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/**
* Changes:
*
* 30-03-07,Nigel Brown(EMBL): renamed variable 'AlignProf1ToProf2WithTree' to
* 'AlignProf2ToProf1WithTree' for consistency with clustalx and user
* interface menu naming.
*/
#ifndef CLUSTALQTPARAMS_H
#define CLUSTALQTPARAMS_H
#include <QColor>
#include <QString>
#include "clustalW/alignment/Alignment.h"
#include <vector>
static QString psColorFile = "/usr/share/clustalx/colprot.xml";
static QString psDNAFile = "/usr/share/clustalx/coldna.xml";
static QString psPrintFile = "/usr/share/clustalx/colprint.xml";
static const int BlackAndWhite = 1;
static const int ColorsBackGround = 2;
static const int ColorsLetters = 3;
//static const int UserColors = 4;
static const int MaxColors = 16;
static const int Simple = 0;
static const int Compound = 1;
static const int Sequences = 0;
static const int Profile1 = 1;
static const int Profile2 = 2;
static const int A4 = 0;
static const int A3 = 1;
static const int USLETTER = 2;
static const int PORTRAIT = 1;
static const int LANDSCAPE = 0;
enum FileNameDialogType
{
CompleteAlign, AlignFromTree, RealignSelectedSeqs, RealignSeqRange, DoGuideTreeOnly,
AlignProf2ToProf1, AlignSeqsToProf1, AlignProf2ToProf1WithTree, AlignSeqsToProf1WithTree
};
enum Viewer
{
SequenceViewer, Profile1Viewer, Profile2Viewer
};
enum AlignType
{
Sequence, Profile
};
struct ColorNamePair
{
QColor color;
QString name;
};
struct rangeParams
{
int firstSeq;
int lastSeq;
int firstRes;
int lastRes;
};
struct residueColors
{
int type;
QChar residue;
QString colorName;
int length;
QColor color;
QString consensusConditionList;
};
struct consensusParams
{
QChar consensusName; // Name of the rule
int cutOffPercent;
int length;
QString cutOffList;
};
struct psPrintParams
{
int firstSeq;
int lastSeq;
int nSeqs;
clustalw::Alignment* alignPtr;
bool showLowScoreRes;
clustalw::Array2D<int> lowScoreRes;
bool showExRes;
clustalw::Array2D<int> exRes;
std::vector<int>* histogram;
clustalw::Array2D<QColor>* colorMask;
std::vector<QString> nameHeader; // Should have 2 elements
std::vector<QString> seqHeader; // Should have 2 elements
bool backGroundColors;
};
#endif
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