Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / multipleAlign / ProfileAlignAlgorithm.h

diff --git a/website/archive/binaries/mac/src/clustalw/src/multipleAlign/ProfileAlignAlgorithm.h b/website/archive/binaries/mac/src/clustalw/src/multipleAlign/ProfileAlignAlgorithm.h
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+++ b/website/archive/binaries/mac/src/clustalw/src/multipleAlign/ProfileAlignAlgorithm.h
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+/**
+ * Author: Mark Larkin
+ * 
+ * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
+ */
+#ifndef PROFILEALIGNALGORITHM_H
+#define PROFILEALIGNALGORITHM_H
+
+#include <vector>
+#include "../alignment/Alignment.h"
+namespace clustalw
+{
+
+class ProfileAlignAlgorithm
+{
+    public:
+  virtual ~ProfileAlignAlgorithm(){};
+
+    /* Functions */
+    virtual int profileAlign(Alignment* alnPtr, DistMatrix* distMat, vector<int>* group, 
+                             int* aligned) = 0;
+    /* Attributes */
+
+    protected:
+    /* Attributes */
+        int prfLength1;
+        int prfLength2;
+        SeqArray seqArray;
+        vector<int> alnWeight;
+        int nseqs1;
+        int nseqs2;     
+    private:
+    /* Functions */
+    
+    /* Attributes */
+       
+};
+
+}
+#endif