-Clazz.declarePackage ("jalview.schemes");\r
-Clazz.load (["jalview.schemes.FollowerColourScheme"], "jalview.schemes.AnnotationColourGradient", ["jalview.datamodel.AlignmentI", "$.GraphLine", "jalview.renderer.AnnotationRenderer", "jalview.schemes.ColourSchemeProperty", "jalview.util.Comparison", "java.awt.Color", "java.util.IdentityHashMap"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.annotation = null;\r
-this.aboveAnnotationThreshold = -1;\r
-this.thresholdIsMinMax = false;\r
-this.annotationThreshold = null;\r
-this.r1 = 0;\r
-this.g1 = 0;\r
-this.b1 = 0;\r
-this.rr = 0;\r
-this.gg = 0;\r
-this.bb = 0;\r
-this.predefinedColours = false;\r
-this.seqAssociated = false;\r
-this.noGradient = false;\r
-this.seqannot = null;\r
-this.aamin = 0;\r
-this.aamax = 0;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.schemes, "AnnotationColourGradient", jalview.schemes.FollowerColourScheme);\r
-Clazz.overrideMethod (c$, "applyTo", \r
-function (sg, hiddenRepSequences) {\r
-var acg = new jalview.schemes.AnnotationColourGradient (this.annotation, this.colourScheme, this.aboveAnnotationThreshold);\r
-acg.thresholdIsMinMax = this.thresholdIsMinMax;\r
-acg.annotationThreshold = (this.annotationThreshold == null) ? null : new jalview.datamodel.GraphLine (this.annotationThreshold);\r
-acg.r1 = this.r1;\r
-acg.g1 = this.g1;\r
-acg.b1 = this.b1;\r
-acg.rr = this.rr;\r
-acg.gg = this.gg;\r
-acg.bb = this.bb;\r
-acg.predefinedColours = this.predefinedColours;\r
-acg.seqAssociated = this.seqAssociated;\r
-acg.noGradient = this.noGradient;\r
-return acg;\r
-}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");\r
-Clazz.makeConstructor (c$, \r
-function (annotation, originalColour, aboveThreshold) {\r
-Clazz.superConstructor (this, jalview.schemes.AnnotationColourGradient, []);\r
-if (Clazz.instanceOf (originalColour, jalview.schemes.AnnotationColourGradient)) {\r
-this.colourScheme = (originalColour).colourScheme;\r
-} else {\r
-this.colourScheme = originalColour;\r
-}this.annotation = annotation;\r
-this.aboveAnnotationThreshold = aboveThreshold;\r
-if (aboveThreshold != -1 && annotation.threshold != null) {\r
-this.annotationThreshold = annotation.threshold;\r
-}this.r1 = 254;\r
-this.g1 = 254;\r
-this.b1 = 254;\r
-this.rr = 0;\r
-this.gg = 0;\r
-this.bb = 0;\r
-this.noGradient = true;\r
-}, "jalview.datamodel.AlignmentAnnotation,jalview.schemes.ColourSchemeI,~N");\r
-Clazz.makeConstructor (c$, \r
-function (annotation, minColour, maxColour, aboveThreshold) {\r
-Clazz.superConstructor (this, jalview.schemes.AnnotationColourGradient, []);\r
-this.annotation = annotation;\r
-this.aboveAnnotationThreshold = aboveThreshold;\r
-if (aboveThreshold != -1 && annotation.threshold != null) {\r
-this.annotationThreshold = annotation.threshold;\r
-}this.r1 = minColour.getRed ();\r
-this.g1 = minColour.getGreen ();\r
-this.b1 = minColour.getBlue ();\r
-this.rr = maxColour.getRed () - this.r1;\r
-this.gg = maxColour.getGreen () - this.g1;\r
-this.bb = maxColour.getBlue () - this.b1;\r
-this.noGradient = false;\r
-this.aamax = annotation.graphMax;\r
-this.aamin = annotation.graphMin;\r
-if (annotation.isRNA ()) {\r
-jalview.schemes.ColourSchemeProperty.initRnaHelicesShading (1 + Clazz.floatToInt (this.aamax));\r
-}}, "jalview.datamodel.AlignmentAnnotation,java.awt.Color,java.awt.Color,~N");\r
-Clazz.defineMethod (c$, "alignmentChanged", \r
-function (alignment, hiddenReps) {\r
-Clazz.superCall (this, jalview.schemes.AnnotationColourGradient, "alignmentChanged", [alignment, hiddenReps]);\r
