+++ /dev/null
-/**
- * Author: Mark Larkin
- *
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
- *
- * Changes:
- *
- * 13-02-07,Nigel Brown(EMBL): Increased maximum sequence identifier
- * width MAXNAMES from 30 to 150.
- * 20-12-07, Paul McGettigan: bug #53 change MAXNAMESTODISPLAY back to 10 from 30
- */
-
-#ifndef CLUSTALW_H
-#define CLUSTALW_H
-/* Mark tidy up Nov 2005 */
-/*********************CLUSTALW.H*********************************************/
-/****************************************************************************/
-
-/*
- *** AW NOT NEEDED ANYMORE since 2.0.9
- *** done via including config.h(clustalw) or DEFINE(clustalx)
- * Main header file for ClustalW. Uncomment ONE of the following 4 lines
- * depending on which compiler you wish to use.
- */
-/* NOT SUPPORTED #define VMS 1 VAX or ALPHA VMS */
-/* Think_C for Macintosh */
-//#define MAC 1 */
-/* Turbo C for PC's */
-// #define WINDOWS 1
-/* unix */
-//#define UNIX 1
-// d
-
-
-#define DEBUGFULL 0
-const bool DEBUGLOG = false;
-/***************************************************************************/
-/***************************************************************************/
-
-
-#include "general.h"
-#include "Array2D.h"
-#include "SquareMat.h"
-#include "SymMatrix.h"
-#include <vector>
-#include <string>
-using namespace std;
-namespace clustalw
-{
-
-typedef SymMatrix DistMatrix;
-typedef std::vector<vector <int> > TreeGroups;
-
-struct TreeNames
-{
- string phylipName;
- string clustalName;
- string distName;
- string nexusName;
- string pimName;
-};
-
-struct AlignmentFileNames
-{
- string treeFile;
- string profile2TreeFile;
- string clustalFile;
- string nrbfFile;
- string gcgFile;
- string phylipFile;
- string gdeFile;
- string nexusFile;
- string fastaFile;
-};
-
-struct TreeNode
-{
- // phylogenetic tree structure
- struct TreeNode *left;
- struct TreeNode *right;
- struct TreeNode *parent;
- float dist;
- int leaf;
- int order;
- string name;
-};
-
-struct PhyloTree
-{
- TreeGroups treeDesc;
- vector<double> leftBranch;
- vector<double> rightBranch;
-};
-struct SeqInfo
-{
- int firstSeq;
- int lastSeq;
- int numSeqs;
-};
-
-struct LowScoreSegParams
-{
- int firstSeq;
- int nSeqs;
- int lastSeq;
- int nCols;
- vector<int>* seqWeight;
- Array2D<int>* lowScoreRes;
- bool seqWeightCalculated;
-};
-/* Global constants */
-const int extraEndElemNum = 2;
-const int ENDALN = 127;
-const int OK = -200;
-const int CANNOTOPENFILE = -300;
-const int NOSEQUENCESINFILE = -400;
-const int OTHERERROR = -500;
-const int ALLNAMESNOTDIFFERENT = -600;
-const int MUSTREADINPROFILE1FIRST = -700;
-const int EMPTYSEQUENCE = -800;
-const int SEQUENCETOOBIG = -900;
-const int BADFORMAT = -1000;
-
-const int AABLOSUM = 0;
-const int AAPAM = 1;
-const int AAGONNET = 2;
-const int AAIDENTITY = 3;
-const int AAUSERDEFINED = 4;
-
-const int PWAABLOSUM = 0;
-const int PWAAPAM = 1;
-const int PWAAGONNET = 2;
-const int PWAAIDENTITY = 3;
-const int PWAAUSER = 4;
-
-const int DNAIUB = 0;
-const int DNACLUSTALW = 1;
-const int DNAUSERDEFINED = 2;
-
-const int AAHISTIDENTITY = 0;
-const int AAHISTGONNETPAM80 = 1;
-const int AAHISTGONNETPAM120 = 2;
-const int AAHISTGONNETPAM250 = 3;
-const int AAHISTGONNETPAM350 = 4;
-const int AAHISTUSER = 5;
-
-const int QTAASEGGONNETPAM80 = 0;
-const int QTAASEGGONNETPAM120 = 1;
-const int QTAASEGGONNETPAM250 = 2;
-const int QTAASEGGONNETPAM350 = 3;
-const int QTAASEGUSER = 4;
-
-const int MAXHYDRESIDUES = 9; // Only allowing 9 hyd residue choices
