site/j2s/jalview/schemes/ClustalxColourScheme.js

   1 Clazz.declarePackage ("jalview.schemes");\r
   2 Clazz.load (["jalview.schemes.ResidueColourScheme", "java.util.HashMap"], ["jalview.schemes.ConsensusColour", "$.ClustalxColourScheme"], ["jalview.schemes.Consensus", "$.ResidueProperties", "java.awt.Color"], function () {\r
   3 c$ = Clazz.decorateAsClass (function () {\r
   4 this.cons2 = null;\r
   5 this.colours = null;\r
   6 this.residueColour = null;\r
   7 this.size = 0;\r
   8 this.conses = null;\r
   9 this.includeGaps = true;\r
  10 Clazz.instantialize (this, arguments);\r
  11 }, jalview.schemes, "ClustalxColourScheme", jalview.schemes.ResidueColourScheme);\r
  12 Clazz.prepareFields (c$, function () {\r
  13 this.conses =  new Array (32);\r
  14 });\r
  15 Clazz.makeConstructor (c$, \r
  16 function (alignment, hiddenReps) {\r
  17 Clazz.superConstructor (this, jalview.schemes.ClustalxColourScheme, []);\r
  18 this.alignmentChanged (alignment, hiddenReps);\r
  19 }, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");\r
  20 Clazz.overrideMethod (c$, "alignmentChanged", \r
  21 function (alignment, hiddenReps) {\r
  22 var maxWidth = alignment.getWidth ();\r
  23 var seqs = alignment.getSequences (hiddenReps);\r
  24 this.cons2 =  Clazz.newIntArray (maxWidth, 24, 0);\r
  25 this.includeGaps = this.isIncludeGaps ();\r
  26 var start = 0;\r
  27 for (var j = 0; j < 24; j++) {\r
  28 for (var i = 0; i < maxWidth; i++) {\r
  29 this.cons2[i][j] = 0;\r
  30 }\r
  31 }\r
  32 var res;\r
  33 var i;\r
  34 var j = 0;\r
  35 var seq;\r
  36 for (var sq, $sq = seqs.iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {\r
  37 seq = sq.getSequence ();\r
  38 var end_j = seq.length - 1;\r
  39 for (i = start; i <= end_j; i++) {\r
  40 if ((seq.length - 1) < i) {\r
  41 res = 23;\r
  42 } else {\r
  43 res = jalview.schemes.ResidueProperties.aaIndex[seq[i].charCodeAt (0)];\r
  44 }this.cons2[i][res]++;\r
  45 }\r
  46 j++;\r
  47 }\r
  48 this.size = seqs.size ();\r
  49 this.makeColours ();\r
  50 }, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");\r
  51 Clazz.defineMethod (c$, "makeColours", \r
  52 function () {\r
  53 this.conses[0] =  new jalview.schemes.Consensus ("WLVIMAFCYHP", 60);\r
  54 this.conses[1] =  new jalview.schemes.Consensus ("WLVIMAFCYHP", 80);\r
  55 this.conses[2] =  new jalview.schemes.Consensus ("ED", 50);\r
  56 this.conses[3] =  new jalview.schemes.Consensus ("KR", 60);\r
  57 this.conses[4] =  new jalview.schemes.Consensus ("G", 50);\r
  58 this.conses[5] =  new jalview.schemes.Consensus ("N", 50);\r
  59 this.conses[6] =  new jalview.schemes.Consensus ("QE", 50);\r
  60 this.conses[7] =  new jalview.schemes.Consensus ("P", 50);\r
  61 this.conses[8] =  new jalview.schemes.Consensus ("TS", 50);\r
  62 this.conses[26] =  new jalview.schemes.Consensus ("A", 85);\r
  63 this.conses[27] =  new jalview.schemes.Consensus ("C", 85);\r
  64 this.conses[10] =  new jalview.schemes.Consensus ("E", 85);\r
  65 this.conses[11] =  new jalview.schemes.Consensus ("F", 85);\r
  66 this.conses[12] =  new jalview.schemes.Consensus ("G", 85);\r
  67 this.conses[13] =  new jalview.schemes.Consensus ("H", 85);\r
  68 this.conses[14] =  new jalview.schemes.Consensus ("I", 85);\r
  69 this.conses[15] =  new jalview.schemes.Consensus ("L", 85);\r
  70 this.conses[16] =  new jalview.schemes.Consensus ("M", 85);\r
  71 this.conses[17] =  new jalview.schemes.Consensus ("N", 85);\r
  72 this.conses[18] =  new jalview.schemes.Consensus ("P", 85);\r
  73 this.conses[19] =  new jalview.schemes.Consensus ("Q", 85);\r
  74 this.conses[20] =  new jalview.schemes.Consensus ("R", 85);\r
  75 this.conses[21] =  new jalview.schemes.Consensus ("S", 85);\r
  76 this.conses[22] =  new jalview.schemes.Consensus ("T", 85);\r
