X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRenderer.js;h=7dc84b1e47d5b249e1101c05bb37dd469927cb3f;hp=019d21830f7f01a2a5bd9b1797f94f94292e980f;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/renderer/seqfeatures/FeatureRenderer.js b/site/j2s/jalview/renderer/seqfeatures/FeatureRenderer.js
index 019d218..7dc84b1 100644
--- a/site/j2s/jalview/renderer/seqfeatures/FeatureRenderer.js
+++ b/site/j2s/jalview/renderer/seqfeatures/FeatureRenderer.js
@@ -1,187 +1,187 @@
-Clazz.declarePackage ("jalview.renderer.seqfeatures");
-Clazz.load (["jalview.viewmodel.seqfeatures.FeatureRendererModel"], "jalview.renderer.seqfeatures.FeatureRenderer", ["jalview.util.Comparison", "java.awt.AlphaComposite", "$.Color", "java.awt.image.BufferedImage", "java.lang.Float"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.fm = null;
-this.charOffset = 0;
-this.offscreenRender = false;
-this.lastSeq = null;
-this.s = '\0';
-this.i = 0;
-this.av_charHeight = 0;
-this.av_charWidth = 0;
-this.av_validCharWidth = false;
-this.av_isShowSeqFeatureHeight = false;
-this.offscreenImage = null;
-this.lastSequenceFeatures = null;
-this.sfSize = 0;
-this.sfindex = 0;
-this.spos = 0;
-this.epos = 0;
-this.transparencyAvailable = true;
-Clazz.instantialize (this, arguments);
-}, jalview.renderer.seqfeatures, "FeatureRenderer", jalview.viewmodel.seqfeatures.FeatureRendererModel);
-Clazz.defineMethod (c$, "updateAvConfig", 
-function () {
-this.av_charHeight = this.av.getCharHeight ();
-this.av_charWidth = this.av.getCharWidth ();
-this.av_validCharWidth = this.av.isValidCharWidth ();
-this.av_isShowSeqFeatureHeight = this.av.isShowSequenceFeaturesHeight ();
-});
-Clazz.defineMethod (c$, "renderFeature", 
-function (g, seq, fstart, fend, featureColour, start, end, y1) {
-this.updateAvConfig ();
-if (((fstart <= end) && (fend >= start))) {
-if (fstart < start) {
-fstart = start;
-}if (fend >= end) {
-fend = end;
-}var pady = (y1 + this.av_charHeight) - Clazz.doubleToInt (this.av_charHeight / 5);
-for (this.i = fstart; this.i <= fend; this.i++) {
-this.s = seq.getCharAt (this.i);
-if (jalview.util.Comparison.isGap (this.s)) {
-continue;
-}g.setColor (featureColour);
-g.fillRect ((this.i - start) * this.av_charWidth, y1, this.av_charWidth, this.av_charHeight);
-if (this.offscreenRender || !this.av_validCharWidth) {
-continue;
-}g.setColor (java.awt.Color.white);
-this.charOffset = Clazz.doubleToInt ((this.av_charWidth - this.fm.charWidth (this.s)) / 2);
-g.drawString (String.valueOf (this.s), this.charOffset + (this.av_charWidth * (this.i - start)), pady);
-}
-}}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,java.awt.Color,~N,~N,~N");
-Clazz.defineMethod (c$, "renderScoreFeature", 
-function (g, seq, fstart, fend, featureColour, start, end, y1, bs) {
-this.updateAvConfig ();
-if (((fstart <= end) && (fend >= start))) {
-if (fstart < start) {
-fstart = start;
-}if (fend >= end) {
-fend = end;
-}var pady = (y1 + this.av_charHeight) - Clazz.doubleToInt (this.av_charHeight / 5);
-var ystrt = 0;
-var yend = this.av_charHeight;
-if (bs[0] != 0) {
-if (bs[1] < 128) {
-yend = Clazz.doubleToInt (this.av_charHeight * (128 - bs[1]) / 512);
-ystrt = this.av_charHeight - Clazz.doubleToInt (yend / 2);
-} else {
-ystrt = Clazz.doubleToInt (this.av_charHeight / 2);
-yend = Clazz.doubleToInt (this.av_charHeight * (bs[1] - 128) / 512);
-}} else {
-yend = Clazz.doubleToInt (this.av_charHeight * bs[1] / 255);
-ystrt = this.av_charHeight - yend;
-}for (this.i = fstart; this.i <= fend; this.i++) {
-this.s = seq.getCharAt (this.i);