-if (this.seqAssociated && this.annotation.getCalcId () != null) {\r
-if (this.seqannot != null) {\r
-this.seqannot.clear ();\r
-} else {\r
-this.seqannot = new java.util.IdentityHashMap ();\r
-}var alcontext = Clazz.instanceOf (alignment, jalview.datamodel.AlignmentI) ? alignment : alignment.getContext ();\r
-var f = true;\r
-var rna = false;\r
-for (var alan, $alan = alcontext.findAnnotation (this.annotation.getCalcId ()).iterator (); $alan.hasNext () && ((alan = $alan.next ()) || true);) {\r
-if (alan.sequenceRef != null && (alan.label != null && this.annotation != null && alan.label.equals (this.annotation.label))) {\r
-if (!rna && alan.isRNA ()) {\r
-rna = true;\r
-}this.seqannot.put (alan.sequenceRef, alan);\r
-if (f || alan.graphMax > this.aamax) {\r
-this.aamax = alan.graphMax;\r
-}if (f || alan.graphMin < this.aamin) {\r
-this.aamin = alan.graphMin;\r
-}f = false;\r
-}}\r
-if (rna) {\r
-jalview.schemes.ColourSchemeProperty.initRnaHelicesShading (1 + Clazz.floatToInt (this.aamax));\r
-}}}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");\r
-Clazz.defineMethod (c$, "getAnnotation", \r
-function () {\r
-return this.annotation.label;\r
-});\r
-Clazz.defineMethod (c$, "getAboveThreshold", \r
-function () {\r
-return this.aboveAnnotationThreshold;\r
-});\r
-Clazz.defineMethod (c$, "getAnnotationThreshold", \r
-function () {\r
-if (this.annotationThreshold == null) {\r
-return 0;\r
-} else {\r
-return this.annotationThreshold.value;\r
-}});\r
-Clazz.defineMethod (c$, "getMinColour", \r
-function () {\r
-return new java.awt.Color (Clazz.floatToInt (this.r1), Clazz.floatToInt (this.g1), Clazz.floatToInt (this.b1));\r
-});\r
-Clazz.defineMethod (c$, "getMaxColour", \r
-function () {\r
-return new java.awt.Color (Clazz.floatToInt (this.r1 + this.rr), Clazz.floatToInt (this.g1 + this.gg), Clazz.floatToInt (this.b1 + this.bb));\r
-});\r
-Clazz.defineMethod (c$, "findColour", \r
-function (c) {\r
-return java.awt.Color.red;\r
-}, "~S");\r
-Clazz.defineMethod (c$, "findColour", \r
-function (c, j, seq) {\r
-var currentColour = java.awt.Color.white;\r
-var annotation = (this.seqAssociated && this.seqannot != null ? this.seqannot.get (seq) : this.annotation);\r
-if (annotation == null) {\r
-return currentColour;\r
-}if ((this.threshold == 0) || this.aboveThreshold (c, j)) {\r
-if (annotation.annotations != null && j < annotation.annotations.length && annotation.annotations[j] != null && !jalview.util.Comparison.isGap (c)) {\r
-var aj = annotation.annotations[j];\r
-if (this.aboveAnnotationThreshold == -1 || (this.annotationThreshold != null && (this.aboveAnnotationThreshold == 1 ? aj.value >= this.annotationThreshold.value : aj.value <= this.annotationThreshold.value))) {\r
-if (this.predefinedColours && aj.colour != null && !aj.colour.equals (java.awt.Color.black)) {\r
-currentColour = aj.colour;\r
-} else if (annotation.hasIcons && annotation.graph == 0) {\r
-if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.' && aj.secondaryStructure != '-') {\r
-if (this.colourScheme != null) {\r
-currentColour = this.colourScheme.findColour (c, j, seq);\r
-} else {\r
-if (annotation.isRNA ()) {\r
-currentColour = jalview.schemes.ColourSchemeProperty.rnaHelices[Clazz.floatToInt (aj.value)];\r
-} else {\r
-currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR : jalview.renderer.AnnotationRenderer.STEM_COLOUR;\r
-}}} else {\r
-return java.awt.Color.white;\r
-}} else if (this.noGradient) {\r
-if (this.colourScheme != null) {\r
-currentColour = this.colourScheme.findColour (c, j, seq);\r
-} else {\r
-if (aj.colour != null) {\r
-currentColour = aj.colour;\r