  77 this.conses[23] =  new jalview.schemes.Consensus ("V", 85);\r
  78 this.conses[24] =  new jalview.schemes.Consensus ("W", 85);\r
  79 this.conses[25] =  new jalview.schemes.Consensus ("Y", 85);\r
  80 this.conses[28] =  new jalview.schemes.Consensus ("K", 85);\r
  81 this.conses[29] =  new jalview.schemes.Consensus ("D", 85);\r
  82 this.conses[30] =  new jalview.schemes.Consensus ("G", 0);\r
  83 this.conses[31] =  new jalview.schemes.Consensus ("P", 0);\r
  84 this.colours =  new Array (11);\r
  85 var tmp8 =  new Array (1);\r
  86 tmp8[0] = this.conses[30];\r
  87 this.colours[7] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.ORANGE), tmp8);\r
  88 var tmp9 =  new Array (1);\r
  89 tmp9[0] = this.conses[31];\r
  90 this.colours[8] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.YELLOW), tmp9);\r
  91 var tmp10 =  new Array (1);\r
  92 tmp10[0] = this.conses[27];\r
  93 this.colours[9] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.PINK), tmp8);\r
  94 var tmp1 =  new Array (14);\r
  95 tmp1[0] = this.conses[0];\r
  96 tmp1[1] = this.conses[1];\r
  97 tmp1[2] = this.conses[26];\r
  98 tmp1[3] = this.conses[27];\r
  99 tmp1[4] = this.conses[11];\r
 100 tmp1[5] = this.conses[13];\r
 101 tmp1[6] = this.conses[14];\r
 102 tmp1[7] = this.conses[15];\r
 103 tmp1[8] = this.conses[16];\r
 104 tmp1[9] = this.conses[23];\r
 105 tmp1[10] = this.conses[24];\r
 106 tmp1[11] = this.conses[25];\r
 107 tmp1[12] = this.conses[18];\r
 108 tmp1[13] = this.conses[19];\r
 109 this.colours[0] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.BLUE), tmp1);\r
 110 this.colours[10] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.CYAN), tmp1);\r
 111 var tmp2 =  new Array (5);\r
 112 tmp2[0] = this.conses[8];\r
 113 tmp2[1] = this.conses[21];\r
 114 tmp2[2] = this.conses[22];\r
 115 tmp2[3] = this.conses[0];\r
 116 tmp2[4] = this.conses[1];\r
 117 this.colours[1] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.GREEN), tmp2);\r
 118 var tmp3 =  new Array (3);\r
 119 tmp3[0] = this.conses[17];\r
 120 tmp3[1] = this.conses[29];\r
 121 tmp3[2] = this.conses[5];\r
 122 this.colours[2] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.GREEN), tmp3);\r
 123 var tmp4 =  new Array (6);\r
 124 tmp4[0] = this.conses[6];\r
 125 tmp4[1] = this.conses[19];\r
 126 tmp4[2] = this.conses[22];\r
 127 tmp4[3] = this.conses[3];\r
 128 tmp4[4] = this.conses[28];\r
 129 tmp4[5] = this.conses[20];\r
 130 this.colours[3] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.GREEN), tmp4);\r
 131 var tmp5 =  new Array (4);\r
 132 tmp5[0] = this.conses[3];\r
 133 tmp5[1] = this.conses[28];\r
 134 tmp5[2] = this.conses[20];\r
 135 tmp5[3] = this.conses[19];\r
 136 this.colours[4] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.RED), tmp5);\r
 137 var tmp6 =  new Array (6);\r
 138 tmp6[0] = this.conses[3];\r
 139 tmp6[1] = this.conses[29];\r
 140 tmp6[2] = this.conses[10];\r
 141 tmp6[3] = this.conses[6];\r
 142 tmp6[4] = this.conses[19];\r
 143 tmp6[5] = this.conses[2];\r
 144 this.colours[5] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.MAGENTA), tmp6);\r
 145 var tmp7 =  new Array (5);\r
 146 tmp7[0] = this.conses[3];\r
 147 tmp7[1] = this.conses[29];\r
 148 tmp7[2] = this.conses[10];\r
 149 tmp7[3] = this.conses[17];\r
 150 tmp7[4] = this.conses[2];\r
 151 this.colours[6] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.MAGENTA), tmp7);\r
 152 this.residueColour =  new Array (20);\r
 153 this.residueColour[0] = this.colours[0];\r
 154 this.residueColour[1] = this.colours[4];\r
 155 this.residueColour[2] = this.colours[2];\r
 156 this.residueColour[3] = this.colours[6];\r
 157 this.residueColour[4] = this.colours[0];\r
 158 this.residueColour[5] = this.colours[3];\r
