X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fschemes%2FResidueProperties.js;h=2a8184572372ef39b9615c97d629ccd2b1469fa5;hp=612edb43866ffcbf15ce5648c6f15cc92b61a1f2;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6

diff --git a/site/j2s/jalview/schemes/ResidueProperties.js b/site/j2s/jalview/schemes/ResidueProperties.js
index 612edb4..2a81845 100644
--- a/site/j2s/jalview/schemes/ResidueProperties.js
+++ b/site/j2s/jalview/schemes/ResidueProperties.js
@@ -1,1090 +1,1090 @@
-Clazz.declarePackage ("jalview.schemes");
-Clazz.load (["jalview.analysis.scoremodels.FeatureScoreModel", "$.PIDScoreModel", "jalview.schemes.ScoreMatrix", "java.awt.Color", "java.util.ArrayList", "$.HashMap", "$.Hashtable", "$.Vector"], "jalview.schemes.ResidueProperties", ["java.lang.StringBuffer"], function () {
-c$ = Clazz.declareType (jalview.schemes, "ResidueProperties");
-c$.buildAmbiguityCodonSet = Clazz.defineMethod (c$, "buildAmbiguityCodonSet", 
-function () {
-if (jalview.schemes.ResidueProperties._ambiguityCodes.size () > 0) {
-System.err.println ("Ignoring multiple calls to buildAmbiguityCodonSet");
-return;
-}for (var acode, $acode = jalview.schemes.ResidueProperties.ambiguityCodes.entrySet ().iterator (); $acode.hasNext () && ((acode = $acode.next ()) || true);) {
-for (var r, $r = 0, $$r = acode.getValue (); $r < $$r.length && ((r = $$r[$r]) || true); $r++) {
-var codesfor = jalview.schemes.ResidueProperties._ambiguityCodes.get (r);
-if (codesfor == null) {
-jalview.schemes.ResidueProperties._ambiguityCodes.put (r, codesfor =  new java.util.ArrayList ());
-}if (!codesfor.contains (acode.getKey ())) {
-codesfor.add (acode.getKey ());
-} else {
-System.err.println ("Inconsistency in the IUBMB ambiguity code nomenclature table: collision for " + acode.getKey () + " in residue " + r);
-}}
-}
-var unambcodons = jalview.schemes.ResidueProperties.codonHash2.keySet ().toArray ( new Array (jalview.schemes.ResidueProperties.codonHash2.size ()));
-for (var codon, $codon = 0, $$codon = unambcodons; $codon < $$codon.length && ((codon = $$codon[$codon]) || true); $codon++) {
-var residue = jalview.schemes.ResidueProperties.codonHash2.get (codon);
-var acodon =  new Array (codon.length);
-for (var i = 0, iSize = codon.length; i < iSize; i++) {
-var _ac = "" + codon.charAt (i);
-var acodes = jalview.schemes.ResidueProperties._ambiguityCodes.get (_ac);
-if (acodes != null) {
-acodon[i] = acodes.toArray ( new Array (acodes.size ()));
-} else {
-acodon[i] =  Clazz.newArray (-1, []);
-}}
-var tpos =  Clazz.newIntArray (codon.length, 0);
-var cpos =  Clazz.newIntArray (codon.length, 0);
-for (var i = 0; i < tpos.length; i++) {
-tpos[i] = -1;
-}
-tpos[acodon.length - 1] = 0;
-var ipos;
-var j;
-while (tpos[0] < acodon[0].length) {
-var allres =  Clazz.newCharArray (tpos.length, '\0');
-var _acodon = "";
-var _anuc;
-for (ipos = 0; ipos < tpos.length; ipos++) {
-if (acodon[ipos].length == 0 || tpos[ipos] < 0) {
-_acodon += codon.charAt (ipos);
-allres[ipos] =  Clazz.newCharArray (-1, [codon.charAt (ipos)]);
-} else {
-_acodon += acodon[ipos][tpos[ipos]];
-var altbase = jalview.schemes.ResidueProperties.ambiguityCodes.get (acodon[ipos][tpos[ipos]]);
-allres[ipos] =  Clazz.newCharArray (altbase.length, '\0');
-j = 0;
-for (var ab, $ab = 0, $$ab = altbase; $ab < $$ab.length && ((ab = $$ab[$ab]) || true); $ab++) {
