bin/jalview/renderer/seqfeatures/FeatureRenderer.js

   1 Clazz.declarePackage ("jalview.renderer.seqfeatures");\r
   2 Clazz.load (["jalview.viewmodel.seqfeatures.FeatureRendererModel"], "jalview.renderer.seqfeatures.FeatureRenderer", ["jalview.util.Comparison", "java.awt.AlphaComposite", "$.Color", "java.awt.image.BufferedImage", "java.lang.Float"], function () {\r
   3 c$ = Clazz.decorateAsClass (function () {\r
   4 this.fm = null;\r
   5 this.charOffset = 0;\r
   6 this.offscreenRender = false;\r
   7 this.lastSeq = null;\r
   8 this.s = '\0';\r
   9 this.i = 0;\r
  10 this.av_charHeight = 0;\r
  11 this.av_charWidth = 0;\r
  12 this.av_validCharWidth = false;\r
  13 this.av_isShowSeqFeatureHeight = false;\r
  14 this.offscreenImage = null;\r
  15 this.lastSequenceFeatures = null;\r
  16 this.sfSize = 0;\r
  17 this.sfindex = 0;\r
  18 this.spos = 0;\r
  19 this.epos = 0;\r
  20 this.transparencyAvailable = true;\r
  21 Clazz.instantialize (this, arguments);\r
  22 }, jalview.renderer.seqfeatures, "FeatureRenderer", jalview.viewmodel.seqfeatures.FeatureRendererModel);\r
  23 Clazz.defineMethod (c$, "updateAvConfig", \r
  24 function () {\r
  25 this.av_charHeight = this.av.getCharHeight ();\r
  26 this.av_charWidth = this.av.getCharWidth ();\r
  27 this.av_validCharWidth = this.av.isValidCharWidth ();\r
  28 this.av_isShowSeqFeatureHeight = this.av.isShowSequenceFeaturesHeight ();\r
  29 });\r
  30 Clazz.defineMethod (c$, "renderFeature", \r
  31 function (g, seq, fstart, fend, featureColour, start, end, y1) {\r
  32 this.updateAvConfig ();\r
  33 if (((fstart <= end) && (fend >= start))) {\r
  34 if (fstart < start) {\r
  35 fstart = start;\r
  36 }if (fend >= end) {\r
  37 fend = end;\r
  38 }var pady = (y1 + this.av_charHeight) - Clazz.doubleToInt (this.av_charHeight / 5);\r
  39 for (this.i = fstart; this.i <= fend; this.i++) {\r
  40 this.s = seq.getCharAt (this.i);\r
  41 if (jalview.util.Comparison.isGap (this.s)) {\r
  42 continue;\r
  43 }g.setColor (featureColour);\r
  44 g.fillRect ((this.i - start) * this.av_charWidth, y1, this.av_charWidth, this.av_charHeight);\r
  45 if (this.offscreenRender || !this.av_validCharWidth) {\r
  46 continue;\r
  47 }g.setColor (java.awt.Color.white);\r
  48 this.charOffset = Clazz.doubleToInt ((this.av_charWidth - this.fm.charWidth (this.s)) / 2);\r
  49 g.drawString (String.valueOf (this.s), this.charOffset + (this.av_charWidth * (this.i - start)), pady);\r
  50 }\r
  51 }}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,java.awt.Color,~N,~N,~N");\r
  52 Clazz.defineMethod (c$, "renderScoreFeature", \r
  53 function (g, seq, fstart, fend, featureColour, start, end, y1, bs) {\r
  54 this.updateAvConfig ();\r
  55 if (((fstart <= end) && (fend >= start))) {\r
  56 if (fstart < start) {\r
  57 fstart = start;\r
  58 }if (fend >= end) {\r
  59 fend = end;\r
  60 }var pady = (y1 + this.av_charHeight) - Clazz.doubleToInt (this.av_charHeight / 5);\r
  61 var ystrt = 0;\r
  62 var yend = this.av_charHeight;\r
  63 if (bs[0] != 0) {\r
  64 if (bs[1] < 128) {\r
  65 yend = Clazz.doubleToInt (this.av_charHeight * (128 - bs[1]) / 512);\r
  66 ystrt = this.av_charHeight - Clazz.doubleToInt (yend / 2);\r
  67 } else {\r
  68 ystrt = Clazz.doubleToInt (this.av_charHeight / 2);\r