-if (jalview.util.Comparison.isGap (this.s)) {
-continue;
-}g.setColor (featureColour);
-var x = (this.i - start) * this.av_charWidth;
-g.drawRect (x, y1, this.av_charWidth, this.av_charHeight);
-g.fillRect (x, y1 + ystrt, this.av_charWidth, yend);
-if (this.offscreenRender || !this.av_validCharWidth) {
-continue;
-}g.setColor (java.awt.Color.black);
-this.charOffset = Clazz.doubleToInt ((this.av_charWidth - this.fm.charWidth (this.s)) / 2);
-g.drawString (String.valueOf (this.s), this.charOffset + (this.av_charWidth * (this.i - start)), pady);
-}
-}}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,java.awt.Color,~N,~N,~N,~A");
-Clazz.defineMethod (c$, "findFeatureColour", 
-function (initialCol, seq, res) {
-return  new java.awt.Color (this.findFeatureColour (initialCol.getRGB (), seq, res));
-}, "java.awt.Color,jalview.datamodel.SequenceI,~N");
-Clazz.defineMethod (c$, "findFeatureColour", 
-function (initialCol, seq, column) {
-if (!this.av.isShowSequenceFeatures ()) {
-return initialCol;
-}var sequenceFeatures = seq.getSequenceFeatures ();
-if (seq !== this.lastSeq) {
-this.lastSeq = seq;
-this.lastSequenceFeatures = sequenceFeatures;
-if (this.lastSequenceFeatures != null) {
-this.sfSize = this.lastSequenceFeatures.length;
-}} else {
-if (this.lastSequenceFeatures !== sequenceFeatures) {
-this.lastSequenceFeatures = sequenceFeatures;
-if (this.lastSequenceFeatures != null) {
-this.sfSize = this.lastSequenceFeatures.length;
-}}}if (this.lastSequenceFeatures == null || this.sfSize == 0) {
-return initialCol;
-}if (jalview.util.Comparison.isGap (this.lastSeq.getCharAt (column))) {
-return java.awt.Color.white.getRGB ();
-}if (this.transparency != 1.0 && this.offscreenImage == null) {
-this.offscreenImage =  new java.awt.image.BufferedImage (1, 1, 2);
-}this.currentColour = null;
-this.offscreenRender = true;
-if (this.offscreenImage != null) {
-this.offscreenImage.setRGB (0, 0, initialCol);
-this.drawSequence (this.offscreenImage.getGraphics (), this.lastSeq, column, column, 0);
-return this.offscreenImage.getRGB (0, 0);
-} else {
-this.drawSequence (null, this.lastSeq, this.lastSeq.findPosition (column), -1, -1);
-if (this.currentColour == null) {
-return initialCol;
-} else {
-return (this.currentColour).intValue ();
-}}}, "~N,jalview.datamodel.SequenceI,~N");
-Clazz.defineMethod (c$, "drawSequence", 
-function (g, seq, start, end, y1) {
-var sequenceFeatures = seq.getSequenceFeatures ();
-if (sequenceFeatures == null || sequenceFeatures.length == 0) {
-return;
-}if (g != null) {
-this.fm = g.getFontMetrics ();
-}this.updateFeatures ();
-if (this.lastSeq == null || seq !== this.lastSeq || sequenceFeatures !== this.lastSequenceFeatures) {
-this.lastSeq = seq;
-this.lastSequenceFeatures = sequenceFeatures;
-}if (this.transparency != 1 && g != null) {
-var g2 = g;
-g2.setComposite (java.awt.AlphaComposite.getInstance (3, this.transparency));
-}if (!this.offscreenRender) {
-this.spos = this.lastSeq.findPosition (start);
-this.epos = this.lastSeq.findPosition (end);
-}this.sfSize = this.lastSequenceFeatures.length;
-var type;
-for (var renderIndex = 0; renderIndex < this.renderOrder.length; renderIndex++) {
-type = this.renderOrder[renderIndex];
-if (type == null || !this.showFeatureOfType (type)) {
-continue;
-}for (this.sfindex = 0; this.sfindex < this.sfSize; this.sfindex++) {
-var sequenceFeature = this.lastSequenceFeatures[this.sfindex];
-if (!sequenceFeature.type.equals (type)) {
-continue;
