X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fschemes%2FClustalxColourScheme.js;h=0556777d48866225d869232638e70e8981be78bb;hp=3897463a3a4fa69c64459b4b4206efcc4b25066f;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/schemes/ClustalxColourScheme.js b/site/j2s/jalview/schemes/ClustalxColourScheme.js
index 3897463..0556777 100644
--- a/site/j2s/jalview/schemes/ClustalxColourScheme.js
+++ b/site/j2s/jalview/schemes/ClustalxColourScheme.js
@@ -1,237 +1,237 @@
-Clazz.declarePackage ("jalview.schemes");
-Clazz.load (["jalview.schemes.ResidueColourScheme", "java.util.HashMap"], ["jalview.schemes.ConsensusColour", "$.ClustalxColourScheme"], ["jalview.schemes.Consensus", "$.ResidueProperties", "java.awt.Color"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.cons2 = null;
-this.colours = null;
-this.residueColour = null;
-this.size = 0;
-this.conses = null;
-this.includeGaps = true;
-Clazz.instantialize (this, arguments);
-}, jalview.schemes, "ClustalxColourScheme", jalview.schemes.ResidueColourScheme);
-Clazz.prepareFields (c$, function () {
-this.conses =  new Array (32);
-});
-Clazz.makeConstructor (c$, 
-function (alignment, hiddenReps) {
-Clazz.superConstructor (this, jalview.schemes.ClustalxColourScheme, []);
-this.alignmentChanged (alignment, hiddenReps);
-}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
-Clazz.overrideMethod (c$, "alignmentChanged", 
-function (alignment, hiddenReps) {
-var maxWidth = alignment.getWidth ();
-var seqs = alignment.getSequences (hiddenReps);
-this.cons2 =  Clazz.newIntArray (maxWidth, 24, 0);
-this.includeGaps = this.isIncludeGaps ();
-var start = 0;
-for (var j = 0; j < 24; j++) {
-for (var i = 0; i < maxWidth; i++) {
-this.cons2[i][j] = 0;
-}
-}
-var res;
-var i;
-var j = 0;
-var seq;
-for (var sq, $sq = seqs.iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {
-seq = sq.getSequence ();
-var end_j = seq.length - 1;
-for (i = start; i <= end_j; i++) {
-if ((seq.length - 1) < i) {
-res = 23;
-} else {
-res = jalview.schemes.ResidueProperties.aaIndex[seq[i].charCodeAt (0)];
-}this.cons2[i][res]++;
-}
-j++;
-}
-this.size = seqs.size ();
-this.makeColours ();
-}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
-Clazz.defineMethod (c$, "makeColours", 
-function () {
-this.conses[0] =  new jalview.schemes.Consensus ("WLVIMAFCYHP", 60);
-this.conses[1] =  new jalview.schemes.Consensus ("WLVIMAFCYHP", 80);
-this.conses[2] =  new jalview.schemes.Consensus ("ED", 50);
-this.conses[3] =  new jalview.schemes.Consensus ("KR", 60);
-this.conses[4] =  new jalview.schemes.Consensus ("G", 50);
-this.conses[5] =  new jalview.schemes.Consensus ("N", 50);
-this.conses[6] =  new jalview.schemes.Consensus ("QE", 50);
-this.conses[7] =  new jalview.schemes.Consensus ("P", 50);
-this.conses[8] =  new jalview.schemes.Consensus ("TS", 50);
-this.conses[26] =  new jalview.schemes.Consensus ("A", 85);
-this.conses[27] =  new jalview.schemes.Consensus ("C", 85);
-this.conses[10] =  new jalview.schemes.Consensus ("E", 85);
-this.conses[11] =  new jalview.schemes.Consensus ("F", 85);
-this.conses[12] =  new jalview.schemes.Consensus ("G", 85);
-this.conses[13] =  new jalview.schemes.Consensus ("H", 85);
-this.conses[14] =  new jalview.schemes.Consensus ("I", 85);
-this.conses[15] =  new jalview.schemes.Consensus ("L", 85);
-this.conses[16] =  new jalview.schemes.Consensus ("M", 85);