-}}} else {\r
-currentColour = this.shadeCalculation (annotation, j);\r
-}}if (this.conservationColouring) {\r
-currentColour = this.applyConservation (currentColour, j);\r
-}}}return currentColour;\r
-}, "~S,~N,jalview.datamodel.SequenceI");\r
-Clazz.defineMethod (c$, "shadeCalculation", \r
- function (annotation, j) {\r
-var range = 1;\r
-if (this.thresholdIsMinMax && annotation.threshold != null && this.aboveAnnotationThreshold == 1 && annotation.annotations[j].value >= annotation.threshold.value) {\r
-range = (annotation.annotations[j].value - annotation.threshold.value) / (annotation.graphMax - annotation.threshold.value);\r
-} else if (this.thresholdIsMinMax && annotation.threshold != null && this.aboveAnnotationThreshold == 0 && annotation.annotations[j].value >= annotation.graphMin) {\r
-range = (annotation.annotations[j].value - annotation.graphMin) / (annotation.threshold.value - annotation.graphMin);\r
-} else {\r
-if (annotation.graphMax != annotation.graphMin) {\r
-range = (annotation.annotations[j].value - annotation.graphMin) / (annotation.graphMax - annotation.graphMin);\r
-} else {\r
-range = 0;\r
-}}var dr = Clazz.floatToInt (this.rr * range + this.r1);\r
-var dg = Clazz.floatToInt (this.gg * range + this.g1);\r
-var db = Clazz.floatToInt (this.bb * range + this.b1);\r
-return new java.awt.Color (dr, dg, db);\r
-}, "jalview.datamodel.AlignmentAnnotation,~N");\r
-Clazz.defineMethod (c$, "isPredefinedColours", \r
-function () {\r
-return this.predefinedColours;\r
-});\r
-Clazz.defineMethod (c$, "setPredefinedColours", \r
-function (predefinedColours) {\r
-this.predefinedColours = predefinedColours;\r
-}, "~B");\r
-Clazz.defineMethod (c$, "isSeqAssociated", \r
-function () {\r
-return this.seqAssociated;\r
-});\r
-Clazz.defineMethod (c$, "setSeqAssociated", \r
-function (sassoc) {\r
-this.seqAssociated = sassoc;\r
-}, "~B");\r
-Clazz.defineStatics (c$,\r
-"NO_THRESHOLD", -1,\r
-"BELOW_THRESHOLD", 0,\r
-"ABOVE_THRESHOLD", 1);\r
-});\r
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (["jalview.schemes.FollowerColourScheme"], "jalview.schemes.AnnotationColourGradient", ["jalview.datamodel.AlignmentI", "$.GraphLine", "jalview.renderer.AnnotationRenderer", "jalview.schemes.ColourSchemeProperty", "jalview.util.Comparison", "java.awt.Color", "java.util.IdentityHashMap"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.annotation = null;
+this.aboveAnnotationThreshold = -1;
+this.thresholdIsMinMax = false;
+this.annotationThreshold = null;
+this.r1 = 0;
+this.g1 = 0;
+this.b1 = 0;
+this.rr = 0;
+this.gg = 0;
+this.bb = 0;
+this.predefinedColours = false;
+this.seqAssociated = false;
+this.noGradient = false;
+this.seqannot = null;
+this.aamin = 0;
+this.aamax = 0;
+Clazz.instantialize (this, arguments);
+}, jalview.schemes, "AnnotationColourGradient", jalview.schemes.FollowerColourScheme);
+Clazz.overrideMethod (c$, "applyTo",
+function (sg, hiddenRepSequences) {
+var acg = new jalview.schemes.AnnotationColourGradient (this.annotation, this.colourScheme, this.aboveAnnotationThreshold);
+acg.thresholdIsMinMax = this.thresholdIsMinMax;
+acg.annotationThreshold = (this.annotationThreshold == null) ? null : new jalview.datamodel.GraphLine (this.annotationThreshold);
+acg.r1 = this.r1;
+acg.g1 = this.g1;
+acg.b1 = this.b1;
+acg.rr = this.rr;
+acg.gg = this.gg;
+acg.bb = this.bb;
+acg.predefinedColours = this.predefinedColours;
+acg.seqAssociated = this.seqAssociated;
+acg.noGradient = this.noGradient;
+return acg;
+}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