-}if (this.featureGroups != null && sequenceFeature.featureGroup != null && sequenceFeature.featureGroup.length != 0 && this.featureGroups.containsKey (sequenceFeature.featureGroup) && !this.featureGroups.get (sequenceFeature.featureGroup).booleanValue ()) {
-continue;
-}if (!this.offscreenRender && (sequenceFeature.getBegin () > this.epos || sequenceFeature.getEnd () < this.spos)) {
-continue;
-}if (this.offscreenRender && this.offscreenImage == null) {
-if (sequenceFeature.begin <= start && sequenceFeature.end >= start) {
-this.currentColour =  new Integer (this.getColour (sequenceFeature).getRGB ());
-}} else if (sequenceFeature.type.equals ("disulfide bond")) {
-this.renderFeature (g, seq, seq.findIndex (sequenceFeature.begin) - 1, seq.findIndex (sequenceFeature.begin) - 1, this.getColour (sequenceFeature), start, end, y1);
-this.renderFeature (g, seq, seq.findIndex (sequenceFeature.end) - 1, seq.findIndex (sequenceFeature.end) - 1, this.getColour (sequenceFeature), start, end, y1);
-} else if (this.showFeature (sequenceFeature)) {
-if (this.av_isShowSeqFeatureHeight && !Float.isNaN (sequenceFeature.score)) {
-this.renderScoreFeature (g, seq, seq.findIndex (sequenceFeature.begin) - 1, seq.findIndex (sequenceFeature.end) - 1, this.getColour (sequenceFeature), start, end, y1, this.normaliseScore (sequenceFeature));
-} else {
-this.renderFeature (g, seq, seq.findIndex (sequenceFeature.begin) - 1, seq.findIndex (sequenceFeature.end) - 1, this.getColour (sequenceFeature), start, end, y1);
-}}}
-}
-if (this.transparency != 1.0 && g != null && this.transparencyAvailable) {
-var g2 = g;
-g2.setComposite (java.awt.AlphaComposite.getInstance (3, 1.0));
-}}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,~N");
-Clazz.defineMethod (c$, "setTransparencyAvailable", 
-function (isTransparencyAvailable) {
-this.transparencyAvailable = isTransparencyAvailable;
-}, "~B");
-Clazz.overrideMethod (c$, "isTransparencyAvailable", 
-function () {
-return this.transparencyAvailable;
-});
-Clazz.overrideMethod (c$, "featuresAdded", 
-function () {
-this.lastSeq = null;
-this.findAllFeatures ();
-});
-});
+Clazz.declarePackage ("jalview.renderer.seqfeatures");
+Clazz.load (["jalview.viewmodel.seqfeatures.FeatureRendererModel"], "jalview.renderer.seqfeatures.FeatureRenderer", ["jalview.util.Comparison", "java.awt.AlphaComposite", "$.Color", "java.awt.image.BufferedImage", "java.lang.Float"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.fm = null;
+this.charOffset = 0;
+this.offscreenRender = false;
+this.lastSeq = null;
+this.s = '\0';
+this.i = 0;
+this.av_charHeight = 0;
+this.av_charWidth = 0;
+this.av_validCharWidth = false;
+this.av_isShowSeqFeatureHeight = false;
+this.offscreenImage = null;
+this.lastSequenceFeatures = null;
+this.sfSize = 0;
+this.sfindex = 0;
+this.spos = 0;
+this.epos = 0;
+this.transparencyAvailable = true;
+Clazz.instantialize (this, arguments);
+}, jalview.renderer.seqfeatures, "FeatureRenderer", jalview.viewmodel.seqfeatures.FeatureRendererModel);
+Clazz.defineMethod (c$, "updateAvConfig", 
+function () {
+this.av_charHeight = this.av.getCharHeight ();
+this.av_charWidth = this.av.getCharWidth ();
+this.av_validCharWidth = this.av.isValidCharWidth ();
+this.av_isShowSeqFeatureHeight = this.av.isShowSequenceFeaturesHeight ();
+});
+Clazz.defineMethod (c$, "renderFeature", 
+function (g, seq, fstart, fend, featureColour, start, end, y1) {
+this.updateAvConfig ();
+if (((fstart <= end) && (fend >= start))) {
+if (fstart < start) {
+fstart = start;
+}if (fend >= end) {
+fend = end;
+}var pady = (y1 + this.av_charHeight) - Clazz.doubleToInt (this.av_charHeight / 5);
