Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/pwpath.h b/website/archive/binaries/mac/src/muscle/pwpath.h
deleted file mode 100644 (file)
index 69628e3..0000000
--- a/website/archive/binaries/mac/src/muscle/pwpath.h
+++ /dev/null
@@ -1,100 +0,0 @@
-#ifndef        PWPath_h\r
-#define PWPath_h\r
-\r
-/***\r
-Each PWEdge in a PWPath specifies a column in a pair-wise (PW) alignment.\r
-"Path" is by analogy with the path through an HMM.\r
-Edge types are:\r
-\r
-       'M'             LetterA + LetterB\r
-       'D'             LetterA + GapB\r
-       'I'             GapB + LetterA\r
-\r
-The mnemomic is Match, Delete, Insert (with respect to A).\r
-Here is a global alignment of sequences A and B.\r
-\r
-       A:      AMQT-F\r
-       B:      -M-TIF\r
-\r
-The path for this example is:\r
-\r
-       Edge    cType   uPrefixLengthA  uPrefixLengthB\r
-       0               D               1                               0\r
-       1               M               2                               1\r
-       2               D               3                               1\r
-       3               M               4                               2\r
-       4               I               4                               3\r
-       5               M               5                               4\r
-\r
-Given the starting positions in each alignment (e.g., column zero for\r
-a global alignment), the prefix length fields are redundant; they are\r
-included only for convenience and as a sanity check, we are not trying\r
-to optimize for speed or space here. We use prefix lengths rather than\r
-column indexes because of the problem of representing the special case\r
-of a gap in the first position.\r
-***/\r
-\r
-class Seq;\r
-class MSA;\r
-class SatchmoParams;\r
-class PW;\r
-class TextFile;\r
-class PWScore;\r
-\r
-class PWEdge\r
-       {\r
-public:\r
-       char cType;\r
-       unsigned uPrefixLengthA;\r
-       unsigned uPrefixLengthB;\r
-\r
-       bool Equal(const PWEdge &e) const\r
-               {\r
-               return uPrefixLengthA == e.uPrefixLengthA &&\r
-                 uPrefixLengthB == e.uPrefixLengthB &&\r
-                 cType == e.cType;\r
-               }\r
-       };\r
-\r
-class PWPath\r
-       {\r
-// Disable compiler defaults\r
-private:\r
-       PWPath &operator=(const PWPath &rhs);\r
-       PWPath(const PWPath &rhs);\r
-\r
-public:\r
-       PWPath();\r
-       virtual ~PWPath();\r
-\r
-public:\r
-       void Clear();\r
-       void FromStr(const char Str[]);\r
-       void Copy(const PWPath &Path);\r
-       void AppendEdge(const PWEdge &Edge);\r
-       void AppendEdge(char cType, unsigned uPrefixLengthA, unsigned uPrefixLengthB);\r
-       void PrependEdge(const PWEdge &Edge);\r
-       unsigned GetEdgeCount() const { return m_uEdgeCount; }\r
-       const PWEdge &GetEdge(unsigned uEdgeIndex) const;\r
-       void Validate(const PWScore &PWS) const;\r
-       void Validate() const;\r
-       void LogMe() const;\r
-       void FromFile(TextFile &File);\r
-       void ToFile(TextFile &File) const;\r
-       void FromMSAPair(const MSA &msaA, const MSA &msaB);\r
-       void AssertEqual(const PWPath &Path) const;\r
-       bool Equal(const PWPath &Path) const;\r
-       unsigned GetMatchCount() const;\r
-       unsigned GetDeleteCount() const;\r
-       unsigned GetInsertCount() const;\r
-\r
-private:\r
-       void ExpandPath(unsigned uAdditionalEdgeCount);\r
-\r
-private:\r
-       unsigned m_uEdgeCount;\r
-       unsigned m_uArraySize;\r
-       PWEdge *m_Edges;\r
-       };\r
-\r
-#endif // PWPath_h\r