-this.conses[17] =  new jalview.schemes.Consensus ("N", 85);
-this.conses[18] =  new jalview.schemes.Consensus ("P", 85);
-this.conses[19] =  new jalview.schemes.Consensus ("Q", 85);
-this.conses[20] =  new jalview.schemes.Consensus ("R", 85);
-this.conses[21] =  new jalview.schemes.Consensus ("S", 85);
-this.conses[22] =  new jalview.schemes.Consensus ("T", 85);
-this.conses[23] =  new jalview.schemes.Consensus ("V", 85);
-this.conses[24] =  new jalview.schemes.Consensus ("W", 85);
-this.conses[25] =  new jalview.schemes.Consensus ("Y", 85);
-this.conses[28] =  new jalview.schemes.Consensus ("K", 85);
-this.conses[29] =  new jalview.schemes.Consensus ("D", 85);
-this.conses[30] =  new jalview.schemes.Consensus ("G", 0);
-this.conses[31] =  new jalview.schemes.Consensus ("P", 0);
-this.colours =  new Array (11);
-var tmp8 =  new Array (1);
-tmp8[0] = this.conses[30];
-this.colours[7] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.ORANGE), tmp8);
-var tmp9 =  new Array (1);
-tmp9[0] = this.conses[31];
-this.colours[8] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.YELLOW), tmp9);
-var tmp10 =  new Array (1);
-tmp10[0] = this.conses[27];
-this.colours[9] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.PINK), tmp8);
-var tmp1 =  new Array (14);
-tmp1[0] = this.conses[0];
-tmp1[1] = this.conses[1];
-tmp1[2] = this.conses[26];
-tmp1[3] = this.conses[27];
-tmp1[4] = this.conses[11];
-tmp1[5] = this.conses[13];
-tmp1[6] = this.conses[14];
-tmp1[7] = this.conses[15];
-tmp1[8] = this.conses[16];
-tmp1[9] = this.conses[23];
-tmp1[10] = this.conses[24];
-tmp1[11] = this.conses[25];
-tmp1[12] = this.conses[18];
-tmp1[13] = this.conses[19];
-this.colours[0] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.BLUE), tmp1);
-this.colours[10] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.CYAN), tmp1);
-var tmp2 =  new Array (5);
-tmp2[0] = this.conses[8];
-tmp2[1] = this.conses[21];
-tmp2[2] = this.conses[22];
-tmp2[3] = this.conses[0];
-tmp2[4] = this.conses[1];
-this.colours[1] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.GREEN), tmp2);
-var tmp3 =  new Array (3);
-tmp3[0] = this.conses[17];
-tmp3[1] = this.conses[29];
-tmp3[2] = this.conses[5];
-this.colours[2] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.GREEN), tmp3);
-var tmp4 =  new Array (6);
-tmp4[0] = this.conses[6];
-tmp4[1] = this.conses[19];
-tmp4[2] = this.conses[22];
-tmp4[3] = this.conses[3];
-tmp4[4] = this.conses[28];
-tmp4[5] = this.conses[20];
-this.colours[3] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.GREEN), tmp4);
-var tmp5 =  new Array (4);
-tmp5[0] = this.conses[3];
-tmp5[1] = this.conses[28];
-tmp5[2] = this.conses[20];
-tmp5[3] = this.conses[19];
-this.colours[4] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.RED), tmp5);
-var tmp6 =  new Array (6);
-tmp6[0] = this.conses[3];
-tmp6[1] = this.conses[29];
-tmp6[2] = this.conses[10];
-tmp6[3] = this.conses[6];
-tmp6[4] = this.conses[19];
-tmp6[5] = this.conses[2];
-this.colours[5] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.MAGENTA), tmp6);
-var tmp7 =  new Array (5);
-tmp7[0] = this.conses[3];
-tmp7[1] = this.conses[29];
-tmp7[2] = this.conses[10];
-tmp7[3] = this.conses[17];
-tmp7[4] = this.conses[2];
-this.colours[6] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.MAGENTA), tmp7);
-this.residueColour =  new Array (20);