+for (this.i = fstart; this.i <= fend; this.i++) {
+this.s = seq.getCharAt (this.i);
+if (jalview.util.Comparison.isGap (this.s)) {
+continue;
+}g.setColor (featureColour);
+g.fillRect ((this.i - start) * this.av_charWidth, y1, this.av_charWidth, this.av_charHeight);
+if (this.offscreenRender || !this.av_validCharWidth) {
+continue;
+}g.setColor (java.awt.Color.white);
+this.charOffset = Clazz.doubleToInt ((this.av_charWidth - this.fm.charWidth (this.s)) / 2);
+g.drawString (String.valueOf (this.s), this.charOffset + (this.av_charWidth * (this.i - start)), pady);
+}
+}}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,java.awt.Color,~N,~N,~N");
+Clazz.defineMethod (c$, "renderScoreFeature", 
+function (g, seq, fstart, fend, featureColour, start, end, y1, bs) {
+this.updateAvConfig ();
+if (((fstart <= end) && (fend >= start))) {
+if (fstart < start) {
+fstart = start;
+}if (fend >= end) {
+fend = end;
+}var pady = (y1 + this.av_charHeight) - Clazz.doubleToInt (this.av_charHeight / 5);
+var ystrt = 0;
+var yend = this.av_charHeight;
+if (bs[0] != 0) {
+if (bs[1] < 128) {
+yend = Clazz.doubleToInt (this.av_charHeight * (128 - bs[1]) / 512);
+ystrt = this.av_charHeight - Clazz.doubleToInt (yend / 2);
+} else {
+ystrt = Clazz.doubleToInt (this.av_charHeight / 2);
+yend = Clazz.doubleToInt (this.av_charHeight * (bs[1] - 128) / 512);
+}} else {
+yend = Clazz.doubleToInt (this.av_charHeight * bs[1] / 255);
+ystrt = this.av_charHeight - yend;
+}for (this.i = fstart; this.i <= fend; this.i++) {
+this.s = seq.getCharAt (this.i);
+if (jalview.util.Comparison.isGap (this.s)) {
+continue;
+}g.setColor (featureColour);
+var x = (this.i - start) * this.av_charWidth;
+g.drawRect (x, y1, this.av_charWidth, this.av_charHeight);
+g.fillRect (x, y1 + ystrt, this.av_charWidth, yend);
+if (this.offscreenRender || !this.av_validCharWidth) {
+continue;
+}g.setColor (java.awt.Color.black);
+this.charOffset = Clazz.doubleToInt ((this.av_charWidth - this.fm.charWidth (this.s)) / 2);
+g.drawString (String.valueOf (this.s), this.charOffset + (this.av_charWidth * (this.i - start)), pady);
+}
+}}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,java.awt.Color,~N,~N,~N,~A");
+Clazz.defineMethod (c$, "findFeatureColour", 
+function (initialCol, seq, res) {
+return  new java.awt.Color (this.findFeatureColour (initialCol.getRGB (), seq, res));
+}, "java.awt.Color,jalview.datamodel.SequenceI,~N");
+Clazz.defineMethod (c$, "findFeatureColour", 
+function (initialCol, seq, column) {
+if (!this.av.isShowSequenceFeatures ()) {
+return initialCol;
+}var sequenceFeatures = seq.getSequenceFeatures ();
+if (seq !== this.lastSeq) {
+this.lastSeq = seq;
+this.lastSequenceFeatures = sequenceFeatures;
+if (this.lastSequenceFeatures != null) {
+this.sfSize = this.lastSequenceFeatures.length;
+}} else {
+if (this.lastSequenceFeatures !== sequenceFeatures) {
+this.lastSequenceFeatures = sequenceFeatures;
+if (this.lastSequenceFeatures != null) {
+this.sfSize = this.lastSequenceFeatures.length;
+}}}if (this.lastSequenceFeatures == null || this.sfSize == 0) {
+return initialCol;
+}if (jalview.util.Comparison.isGap (this.lastSeq.getCharAt (column))) {
+return java.awt.Color.white.getRGB ();
+}if (this.transparency != 1.0 && this.offscreenImage == null) {
+this.offscreenImage =  new java.awt.image.BufferedImage (1, 1, 2);
+}this.currentColour = null;
+this.offscreenRender = true;
+if (this.offscreenImage != null) {
+this.offscreenImage.setRGB (0, 0, initialCol);
+this.drawSequence (this.offscreenImage.getGraphics (), this.lastSeq, column, column, 0);
