\r
-\r
-const unsigned EMPTY = (unsigned) ~0;\r
-const unsigned MAX_DIAGS = 1024;\r
-\r
-struct Diag\r
-       {\r
-       unsigned m_uStartPosA;\r
-       unsigned m_uStartPosB;\r
-       unsigned m_uLength;\r
-       };\r
-\r
-struct Rect\r
-       {\r
-       unsigned m_uStartPosA;\r
-       unsigned m_uStartPosB;\r
-       unsigned m_uLengthA;\r
-       unsigned m_uLengthB;\r
-       };\r
-\r
-class DiagList\r
-       {\r
-public:\r
-       DiagList()\r
-               {\r
-               m_uCount = 0;\r
-               }\r
-       ~DiagList()\r
-               {\r
-               Free();\r
-               }\r
-\r
-public:\r
-// Creation\r
-       void Clear()\r
-               {\r
-               Free();\r
-               }\r
-       void FromPath(const PWPath &Path);\r
-       void Add(const Diag &d);\r
-       void Add(unsigned uStartPosA, unsigned uStartPosB, unsigned uLength);\r
-       void DeleteIncompatible();\r
-\r
-// Accessors\r
-       unsigned GetCount() const\r
-               {\r
-               return m_uCount;\r
-               }\r
-       const Diag &Get(unsigned uIndex) const;\r
-\r
-// Operations\r
-       void Sort();\r
-       void Copy(const DiagList &DL);\r
-\r
-// Query\r
-       // returns true iff given diagonal is included in the list\r
-       // in whole or in part.\r
-       bool NonZeroIntersection(const Diag &d) const;\r
-       bool IsSorted() const;\r
-\r
-// Diagnostics\r
-       void LogMe() const;\r
-\r
-private:\r
-       void Free()\r
-               {\r
-               m_uCount = 0;\r
-               }\r
-\r
-private:\r
-       unsigned m_uCount;\r
-       Diag m_Diags[MAX_DIAGS];\r
-       };\r
-\r
-unsigned DiagOverlap(const Diag &d1, const Diag &d2);\r
-unsigned DiagOverlapA(const Diag &d1, const Diag &d2);\r
-unsigned DiagOverlapB(const Diag &d1, const Diag &d2);\r
-unsigned DiagBreak(const Diag &d1, const Diag &d2);\r
-bool DiagCompatible(const Diag &d1, const Diag &d2);\r
-void CheckDiags(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
-  unsigned uLengthB, const MSA &msaA, const MSA &msaB, const PWPath &Path);\r
-void FindDiags(const ProfPos *PX, unsigned uLengthX, const ProfPos *PY,\r
-  unsigned uLengthY, DiagList &DL);\r
-void FindDiagsNuc(const ProfPos *PX, unsigned uLengthX, const ProfPos *PY,\r
-  unsigned uLengthY, DiagList &DL);\r
-void MergeDiags(DiagList &DL);\r
-\r
-#endif // diaglist_h\r