bin/jalview/renderer/seqfeatures/FeatureRenderer.js

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