+return this.offscreenImage.getRGB (0, 0);
+} else {
+this.drawSequence (null, this.lastSeq, this.lastSeq.findPosition (column), -1, -1);
+if (this.currentColour == null) {
+return initialCol;
+} else {
+return (this.currentColour).intValue ();
+}}}, "~N,jalview.datamodel.SequenceI,~N");
+Clazz.defineMethod (c$, "drawSequence", 
+function (g, seq, start, end, y1) {
+var sequenceFeatures = seq.getSequenceFeatures ();
+if (sequenceFeatures == null || sequenceFeatures.length == 0) {
+return;
+}if (g != null) {
+this.fm = g.getFontMetrics ();
+}this.updateFeatures ();
+if (this.lastSeq == null || seq !== this.lastSeq || sequenceFeatures !== this.lastSequenceFeatures) {
+this.lastSeq = seq;
+this.lastSequenceFeatures = sequenceFeatures;
+}if (this.transparency != 1 && g != null) {
+var g2 = g;
+g2.setComposite (java.awt.AlphaComposite.getInstance (3, this.transparency));
+}if (!this.offscreenRender) {
+this.spos = this.lastSeq.findPosition (start);
+this.epos = this.lastSeq.findPosition (end);
+}this.sfSize = this.lastSequenceFeatures.length;
+var type;
+for (var renderIndex = 0; renderIndex < this.renderOrder.length; renderIndex++) {
+type = this.renderOrder[renderIndex];
+if (type == null || !this.showFeatureOfType (type)) {
+continue;
+}for (this.sfindex = 0; this.sfindex < this.sfSize; this.sfindex++) {
+var sequenceFeature = this.lastSequenceFeatures[this.sfindex];
+if (!sequenceFeature.type.equals (type)) {
+continue;
+}if (this.featureGroups != null && sequenceFeature.featureGroup != null && sequenceFeature.featureGroup.length != 0 && this.featureGroups.containsKey (sequenceFeature.featureGroup) && !this.featureGroups.get (sequenceFeature.featureGroup).booleanValue ()) {
+continue;
+}if (!this.offscreenRender && (sequenceFeature.getBegin () > this.epos || sequenceFeature.getEnd () < this.spos)) {
+continue;
+}if (this.offscreenRender && this.offscreenImage == null) {
+if (sequenceFeature.begin <= start && sequenceFeature.end >= start) {
+this.currentColour =  new Integer (this.getColour (sequenceFeature).getRGB ());
+}} else if (sequenceFeature.type.equals ("disulfide bond")) {
+this.renderFeature (g, seq, seq.findIndex (sequenceFeature.begin) - 1, seq.findIndex (sequenceFeature.begin) - 1, this.getColour (sequenceFeature), start, end, y1);
+this.renderFeature (g, seq, seq.findIndex (sequenceFeature.end) - 1, seq.findIndex (sequenceFeature.end) - 1, this.getColour (sequenceFeature), start, end, y1);
+} else if (this.showFeature (sequenceFeature)) {
+if (this.av_isShowSeqFeatureHeight && !Float.isNaN (sequenceFeature.score)) {
+this.renderScoreFeature (g, seq, seq.findIndex (sequenceFeature.begin) - 1, seq.findIndex (sequenceFeature.end) - 1, this.getColour (sequenceFeature), start, end, y1, this.normaliseScore (sequenceFeature));
+} else {
+this.renderFeature (g, seq, seq.findIndex (sequenceFeature.begin) - 1, seq.findIndex (sequenceFeature.end) - 1, this.getColour (sequenceFeature), start, end, y1);
+}}}
+}
+if (this.transparency != 1.0 && g != null && this.transparencyAvailable) {
+var g2 = g;
+g2.setComposite (java.awt.AlphaComposite.getInstance (3, 1.0));
+}}, "java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,~N");
+Clazz.defineMethod (c$, "setTransparencyAvailable", 
+function (isTransparencyAvailable) {
+this.transparencyAvailable = isTransparencyAvailable;
+}, "~B");
+Clazz.overrideMethod (c$, "isTransparencyAvailable", 
+function () {
+return this.transparencyAvailable;
+});
+Clazz.overrideMethod (c$, "featuresAdded", 
+function () {
+this.lastSeq = null;
+this.findAllFeatures ();
+});
+});