+Clazz.makeConstructor (c$,
+function (annotation, originalColour, aboveThreshold) {
+Clazz.superConstructor (this, jalview.schemes.AnnotationColourGradient, []);
+if (Clazz.instanceOf (originalColour, jalview.schemes.AnnotationColourGradient)) {
+this.colourScheme = (originalColour).colourScheme;
+} else {
+this.colourScheme = originalColour;
+}this.annotation = annotation;
+this.aboveAnnotationThreshold = aboveThreshold;
+if (aboveThreshold != -1 && annotation.threshold != null) {
+this.annotationThreshold = annotation.threshold;
+}this.r1 = 254;
+this.g1 = 254;
+this.b1 = 254;
+this.rr = 0;
+this.gg = 0;
+this.bb = 0;
+this.noGradient = true;
+}, "jalview.datamodel.AlignmentAnnotation,jalview.schemes.ColourSchemeI,~N");
+Clazz.makeConstructor (c$,
+function (annotation, minColour, maxColour, aboveThreshold) {
+Clazz.superConstructor (this, jalview.schemes.AnnotationColourGradient, []);
+this.annotation = annotation;
+this.aboveAnnotationThreshold = aboveThreshold;
+if (aboveThreshold != -1 && annotation.threshold != null) {
+this.annotationThreshold = annotation.threshold;
+}this.r1 = minColour.getRed ();
+this.g1 = minColour.getGreen ();
+this.b1 = minColour.getBlue ();
+this.rr = maxColour.getRed () - this.r1;
+this.gg = maxColour.getGreen () - this.g1;
+this.bb = maxColour.getBlue () - this.b1;
+this.noGradient = false;
+this.aamax = annotation.graphMax;
+this.aamin = annotation.graphMin;
+if (annotation.isRNA ()) {
+jalview.schemes.ColourSchemeProperty.initRnaHelicesShading (1 + Clazz.floatToInt (this.aamax));
+}}, "jalview.datamodel.AlignmentAnnotation,java.awt.Color,java.awt.Color,~N");
+Clazz.defineMethod (c$, "alignmentChanged",
+function (alignment, hiddenReps) {
+Clazz.superCall (this, jalview.schemes.AnnotationColourGradient, "alignmentChanged", [alignment, hiddenReps]);
+if (this.seqAssociated && this.annotation.getCalcId () != null) {
+if (this.seqannot != null) {
+this.seqannot.clear ();
+} else {
+this.seqannot = new java.util.IdentityHashMap ();
+}var alcontext = Clazz.instanceOf (alignment, jalview.datamodel.AlignmentI) ? alignment : alignment.getContext ();
+var f = true;
+var rna = false;
+for (var alan, $alan = alcontext.findAnnotation (this.annotation.getCalcId ()).iterator (); $alan.hasNext () && ((alan = $alan.next ()) || true);) {
+if (alan.sequenceRef != null && (alan.label != null && this.annotation != null && alan.label.equals (this.annotation.label))) {
+if (!rna && alan.isRNA ()) {
+rna = true;
+}this.seqannot.put (alan.sequenceRef, alan);
+if (f || alan.graphMax > this.aamax) {
+this.aamax = alan.graphMax;
+}if (f || alan.graphMin < this.aamin) {
+this.aamin = alan.graphMin;
+}f = false;
+}}
+if (rna) {
+jalview.schemes.ColourSchemeProperty.initRnaHelicesShading (1 + Clazz.floatToInt (this.aamax));
+}}}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
+Clazz.defineMethod (c$, "getAnnotation",
+function () {
+return this.annotation.label;
+});
+Clazz.defineMethod (c$, "getAboveThreshold",
+function () {
+return this.aboveAnnotationThreshold;
+});
+Clazz.defineMethod (c$, "getAnnotationThreshold",
+function () {
+if (this.annotationThreshold == null) {
+return 0;
+} else {
+return this.annotationThreshold.value;
+}});
+Clazz.defineMethod (c$, "getMinColour",
+function () {
+return new java.awt.Color (Clazz.floatToInt (this.r1), Clazz.floatToInt (this.g1), Clazz.floatToInt (this.b1));
+});
+Clazz.defineMethod (c$, "getMaxColour",
+function () {
+return new java.awt.Color (Clazz.floatToInt (this.r1 + this.rr), Clazz.floatToInt (this.g1 + this.gg), Clazz.floatToInt (this.b1 + this.bb));