  69 yend = Clazz.doubleToInt (this.av_charHeight * (bs[1] - 128) / 512);\r
  70 }} else {\r
  71 yend = Clazz.doubleToInt (this.av_charHeight * bs[1] / 255);\r
  72 ystrt = this.av_charHeight - yend;\r
  73 }for (this.i = fstart; this.i <= fend; this.i++) {\r
  74 this.s = seq.getCharAt (this.i);\r
  75 if (jalview.util.Comparison.isGap (this.s)) {\r
  76 continue;\r
  77 }g.setColor (featureColour);\r
  78 var x = (this.i - start) * this.av_charWidth;\r
  79 g.drawRect (x, y1, this.av_charWidth, this.av_charHeight);\r
  80 g.fillRect (x, y1 + ystrt, this.av_charWidth, yend);\r
  81 if (this.offscreenRender || !this.av_validCharWidth) {\r
  82 continue;\r
  83 }g.setColor (java.awt.Color.black);\r
  84 this.charOffset = Clazz.doubleToInt ((this.av_charWidth - this.fm.charWidth (this.s)) / 2);\r
  85 g.drawString (String.valueOf (this.s), this.charOffset + (this.av_charWidth * (this.i - start)), pady);\r
  86 }\r
  87 }}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,java.awt.Color,~N,~N,~N,~A");\r
  88 Clazz.defineMethod (c$, "findFeatureColour", \r
  89 function (initialCol, seq, res) {\r
  90 return  new java.awt.Color (this.findFeatureColour (initialCol.getRGB (), seq, res));\r
  91 }, "java.awt.Color,jalview.datamodel.SequenceI,~N");\r
  92 Clazz.defineMethod (c$, "findFeatureColour", \r
  93 function (initialCol, seq, column) {\r
  94 if (!this.av.isShowSequenceFeatures ()) {\r
  95 return initialCol;\r
  96 }var sequenceFeatures = seq.getSequenceFeatures ();\r
  97 if (seq !== this.lastSeq) {\r
  98 this.lastSeq = seq;\r
  99 this.lastSequenceFeatures = sequenceFeatures;\r
 100 if (this.lastSequenceFeatures != null) {\r
 101 this.sfSize = this.lastSequenceFeatures.length;\r
 102 }} else {\r
 103 if (this.lastSequenceFeatures !== sequenceFeatures) {\r
 104 this.lastSequenceFeatures = sequenceFeatures;\r
 105 if (this.lastSequenceFeatures != null) {\r
 106 this.sfSize = this.lastSequenceFeatures.length;\r
 107 }}}if (this.lastSequenceFeatures == null || this.sfSize == 0) {\r
 108 return initialCol;\r
 109 }if (jalview.util.Comparison.isGap (this.lastSeq.getCharAt (column))) {\r
 110 return java.awt.Color.white.getRGB ();\r
 111 }if (this.transparency != 1.0 && this.offscreenImage == null) {\r
 112 this.offscreenImage =  new java.awt.image.BufferedImage (1, 1, 2);\r
 113 }this.currentColour = null;\r
 114 this.offscreenRender = true;\r
 115 if (this.offscreenImage != null) {\r
 116 this.offscreenImage.setRGB (0, 0, initialCol);\r
 117 this.drawSequence (this.offscreenImage.getGraphics (), this.lastSeq, column, column, 0);\r
 118 return this.offscreenImage.getRGB (0, 0);\r
 119 } else {\r
 120 this.drawSequence (null, this.lastSeq, this.lastSeq.findPosition (column), -1, -1);\r
 121 if (this.currentColour == null) {\r
 122 return initialCol;\r
 123 } else {\r
 124 return (this.currentColour).intValue ();\r
 125 }}}, "~N,jalview.datamodel.SequenceI,~N");\r
 126 Clazz.defineMethod (c$, "drawSequence", \r
 127 function (g, seq, start, end, y1) {\r
 128 var sequenceFeatures = seq.getSequenceFeatures ();\r
 129 if (sequenceFeatures == null || sequenceFeatures.length == 0) {\r
 130 return;\r
 131 }if (g != null) {\r
 132 this.fm = g.getFontMetrics ();\r
 133 }this.updateFeatures ();\r