-this.residueColour[0] = this.colours[0];
-this.residueColour[1] = this.colours[4];
-this.residueColour[2] = this.colours[2];
-this.residueColour[3] = this.colours[6];
-this.residueColour[4] = this.colours[0];
-this.residueColour[5] = this.colours[3];
-this.residueColour[6] = this.colours[5];
-this.residueColour[7] = this.colours[7];
-this.residueColour[8] = this.colours[10];
-this.residueColour[9] = this.colours[0];
-this.residueColour[10] = this.colours[0];
-this.residueColour[11] = this.colours[4];
-this.residueColour[12] = this.colours[0];
-this.residueColour[13] = this.colours[0];
-this.residueColour[14] = this.colours[8];
-this.residueColour[15] = this.colours[1];
-this.residueColour[16] = this.colours[1];
-this.residueColour[17] = this.colours[0];
-this.residueColour[18] = this.colours[10];
-this.residueColour[19] = this.colours[0];
-});
-Clazz.defineMethod (c$, "findColour", 
-function (c) {
-return java.awt.Color.pink;
-}, "~S");
-Clazz.defineMethod (c$, "findColour", 
-function (c, j, seq) {
-var currentColour;
-if (this.cons2.length <= j || (this.includeGaps && this.threshold != 0 && !this.aboveThreshold (c, j))) {
-return java.awt.Color.white;
-}var i = jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)];
-currentColour = java.awt.Color.white;
-if (i > 19) {
-return currentColour;
-}for (var k = 0; k < this.residueColour[i].conses.length; k++) {
-if (this.residueColour[i].conses[k].isConserved (this.cons2, j, this.size, this.includeGaps)) {
-currentColour = this.residueColour[i].c;
-}}
-if (i == 4) {
-if (this.conses[27].isConserved (this.cons2, j, this.size, this.includeGaps)) {
-currentColour = jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.PINK);
-}}if (this.conservationColouring) {
-currentColour = this.applyConservation (currentColour, j);
-}return currentColour;
-}, "~S,~N,jalview.datamodel.SequenceI");
-Clazz.defineMethod (c$, "isIncludeGaps", 
-function () {
-return this.includeGaps;
-});
-Clazz.defineMethod (c$, "setIncludeGaps", 
-function (includeGaps) {
-this.includeGaps = includeGaps;
-}, "~B");
-Clazz.overrideMethod (c$, "applyTo", 
-function (sg, hiddenRepSequences) {
-var css =  new jalview.schemes.ClustalxColourScheme (sg, hiddenRepSequences);
-css.includeGaps = this.includeGaps;
-return css;
-}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
-Clazz.defineStatics (c$,
-"EIGHTY_FIVE", 85,
-"FIFTY", 50,
-"EIGHTY", 80,
-"SIXTY", 60);
-c$.colhash = c$.prototype.colhash =  new java.util.HashMap ();
-{
-jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.RED,  new java.awt.Color (0.9, 0.2, 0.1));
-jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.BLUE,  new java.awt.Color (0.5, 0.7, 0.9));
-jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.GREEN,  new java.awt.Color (0.1, 0.8, 0.1));
-jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.ORANGE,  new java.awt.Color (0.9, 0.6, 0.3));
-jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.CYAN,  new java.awt.Color (0.1, 0.7, 0.7));
-jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.PINK,  new java.awt.Color (0.9, 0.5, 0.5));
-jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.MAGENTA,  new java.awt.Color (0.8, 0.3, 0.8));
-jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.YELLOW,  new java.awt.Color (0.8, 0.8, 0.0));
-}c$ = Clazz.decorateAsClass (function () {
-this.conses = null;
-this.c = null;