-const int Protein = 0;
-const int DNA = 1;
-const int Pairwise = 0;
-const int MultipleAlign = 1;
-
-const int OUTSECST = 0;
-const int OUTGAP = 1;
-const int OUTBOTH = 2;
-const int OUTNONE = 3;
-
-const int MAXNAMES = 150; /* Max chars read for seq. names */ //nige, was 30
-//const int MAXNAMESTODISPLAY = 30; // Used for printout. Mark 18-7-07
-//const int MAXNAMESTODISPLAY = 10; // Bug #53. Paul 20-12-07
-const int MAXNAMESTODISPLAY = 30; //Paul replicate 1.83 behavour 9-2-08
-const int MINNAMESTODISPLAY = 10; //Paul replicate 1.83 behavour 9-2-08
-const int MAXTITLES = 60; /* Title length */
-const int FILENAMELEN = 256; /* Max. file name length */
-
-const int UNKNOWN = 0;
-const int EMBLSWISS = 1;
-const int PIR = 2;
-const int PEARSON = 3;
-const int GDE = 4;
-const int CLUSTAL = 5; /* DES */
-const int MSF = 6; /* DES */
-const int RSF = 7; /* JULIE */
-const int USER = 8; /* DES */
-const int PHYLIP = 9; /* DES */
-const int NEXUS = 10; /* DES */
-const int FASTA = 11; /* Ramu */
-
-const int NONE = 0;
-const int SECST = 1;
-const int GMASK = 2;
-
-const int PROFILE = 0;
-const int SEQUENCE = 1;
-
-const int BS_NODE_LABELS = 2;
-const int BS_BRANCH_LABELS = 1;
-
-const int PAGE_LEN = 22; /* Number of lines of help sent to screen */
-
-const int PAGEWIDTH = 80; /* maximum characters on output file page */
-const int LINELENGTH = 60; /* Output file line length */
-const int GCG_LINELENGTH = 50;
-
-const int NJ = 1;
-const int UPGMA = 2;
-
-const int ALIGNMENT = 1;
-const int TREE = 2;
-
-const int MinIdentifier = 1;
-
-const string VALID_COMMAND_SEP = "-/";
-
-#ifdef OS_MAC
- const char default_commandsep = '-';
- const char DIRDELIM = '/';
- const int INT_SCALE_FACTOR = 100; /* Scaling factor to convert float to integer
- for profile scores */
-
-#elif OS_WINDOWS
- const char default_commandsep = '/';
- const char DIRDELIM = '\\';
- const int INT_SCALE_FACTOR = 100; /* Scaling factor to convert float to integer
- for profile scores */
-
-#elif OS_UNIX
- const char default_commandsep = '-';
- const char DIRDELIM = '/';
- const int INT_SCALE_FACTOR = 1000; /* Scaling factor to convert float to integer
- for profile scores */
-#endif
-
-
-const int NUMRES = 32; /* max size of comparison matrix */
-const int INPUT = 0;
-const int ALIGNED = 1;
-
-const int LEFT = 1;
-const int RIGHT = 2;
-
-const int NODE = 0;
-const int LEAF = 1;
-
-const int GAPCOL = 32; /* position of gap open penalty in profile */
-const int LENCOL = 33; /* position of gap extension penalty in profile */
-
-typedef struct
-{
- /* Holds values for the pairwise scales */
- float gapOpenScale;
- float gapExtendScale;
- int intScale;
-}PairScaleValues;
-
-typedef struct
-{
- float scale;
- float intScale;
-}PrfScaleValues;
-
-typedef struct node
-{
- /* phylogenetic tree structure */
- struct node *left;
- struct node *right;
- struct node *parent;
- float dist;
- int leaf;
- int order;
- char name[64];
-} stree, *treeptr;
-
-typedef struct
-{
- char title[30];
- char string[30];
-} MatMenuEntry;
-
-typedef struct
-{
- int noptions;
- MatMenuEntry opt[10];
-} MatMenu;
-
-const int MAXMAT = 10;
-
-typedef struct
-{
- int llimit;
- int ulimit;
- vector<short>* matptr;
- vector<short>* AAXref;
-} SeriesMat;
-
-/*
- * UserMatSeries holds the number of matrices in the series and
- */
-typedef struct
-{
- int nmat;
- SeriesMat mat[MAXMAT];
-} UserMatrixSeries;
-
-}
-#endif
-
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