 134 if (this.lastSeq == null || seq !== this.lastSeq || sequenceFeatures !== this.lastSequenceFeatures) {\r
 135 this.lastSeq = seq;\r
 136 this.lastSequenceFeatures = sequenceFeatures;\r
 137 }if (this.transparency != 1 && g != null) {\r
 138 var g2 = g;\r
 139 g2.setComposite (java.awt.AlphaComposite.getInstance (3, this.transparency));\r
 140 }if (!this.offscreenRender) {\r
 141 this.spos = this.lastSeq.findPosition (start);\r
 142 this.epos = this.lastSeq.findPosition (end);\r
 143 }this.sfSize = this.lastSequenceFeatures.length;\r
 144 var type;\r
 145 for (var renderIndex = 0; renderIndex < this.renderOrder.length; renderIndex++) {\r
 146 type = this.renderOrder[renderIndex];\r
 147 if (type == null || !this.showFeatureOfType (type)) {\r
 148 continue;\r
 149 }for (this.sfindex = 0; this.sfindex < this.sfSize; this.sfindex++) {\r
 150 var sequenceFeature = this.lastSequenceFeatures[this.sfindex];\r
 151 if (!sequenceFeature.type.equals (type)) {\r
 152 continue;\r
 153 }if (this.featureGroups != null && sequenceFeature.featureGroup != null && sequenceFeature.featureGroup.length != 0 && this.featureGroups.containsKey (sequenceFeature.featureGroup) && !this.featureGroups.get (sequenceFeature.featureGroup).booleanValue ()) {\r
 154 continue;\r
 155 }if (!this.offscreenRender && (sequenceFeature.getBegin () > this.epos || sequenceFeature.getEnd () < this.spos)) {\r
 156 continue;\r
 157 }if (this.offscreenRender && this.offscreenImage == null) {\r
 158 if (sequenceFeature.begin <= start && sequenceFeature.end >= start) {\r
 159 this.currentColour =  new Integer (this.getColour (sequenceFeature).getRGB ());\r
 160 }} else if (sequenceFeature.type.equals ("disulfide bond")) {\r
 161 this.renderFeature (g, seq, seq.findIndex (sequenceFeature.begin) - 1, seq.findIndex (sequenceFeature.begin) - 1, this.getColour (sequenceFeature), start, end, y1);\r
 162 this.renderFeature (g, seq, seq.findIndex (sequenceFeature.end) - 1, seq.findIndex (sequenceFeature.end) - 1, this.getColour (sequenceFeature), start, end, y1);\r
 163 } else if (this.showFeature (sequenceFeature)) {\r
 164 if (this.av_isShowSeqFeatureHeight && !Float.isNaN (sequenceFeature.score)) {\r
 165 this.renderScoreFeature (g, seq, seq.findIndex (sequenceFeature.begin) - 1, seq.findIndex (sequenceFeature.end) - 1, this.getColour (sequenceFeature), start, end, y1, this.normaliseScore (sequenceFeature));\r
 166 } else {\r
 167 this.renderFeature (g, seq, seq.findIndex (sequenceFeature.begin) - 1, seq.findIndex (sequenceFeature.end) - 1, this.getColour (sequenceFeature), start, end, y1);\r
 168 }}}\r
 169 }\r
 170 if (this.transparency != 1.0 && g != null && this.transparencyAvailable) {\r
 171 var g2 = g;\r
 172 g2.setComposite (java.awt.AlphaComposite.getInstance (3, 1.0));\r
 173 }}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,~N");\r
 174 Clazz.defineMethod (c$, "setTransparencyAvailable", \r
 175 function (isTransparencyAvailable) {\r
 176 this.transparencyAvailable = isTransparencyAvailable;\r
 177 }, "~B");\r
 178 Clazz.overrideMethod (c$, "isTransparencyAvailable", \r
 179 function () {\r
 180 return this.transparencyAvailable;\r
 181 });\r
 182 Clazz.overrideMethod (c$, "featuresAdded", \r
 183 function () {\r
 184 this.lastSeq = null;\r
 185 this.findAllFeatures ();\r
 186 });\r
 187 });\r