Mac binaries

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

diff --git a/website/archive/binaries/mac/src/clustalw/src/multipleAlign/LowScoreSegProfile.h b/website/archive/binaries/mac/src/clustalw/src/multipleAlign/LowScoreSegProfile.h
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+/**
+ * Author: Mark Larkin
+ * 
+ * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
+ */
+/**
+ * NOTE: This profile is not used in the multiple alignment part. It is used for the
+ * the clustal Qt part. It is used in the calculation of low scoring segments.
+ */
+#ifndef LOWSCORESEGPROFILE_H
+#define LOWSCORESEGPROFILE_H
+
+#include "../alignment/Alignment.h"
+
+namespace clustalw
+{
+
+class LowScoreSegProfile
+{
+    public:
+        /* Functions */
+        LowScoreSegProfile(int prfLen, int firstS, int lastS);
+        void calcLowScoreSegProfile(const SeqArray* seqArray, 
+                                int matrix[NUMRES][NUMRES], vector<int>* seqWeight);
+        const SeqArray* getProfilePtr(){return &profile;};                        
+        /* Attributes */
+
+    protected:
+        /* Functions */
+
+        /* Attributes */
+        SeqArray profile; 
+        int prfLength;
+        int firstSeq, lastSeq;
+    private:
+        /* Functions */
+
+        /* Attributes */
+
+};
+
+}
+#endif