website/archive/binaries/mac/src/clustalw/src/Clustal.h

   1 /**
   2  * Author: Mark Larkin
   3  *
   4  * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
   5  */
   6 /**
   7  * The class Clustal is the main class in the program. It is used by the interactive
   8  * menu, command line parser and clustal x to perform the algorithmic part of the
   9  * program.
  10  */
  11 #ifndef CLUSTAL_H
  12 #define CLUSTAL_H
  13
  14 #include <string>
  15 #include "general/clustalw.h"
  16 #include "general/utils.h"
  17 #include "general/userparams.h"
  18 #include "fileInput/FileReader.h"
  19 #include "alignment/Alignment.h"
  20 #include "alignment/AlignmentOutput.h"
  21
  22 using namespace std;
  23
  24 namespace clustalw
  25 {
  26
  27 class Clustal
  28 {
  29     public:
  30         /* Functions */
  31         Clustal();
  32         void align(string* phylipName, bool createOutput = true);
  33         void sequencesAlignToProfile(string* phylipName);
  34         void profileAlign(string* p1TreeName, string* p2TreeName);
  35         void doGuideTreeOnly(string* phylipName);
  36         void doAlignUseOldTree(string* phylipName);
  37         void getHelp(string helpPointer, bool printTitle = false);
  38         void getHelp(char helpPointer, bool printTitle = false);
  39         void getFullHelp();
  40         int sequenceInput(bool append, string *offendingSeq);
  41         int profile1Input(string profile1Name = "");
  42         int profile2Input(string profile2Name = "");
  43         int commandLineReadSeq(int firstSeq);
  44         void outputNow();
  45         void phylogeneticTree(string* phylip_name, string* clustal_name, string* dist_name,
  46                               string* nexus_name, string pimName);
  47         void bootstrapTree(string* phylip_name, string* clustal_name, string* nexus_name);
  48         Alignment* getAlignmentPtr(){return &alignmentObj;}
  49         void QTcalcLowScoreSegments(LowScoreSegParams* params);
  50         void QTcalcWeightsForLowScoreSeg(LowScoreSegParams* params);
  51         void QTremoveShortSegments(LowScoreSegParams* params);
  52         void QTSetFileNamesForOutput(AlignmentFileNames fileNames);
  53         bool QTRealignSelectedRange(AlignmentFileNames fileNames, int beginPos, int endPos,
  54                                     bool realignEndGapPen);
  55         void test();
  56         /* Attributes */
  57
  58     private:
  59         /* Functions */
  60         void initInterface();
  61         void calcGapPenaltyMask(int prfLength, vector<char>* mask, vector<char>* gapMask);
  62         bool useExistingGuideTree(int type, string* phylipName, const string& path);
  63         void promptForNewGuideTreeName(int type, string* treeName, const string& path);
  64         //bool removeFirstIterate(Alignment* alnPtr, DistMatrix* distMat);
  65         /* Attributes */
  66         enum{Sequences, Profile1, Profile2};
  67         string sequencesMsg, profile1Msg, profile2Msg;
  68         string newProfile1TreePrompt, newProfile2TreePrompt;
  69
  70         Alignment alignmentObj;
  71         string helpFileName;
  72         int newSeq;
  73         bool checkTree;
  74         AlignmentFileNames QTFileNames;
  75 };
  76 }
  77 #endif