Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/clustalw/src/Clustal.h b/website/archive/binaries/mac/src/clustalw/src/Clustal.h
deleted file mode 100644 (file)
index 4a8c4cd..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/Clustal.h
+++ /dev/null
@@ -1,77 +0,0 @@
-/**
- * Author: Mark Larkin
- *
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-/**
- * The class Clustal is the main class in the program. It is used by the interactive
- * menu, command line parser and clustal x to perform the algorithmic part of the
- * program. 
- */
-#ifndef CLUSTAL_H
-#define CLUSTAL_H
-
-#include <string>
-#include "general/clustalw.h"
-#include "general/utils.h"
-#include "general/userparams.h"
-#include "fileInput/FileReader.h"
-#include "alignment/Alignment.h"
-#include "alignment/AlignmentOutput.h"
-
-using namespace std;
-
-namespace clustalw
-{
-
-class Clustal
-{
-    public:
-        /* Functions */
-        Clustal();
-        void align(string* phylipName, bool createOutput = true);
-        void sequencesAlignToProfile(string* phylipName);
-        void profileAlign(string* p1TreeName, string* p2TreeName);
-        void doGuideTreeOnly(string* phylipName);
-        void doAlignUseOldTree(string* phylipName);        
-        void getHelp(string helpPointer, bool printTitle = false);
-        void getHelp(char helpPointer, bool printTitle = false);
-        void getFullHelp();
-        int sequenceInput(bool append, string *offendingSeq);
-        int profile1Input(string profile1Name = "");
-        int profile2Input(string profile2Name = "");
-        int commandLineReadSeq(int firstSeq);
-        void outputNow();
-        void phylogeneticTree(string* phylip_name, string* clustal_name, string* dist_name,
-                              string* nexus_name, string pimName);
-        void bootstrapTree(string* phylip_name, string* clustal_name, string* nexus_name);
-        Alignment* getAlignmentPtr(){return &alignmentObj;} 
-        void QTcalcLowScoreSegments(LowScoreSegParams* params);
-        void QTcalcWeightsForLowScoreSeg(LowScoreSegParams* params);
-        void QTremoveShortSegments(LowScoreSegParams* params);
-        void QTSetFileNamesForOutput(AlignmentFileNames fileNames);
-        bool QTRealignSelectedRange(AlignmentFileNames fileNames, int beginPos, int endPos,
-                                    bool realignEndGapPen);
-        void test();
-        /* Attributes */
-
-    private:
-        /* Functions */
-        void initInterface();
-        void calcGapPenaltyMask(int prfLength, vector<char>* mask, vector<char>* gapMask);
-        bool useExistingGuideTree(int type, string* phylipName, const string& path);
-        void promptForNewGuideTreeName(int type, string* treeName, const string& path);
-        //bool removeFirstIterate(Alignment* alnPtr, DistMatrix* distMat);
-        /* Attributes */
-        enum{Sequences, Profile1, Profile2};
-        string sequencesMsg, profile1Msg, profile2Msg;
-        string newProfile1TreePrompt, newProfile2TreePrompt;
-        
-        Alignment alignmentObj;
-        string helpFileName;
-        int newSeq;
-        bool checkTree;
-        AlignmentFileNames QTFileNames;
-};
-}
-#endif