-Clazz.instantialize (this, arguments);
-}, jalview.schemes, "ConsensusColour");
-Clazz.makeConstructor (c$, 
-function (c, conses) {
-this.conses = conses;
-this.c = c;
-}, "java.awt.Color,~A");
-});
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (["jalview.schemes.ResidueColourScheme", "java.util.HashMap"], ["jalview.schemes.ConsensusColour", "$.ClustalxColourScheme"], ["jalview.schemes.Consensus", "$.ResidueProperties", "java.awt.Color"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.cons2 = null;
+this.colours = null;
+this.residueColour = null;
+this.size = 0;
+this.conses = null;
+this.includeGaps = true;
+Clazz.instantialize (this, arguments);
+}, jalview.schemes, "ClustalxColourScheme", jalview.schemes.ResidueColourScheme);
+Clazz.prepareFields (c$, function () {
+this.conses =  new Array (32);
+});
+Clazz.makeConstructor (c$, 
+function (alignment, hiddenReps) {
+Clazz.superConstructor (this, jalview.schemes.ClustalxColourScheme, []);
+this.alignmentChanged (alignment, hiddenReps);
+}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
+Clazz.overrideMethod (c$, "alignmentChanged", 
+function (alignment, hiddenReps) {
+var maxWidth = alignment.getWidth ();
+var seqs = alignment.getSequences (hiddenReps);
+this.cons2 =  Clazz.newIntArray (maxWidth, 24, 0);
+this.includeGaps = this.isIncludeGaps ();
+var start = 0;
+for (var j = 0; j < 24; j++) {
+for (var i = 0; i < maxWidth; i++) {
+this.cons2[i][j] = 0;
+}
+}
+var res;
+var i;
+var j = 0;
+var seq;
+for (var sq, $sq = seqs.iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {
+seq = sq.getSequence ();
+var end_j = seq.length - 1;
+for (i = start; i <= end_j; i++) {
+if ((seq.length - 1) < i) {
+res = 23;
+} else {
+res = jalview.schemes.ResidueProperties.aaIndex[seq[i].charCodeAt (0)];
+}this.cons2[i][res]++;
+}
+j++;
+}
+this.size = seqs.size ();
+this.makeColours ();
+}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
+Clazz.defineMethod (c$, "makeColours", 
+function () {
+this.conses[0] =  new jalview.schemes.Consensus ("WLVIMAFCYHP", 60);
+this.conses[1] =  new jalview.schemes.Consensus ("WLVIMAFCYHP", 80);
+this.conses[2] =  new jalview.schemes.Consensus ("ED", 50);
+this.conses[3] =  new jalview.schemes.Consensus ("KR", 60);
+this.conses[4] =  new jalview.schemes.Consensus ("G", 50);
+this.conses[5] =  new jalview.schemes.Consensus ("N", 50);
+this.conses[6] =  new jalview.schemes.Consensus ("QE", 50);
+this.conses[7] =  new jalview.schemes.Consensus ("P", 50);
+this.conses[8] =  new jalview.schemes.Consensus ("TS", 50);
+this.conses[26] =  new jalview.schemes.Consensus ("A", 85);
+this.conses[27] =  new jalview.schemes.Consensus ("C", 85);
+this.conses[10] =  new jalview.schemes.Consensus ("E", 85);
+this.conses[11] =  new jalview.schemes.Consensus ("F", 85);
+this.conses[12] =  new jalview.schemes.Consensus ("G", 85);
+this.conses[13] =  new jalview.schemes.Consensus ("H", 85);
+this.conses[14] =  new jalview.schemes.Consensus ("I", 85);
+this.conses[15] =  new jalview.schemes.Consensus ("L", 85);
+this.conses[16] =  new jalview.schemes.Consensus ("M", 85);
+this.conses[17] =  new jalview.schemes.Consensus ("N", 85);
+this.conses[18] =  new jalview.schemes.Consensus ("P", 85);
+this.conses[19] =  new jalview.schemes.Consensus ("Q", 85);
+this.conses[20] =  new jalview.schemes.Consensus ("R", 85);
