text: //
  // tweakseq - provides an editor for and interface to various sequence alignment tools
  //
  // The MIT License (MIT)
  //
  // Copyright (c) 2000-2017  Michael J. Wouters, Merridee A. Wouters
  // 
  // Permission is hereby granted, free of charge, to any person obtaining a copy
  // of this software and associated documentation files (the "Software"), to deal
  // in the Software without restriction, including without limitation the rights
  // to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  // copies of the Software, and to permit persons to whom the Software is
  // furnished to do so, subject to the following conditions:
  // 
  // The above copyright notice and this permission notice shall be included in
  // all copies or substantial portions of the Software.
  // 
  // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  // IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  // FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  // AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  // THE SOFTWARE.
  //
  
  #ifndef __AMINO_ACIDS_H_
  #define __AMINO_ACIDS_H_
  
  // A ala alanine
  // B asx asparagine or aspartic acid
  // C cys cysteine
  // D asp aspartic acid
  // E glu glutamic acid
  // F phe phenylalanine
  // G gly glycine
  // H his histidine
  // I ile isoleucine
  // J
  // K lys lysine
  // L leu leucine 
  // M met methionine
  // N asn asparagine
  // O
  // P pro proline
  // Q gln glutamine
  // R arg arginine
  // S ser serine
  // T thr threonine
  // U 
  // V val valine
  // W trp tryptophan
  // X
  // Y tyr tyrosine
  // Z glx glutamine or glutamic acid
  
  
  // Physico-chemical Map
  int PhysicoChemicalColours[26][3]= {
  	{224,224,224}, // A ala alanine
  	{255,0,128},   // B asx asparagine or aspartic acid UNDEFINED use mean
  	{255,255,0},   // C cys cysteine
  	{255,0,0},     // D asp aspartic acid
  	{255,0,0},     // E glu glutamic acid
  	{254,172,0},   // F phe phenylalanine
  	{224,224,224}, // G gly glycine
  	{135,206,235}, // H his histidine
  	{224,224,224}, // I ile isoleucine
  	{0,0,0},       // J
  	{135,206,235}, // K lys lysine
  	{224,224,224}, // L leu leucine 
  	{255,255,0},   // M met methionine
  	{255,0,255},   // N asn asparagine
  	{0,0,0},       // O
  	{0,255,0},     // P pro proline
  	{255,0,255},   // Q gln glutamine
  	{135,206,235}, // R arg arginine
  	{255,0,0},     // S ser serine
  	{255,0,0},     // T thr threonine
  	{0,0,0},       // U 
  	{224,224,224}, // V val valine
  	{254,172,0},   // W trp tryptophan
  	{0,0,0},       // X
  	{254,172,0},   // Y tyr tyrosine
  	{255,0,128},// Z glx glutamine or glutamic acid UNDEFINED use mean
  };
  
  // Taylor Map
  int TaylorColours[26][3] = {
  	{204,255,0}, // A ala alanine [0.8 1 0]
  	{230,0,128}, // B asx asparagine or aspartic acid UNDEFINED use mean
  	{255,255,0}, // C cys cysteine [1 1 0]
  	{255,0,0},   // D asp aspartic acid [1 0 0] 
  	{255,0,102}, // E glu glutamic acid [1 0 0.4]
  	{0,255,102}, // F phe phenylalanine [0 1 0.4]
  	{255,153,0}, // G gly glycine [1 0.6 0]
  	{0,102,255}, // H his histidine [0 0.4 1]
  	{102,255,0}, // I ile isoleucine [0.4 1 0]
  	{0,0,0},     // J
  	{102,0,255}, // K lys lysine [0.4 0 1]
  	{51,255,0},  // L leu leucine [0.2 1 0]
  	{0,255,0},   // M met methionine [0 1 0]
  	{204,0,255}, // N asn asparagine [0.8 0 1]
  	{0,0,0},     // O
  	{255,204,0}, // P pro proline [1 0.8 0]
  	{255,0,204}, // Q gln glutamine [1 0 0.8]
  	{0,0,255},   // R arg arginine [0 0 1]
  	{255,51,0},  // S ser serine [1 0.2 0]
  	{255,102,0}, // T thr threonine [1 0.4 0]
  	{0,0,0},     // U 
  	{153, 255, 0}, // V val valine [0.6 1 0]
  	{0,204,255},  // W trp tryptophan [0 0.8 1]
  	{0,0,0},      // X
  	{0,255,204},  // Y tyr tyrosine [0 1 0.8]
  	{255,0,153}   // Z glx glutamine or glutamic acid UNDEFINED use mean
  };
  
  // RasMol "amino" scheme
  int RasMolColours[26][3]={
  	{200,200,200}, // A ala alanine
  	{190,160,110}, // B asx asparagine or aspartic acid
  	{230,230, 0},  // C cys cysteine
  	{230,230, 10}, // D asp aspartic acid
  	{230,230, 10}, // E glu glutamic acid
  	{ 50, 50,170}, // F phe phenylalanine
  	{235,235,235}, // G gly glycine
  	{130,130,210}, // H his histidine
  	{ 15,130, 15}, // I ile isoleucine
  	{0,0,0},       // J
  	{ 20, 90,255}, // K lys lysine
  	{ 15,130, 15}, // L leu leucine 
  	{230,230, 0},  // M met methionine
  	{ 0,220,220},  // N asn asparagine
  	{0,0,0},       // O
  	{220,150,130}, // P pro proline
  	{ 0,220,220},  // Q gln glutamine
  	{ 20, 90,255}, // R arg arginine
  	{250,150, 0},  // S ser serine
  	{250,150, 0},  // T thr threonine
  	{0,0,0},       // U 
  	{ 15,130, 15}, // V val valine
  	{180, 90,180}, // W trp tryptophan
  	{0,0,0},       // X
  	{ 50, 50,170}, // Y tyr tyrosine
  	{190,160,110}  // Z glx glutamine or glutamic acid
  };
  
  #endif