 159 this.residueColour[6] = this.colours[5];\r
 160 this.residueColour[7] = this.colours[7];\r
 161 this.residueColour[8] = this.colours[10];\r
 162 this.residueColour[9] = this.colours[0];\r
 163 this.residueColour[10] = this.colours[0];\r
 164 this.residueColour[11] = this.colours[4];\r
 165 this.residueColour[12] = this.colours[0];\r
 166 this.residueColour[13] = this.colours[0];\r
 167 this.residueColour[14] = this.colours[8];\r
 168 this.residueColour[15] = this.colours[1];\r
 169 this.residueColour[16] = this.colours[1];\r
 170 this.residueColour[17] = this.colours[0];\r
 171 this.residueColour[18] = this.colours[10];\r
 172 this.residueColour[19] = this.colours[0];\r
 173 });\r
 174 Clazz.defineMethod (c$, "findColour", \r
 175 function (c) {\r
 176 return java.awt.Color.pink;\r
 177 }, "~S");\r
 178 Clazz.defineMethod (c$, "findColour", \r
 179 function (c, j, seq) {\r
 180 var currentColour;\r
 181 if (this.cons2.length <= j || (this.includeGaps && this.threshold != 0 && !this.aboveThreshold (c, j))) {\r
 182 return java.awt.Color.white;\r
 183 }var i = jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)];\r
 184 currentColour = java.awt.Color.white;\r
 185 if (i > 19) {\r
 186 return currentColour;\r
 187 }for (var k = 0; k < this.residueColour[i].conses.length; k++) {\r
 188 if (this.residueColour[i].conses[k].isConserved (this.cons2, j, this.size, this.includeGaps)) {\r
 189 currentColour = this.residueColour[i].c;\r
 190 }}\r
 191 if (i == 4) {\r
 192 if (this.conses[27].isConserved (this.cons2, j, this.size, this.includeGaps)) {\r
 193 currentColour = jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.PINK);\r
 194 }}if (this.conservationColouring) {\r
 195 currentColour = this.applyConservation (currentColour, j);\r
 196 }return currentColour;\r
 197 }, "~S,~N,jalview.datamodel.SequenceI");\r
 198 Clazz.defineMethod (c$, "isIncludeGaps", \r
 199 function () {\r
 200 return this.includeGaps;\r
 201 });\r
 202 Clazz.defineMethod (c$, "setIncludeGaps", \r
 203 function (includeGaps) {\r
 204 this.includeGaps = includeGaps;\r
 205 }, "~B");\r
 206 Clazz.overrideMethod (c$, "applyTo", \r
 207 function (sg, hiddenRepSequences) {\r
 208 var css =  new jalview.schemes.ClustalxColourScheme (sg, hiddenRepSequences);\r
 209 css.includeGaps = this.includeGaps;\r
 210 return css;\r
 211 }, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");\r
 212 Clazz.defineStatics (c$,\r
 213 "EIGHTY_FIVE", 85,\r
 214 "FIFTY", 50,\r
 215 "EIGHTY", 80,\r
 216 "SIXTY", 60);\r
 217 c$.colhash = c$.prototype.colhash =  new java.util.HashMap ();\r
 218 {\r
 219 jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.RED,  new java.awt.Color (0.9, 0.2, 0.1));\r
 220 jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.BLUE,  new java.awt.Color (0.5, 0.7, 0.9));\r
 221 jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.GREEN,  new java.awt.Color (0.1, 0.8, 0.1));\r
 222 jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.ORANGE,  new java.awt.Color (0.9, 0.6, 0.3));\r
 223 jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.CYAN,  new java.awt.Color (0.1, 0.7, 0.7));\r
 224 jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.PINK,  new java.awt.Color (0.9, 0.5, 0.5));\r
 225 jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.MAGENTA,  new java.awt.Color (0.8, 0.3, 0.8));\r
 226 jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.YELLOW,  new java.awt.Color (0.8, 0.8, 0.0));\r
 227 }c$ = Clazz.decorateAsClass (function () {\r
 228 this.conses = null;\r
 229 this.c = null;\r
 230 Clazz.instantialize (this, arguments);\r
 231 }, jalview.schemes, "ConsensusColour");\r
 232 Clazz.makeConstructor (c$, \r
 233 function (c, conses) {\r
 234 this.conses = conses;\r
 235 this.c = c;\r
 236 }, "java.awt.Color,~A");\r
 237 });\r