+});
+Clazz.defineMethod (c$, "findColour",
+function (c) {
+return java.awt.Color.red;
+}, "~S");
+Clazz.defineMethod (c$, "findColour",
+function (c, j, seq) {
+var currentColour = java.awt.Color.white;
+var annotation = (this.seqAssociated && this.seqannot != null ? this.seqannot.get (seq) : this.annotation);
+if (annotation == null) {
+return currentColour;
+}if ((this.threshold == 0) || this.aboveThreshold (c, j)) {
+if (annotation.annotations != null && j < annotation.annotations.length && annotation.annotations[j] != null && !jalview.util.Comparison.isGap (c)) {
+var aj = annotation.annotations[j];
+if (this.aboveAnnotationThreshold == -1 || (this.annotationThreshold != null && (this.aboveAnnotationThreshold == 1 ? aj.value >= this.annotationThreshold.value : aj.value <= this.annotationThreshold.value))) {
+if (this.predefinedColours && aj.colour != null && !aj.colour.equals (java.awt.Color.black)) {
+currentColour = aj.colour;
+} else if (annotation.hasIcons && annotation.graph == 0) {
+if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.' && aj.secondaryStructure != '-') {
+if (this.colourScheme != null) {
+currentColour = this.colourScheme.findColour (c, j, seq);
+} else {
+if (annotation.isRNA ()) {
+currentColour = jalview.schemes.ColourSchemeProperty.rnaHelices[Clazz.floatToInt (aj.value)];
+} else {
+currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
+}}} else {
+return java.awt.Color.white;
+}} else if (this.noGradient) {
+if (this.colourScheme != null) {
+currentColour = this.colourScheme.findColour (c, j, seq);
+} else {
+if (aj.colour != null) {
+currentColour = aj.colour;
+}}} else {
+currentColour = this.shadeCalculation (annotation, j);
+}}if (this.conservationColouring) {
+currentColour = this.applyConservation (currentColour, j);
+}}}return currentColour;
+}, "~S,~N,jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "shadeCalculation",
+ function (annotation, j) {
+var range = 1;
+if (this.thresholdIsMinMax && annotation.threshold != null && this.aboveAnnotationThreshold == 1 && annotation.annotations[j].value >= annotation.threshold.value) {
+range = (annotation.annotations[j].value - annotation.threshold.value) / (annotation.graphMax - annotation.threshold.value);
+} else if (this.thresholdIsMinMax && annotation.threshold != null && this.aboveAnnotationThreshold == 0 && annotation.annotations[j].value >= annotation.graphMin) {
+range = (annotation.annotations[j].value - annotation.graphMin) / (annotation.threshold.value - annotation.graphMin);
+} else {
+if (annotation.graphMax != annotation.graphMin) {
+range = (annotation.annotations[j].value - annotation.graphMin) / (annotation.graphMax - annotation.graphMin);
+} else {
+range = 0;
+}}var dr = Clazz.floatToInt (this.rr * range + this.r1);
+var dg = Clazz.floatToInt (this.gg * range + this.g1);
+var db = Clazz.floatToInt (this.bb * range + this.b1);
+return new java.awt.Color (dr, dg, db);
+}, "jalview.datamodel.AlignmentAnnotation,~N");
+Clazz.defineMethod (c$, "isPredefinedColours",
+function () {
+return this.predefinedColours;
+});
+Clazz.defineMethod (c$, "setPredefinedColours",
+function (predefinedColours) {
+this.predefinedColours = predefinedColours;
+}, "~B");
+Clazz.defineMethod (c$, "isSeqAssociated",
+function () {
+return this.seqAssociated;
+});
+Clazz.defineMethod (c$, "setSeqAssociated",
+function (sassoc) {
+this.seqAssociated = sassoc;
+}, "~B");
+Clazz.defineStatics (c$,
+"NO_THRESHOLD", -1,
+"BELOW_THRESHOLD", 0,
+"ABOVE_THRESHOLD", 1);
+});
git://source.jalview.org / jalviewjs.git / blobdiff