Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / alignment / AlignmentOutput.h

diff --git a/website/archive/binaries/mac/src/clustalw/src/alignment/AlignmentOutput.h b/website/archive/binaries/mac/src/clustalw/src/alignment/AlignmentOutput.h
deleted file mode 100644 (file)
index 5a75dbf..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/alignment/AlignmentOutput.h
+++ /dev/null
@@ -1,98 +0,0 @@
-/**
- * Author: Mark Larkin
- * 
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-/*
- * The class AlignmentOutput is used to output the Alignment in all the different
- * formats that have been selected. It will output all the different file types if
- * these have been selected from the menu or the commandline.
- * To use this class we must call openAlignmentOutput first. Then we call the function
- * createAlignmentOutput with an Alignment to be output and the first and last sequence
- * to be output as well. 
- */
-#ifndef ALIGNMENTOUTPUT_H
-#define ALIGNMENTOUTPUT_H
-
-#include <string>
-#include <vector>
-#include <fstream>
-#include <memory>
-#include <sstream>
-#include <exception>
-#include <cassert>
-#include "Alignment.h"
-
-
-namespace clustalw
-{
-
-typedef struct rangeNum 
-{
-    int start;
-    int end;
-} rangeNum;
-
-typedef struct outputRegion 
-{
-    int _firstSeq;
-    int _lastSeq;
-    int _firstRes;
-    int _lastRes;
-} outputRegion;
-
-class AlignmentOutput
-{
-    public:
-        /* Functions */
-        AlignmentOutput();
-        bool openAlignmentOutput(string path);
-        bool QTOpenFilesForOutput(AlignmentFileNames fileNames);
-        void createAlignmentOutput(Alignment* alignPtr, int firstSeq, int lastSeq);
-        void printSecStructMask(int prfLength, vector<char>* mask, vector<char>* structMask);
-        /* Attributes */
-
-    private:
-        /* Functions */
-        void fastaOut(Alignment* alignPtr, outputRegion partToOutput);
-        void clustalOut(Alignment* alignPtr, outputRegion partToOutput);
-        void gcgOut(Alignment* alignPtr, outputRegion partToOutput);
-        void nexusOut(Alignment* alignPtr, outputRegion partToOutput);
-        void phylipOut(Alignment* alignPtr, outputRegion partToOutput);
-        void nbrfOut(Alignment* alignPtr, outputRegion partToOutput);
-        void gdeOut(Alignment* alignPtr, outputRegion partToOutput);
-        string nameonly(string s);
-        
-        void findRangeValues(Alignment* alignPtr, rangeNum *rnum, int firstRes, int lastRes, 
-                             int firstSeq);
-        bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
-        string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path, 
-                              string fileExtension);
-        int SeqGCGCheckSum(vector<char>* sequence, int length);
-        void showAlign();
-        /* Attributes */
-   
-        auto_ptr<ofstream> clustalOutFile;
-        auto_ptr<ofstream> gcgOutFile;
-        auto_ptr<ofstream> nbrfOutFile;
-        auto_ptr<ofstream> phylipOutFile;
-        auto_ptr<ofstream> gdeOutFile;
-        auto_ptr<ofstream> nexusOutFile;
-        auto_ptr<ofstream> fastaOutFile;
-        
-        string clustalOutName;
-        string gcgOutName;
-        string phylipOutName;
-        string nbrfOutName;
-        string gdeOutName;
-        string nexusOutName;
-        string fastaOutName;
-        vector<string> strongGroup; 
-        vector<string> weakGroup;
-        int clusSecStructOffset;
-        int clusSequenceOffset;        
-};
-
-}
-#endif
-