+this.conses[21] =  new jalview.schemes.Consensus ("S", 85);
+this.conses[22] =  new jalview.schemes.Consensus ("T", 85);
+this.conses[23] =  new jalview.schemes.Consensus ("V", 85);
+this.conses[24] =  new jalview.schemes.Consensus ("W", 85);
+this.conses[25] =  new jalview.schemes.Consensus ("Y", 85);
+this.conses[28] =  new jalview.schemes.Consensus ("K", 85);
+this.conses[29] =  new jalview.schemes.Consensus ("D", 85);
+this.conses[30] =  new jalview.schemes.Consensus ("G", 0);
+this.conses[31] =  new jalview.schemes.Consensus ("P", 0);
+this.colours =  new Array (11);
+var tmp8 =  new Array (1);
+tmp8[0] = this.conses[30];
+this.colours[7] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.ORANGE), tmp8);
+var tmp9 =  new Array (1);
+tmp9[0] = this.conses[31];
+this.colours[8] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.YELLOW), tmp9);
+var tmp10 =  new Array (1);
+tmp10[0] = this.conses[27];
+this.colours[9] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.PINK), tmp8);
+var tmp1 =  new Array (14);
+tmp1[0] = this.conses[0];
+tmp1[1] = this.conses[1];
+tmp1[2] = this.conses[26];
+tmp1[3] = this.conses[27];
+tmp1[4] = this.conses[11];
+tmp1[5] = this.conses[13];
+tmp1[6] = this.conses[14];
+tmp1[7] = this.conses[15];
+tmp1[8] = this.conses[16];
+tmp1[9] = this.conses[23];
+tmp1[10] = this.conses[24];
+tmp1[11] = this.conses[25];
+tmp1[12] = this.conses[18];
+tmp1[13] = this.conses[19];
+this.colours[0] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.BLUE), tmp1);
+this.colours[10] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.CYAN), tmp1);
+var tmp2 =  new Array (5);
+tmp2[0] = this.conses[8];
+tmp2[1] = this.conses[21];
+tmp2[2] = this.conses[22];
+tmp2[3] = this.conses[0];
+tmp2[4] = this.conses[1];
+this.colours[1] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.GREEN), tmp2);
+var tmp3 =  new Array (3);
+tmp3[0] = this.conses[17];
+tmp3[1] = this.conses[29];
+tmp3[2] = this.conses[5];
+this.colours[2] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.GREEN), tmp3);
+var tmp4 =  new Array (6);
+tmp4[0] = this.conses[6];
+tmp4[1] = this.conses[19];
+tmp4[2] = this.conses[22];
+tmp4[3] = this.conses[3];
+tmp4[4] = this.conses[28];
+tmp4[5] = this.conses[20];
+this.colours[3] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.GREEN), tmp4);
+var tmp5 =  new Array (4);
+tmp5[0] = this.conses[3];
+tmp5[1] = this.conses[28];
+tmp5[2] = this.conses[20];
+tmp5[3] = this.conses[19];
+this.colours[4] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.RED), tmp5);
+var tmp6 =  new Array (6);
+tmp6[0] = this.conses[3];
+tmp6[1] = this.conses[29];
+tmp6[2] = this.conses[10];
+tmp6[3] = this.conses[6];
+tmp6[4] = this.conses[19];
+tmp6[5] = this.conses[2];
+this.colours[5] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.MAGENTA), tmp6);
+var tmp7 =  new Array (5);
+tmp7[0] = this.conses[3];
+tmp7[1] = this.conses[29];
+tmp7[2] = this.conses[10];
+tmp7[3] = this.conses[17];
+tmp7[4] = this.conses[2];
+this.colours[6] =  new jalview.schemes.ConsensusColour (jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.MAGENTA), tmp7);
+this.residueColour =  new Array (20);
+this.residueColour[0] = this.colours[0];
+this.residueColour[1] = this.colours[4];
+this.residueColour[2] = this.colours[2];
+this.residueColour[3] = this.colours[6];
+this.residueColour[4] = this.colours[0];
+this.residueColour[5] = this.colours[3];
+this.residueColour[6] = this.colours[5];
+this.residueColour[7] = this.colours[7];
+this.residueColour[8] = this.colours[10];
+this.residueColour[9] = this.colours[0];
+this.residueColour[10] = this.colours[0];
+this.residueColour[11] = this.colours[4];
+this.residueColour[12] = this.colours[0];
+this.residueColour[13] = this.colours[0];
+this.residueColour[14] = this.colours[8];
+this.residueColour[15] = this.colours[1];
+this.residueColour[16] = this.colours[1];
+this.residueColour[17] = this.colours[0];
+this.residueColour[18] = this.colours[10];
+this.residueColour[19] = this.colours[0];
+});
+Clazz.defineMethod (c$, "findColour", 
+function (c) {
+return java.awt.Color.pink;
+}, "~S");
+Clazz.defineMethod (c$, "findColour", 
+function (c, j, seq) {
+var currentColour;
+if (this.cons2.length <= j || (this.includeGaps && this.threshold != 0 && !this.aboveThreshold (c, j))) {
+return java.awt.Color.white;
+}var i = jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)];
+currentColour = java.awt.Color.white;
+if (i > 19) {
+return currentColour;
+}for (var k = 0; k < this.residueColour[i].conses.length; k++) {
+if (this.residueColour[i].conses[k].isConserved (this.cons2, j, this.size, this.includeGaps)) {
+currentColour = this.residueColour[i].c;
+}}
+if (i == 4) {
+if (this.conses[27].isConserved (this.cons2, j, this.size, this.includeGaps)) {
+currentColour = jalview.schemes.ClustalxColourScheme.colhash.get (java.awt.Color.PINK);
+}}if (this.conservationColouring) {
+currentColour = this.applyConservation (currentColour, j);
+}return currentColour;
+}, "~S,~N,jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "isIncludeGaps", 
+function () {
+return this.includeGaps;
+});
+Clazz.defineMethod (c$, "setIncludeGaps", 
+function (includeGaps) {
+this.includeGaps = includeGaps;
+}, "~B");
+Clazz.overrideMethod (c$, "applyTo", 
+function (sg, hiddenRepSequences) {
+var css =  new jalview.schemes.ClustalxColourScheme (sg, hiddenRepSequences);
+css.includeGaps = this.includeGaps;
+return css;
+}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
+Clazz.defineStatics (c$,
+"EIGHTY_FIVE", 85,
+"FIFTY", 50,
+"EIGHTY", 80,
+"SIXTY", 60);
+c$.colhash = c$.prototype.colhash =  new java.util.HashMap ();
+{
+jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.RED,  new java.awt.Color (0.9, 0.2, 0.1));
+jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.BLUE,  new java.awt.Color (0.5, 0.7, 0.9));
+jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.GREEN,  new java.awt.Color (0.1, 0.8, 0.1));
+jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.ORANGE,  new java.awt.Color (0.9, 0.6, 0.3));
+jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.CYAN,  new java.awt.Color (0.1, 0.7, 0.7));
+jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.PINK,  new java.awt.Color (0.9, 0.5, 0.5));
+jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.MAGENTA,  new java.awt.Color (0.8, 0.3, 0.8));
+jalview.schemes.ClustalxColourScheme.colhash.put (java.awt.Color.YELLOW,  new java.awt.Color (0.8, 0.8, 0.0));
+}c$ = Clazz.decorateAsClass (function () {
+this.conses = null;
+this.c = null;
+Clazz.instantialize (this, arguments);
+}, jalview.schemes, "ConsensusColour");
+Clazz.makeConstructor (c$, 
+function (c, conses) {
+this.conses = conses;
+this.c = c;
+}, "java.awt.Color,~A");
+});