-allres[ipos][j++] = ab.charAt (0);
-}
-}}
-for (ipos = 0; ipos < cpos.length; ipos++) {
-cpos[ipos] = 0;
-}
-var valid = true;
-do {
-var _codon = "";
-for (j = 0; j < cpos.length; j++) {
-_codon += allres[j][cpos[j]];
-}
-var tr = jalview.schemes.ResidueProperties.codonHash2.get (_codon);
-if (valid = (tr != null && tr.equals (residue))) {
-ipos = acodon.length - 1;
-while (++cpos[ipos] >= allres[ipos].length && ipos > 0) {
-cpos[ipos] = 0;
-ipos--;
-}
-}} while (valid && cpos[0] < allres[0].length);
-if (valid) {
-jalview.schemes.ResidueProperties.codonHash2.put (_acodon, residue);
-} else {
-}ipos = acodon.length - 1;
-while (++tpos[ipos] >= acodon[ipos].length && ipos > 0) {
-tpos[ipos] = -1;
-ipos--;
-}
-}
-}
-});
-c$.getHydmax = Clazz.defineMethod (c$, "getHydmax", 
-function () {
-return 4.5;
-});
-c$.getHydmin = Clazz.defineMethod (c$, "getHydmin", 
-function () {
-return -3.9;
-});
-c$.getHyd = Clazz.defineMethod (c$, "getHyd", 
-function () {
-return jalview.schemes.ResidueProperties.hyd;
-});
-c$.getAA3Hash = Clazz.defineMethod (c$, "getAA3Hash", 
-function () {
-return jalview.schemes.ResidueProperties.aa3Hash;
-});
-c$.getDNA = Clazz.defineMethod (c$, "getDNA", 
-function () {
-return jalview.schemes.ResidueProperties.DNA;
-});
-c$.getBLOSUM62 = Clazz.defineMethod (c$, "getBLOSUM62", 
-function () {
-return jalview.schemes.ResidueProperties.BLOSUM62;
-});
-c$.getPAM250 = Clazz.defineMethod (c$, "getPAM250", 
-function (A1, A2) {
-return jalview.schemes.ResidueProperties.getPAM250 (A1.charAt (0), A2.charAt (0));
-}, "~S,~S");
-c$.getBLOSUM62 = Clazz.defineMethod (c$, "getBLOSUM62", 
-function (c1, c2) {
-var pog = 0;
-try {
-var a = jalview.schemes.ResidueProperties.aaIndex[c1.charCodeAt (0)];
-var b = jalview.schemes.ResidueProperties.aaIndex[c2.charCodeAt (0)];
-pog = jalview.schemes.ResidueProperties.BLOSUM62[a][b];
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-} else {
-throw e;
-}
-}
-return pog;
-}, "~S,~S");
-c$.getCodons = Clazz.defineMethod (c$, "getCodons", 
-function (res) {
-if (jalview.schemes.ResidueProperties.codonHash.containsKey (res)) {
-return jalview.schemes.ResidueProperties.codonHash.get (res);
-}return null;
-}, "~S");
-c$.codonTranslate = Clazz.defineMethod (c$, "codonTranslate", 
-function (lccodon) {
-if (false) {
-return jalview.schemes.ResidueProperties._codonTranslate (lccodon);
-}var cdn = jalview.schemes.ResidueProperties.codonHash2.get (lccodon.toUpperCase ());
-if (cdn != null && cdn.equals ("*")) {
-return "STOP";
-}return cdn;
-}, "~S");
-c$._codonTranslate = Clazz.defineMethod (c$, "_codonTranslate", 
-function (lccodon) {
-var codon = lccodon.toUpperCase ();
-if (codon.indexOf ('X') > -1 || codon.indexOf ('N') > -1) {
-return "X";
-}for (var key, $key = jalview.schemes.ResidueProperties.codonHash.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) {
-if (jalview.schemes.ResidueProperties.codonHash.get (key).contains (codon)) {
-return key;
-}}
-return null;
-}, "~S");
-c$.getDefaultPeptideMatrix = Clazz.defineMethod (c$, "getDefaultPeptideMatrix", 
-function () {
-return jalview.schemes.ResidueProperties.getBLOSUM62 ();
-});
-c$.getDefaultDnaMatrix = Clazz.defineMethod (c$, "getDefaultDnaMatrix", 
-function () {
-return jalview.schemes.ResidueProperties.getDNA ();
-});
-c$.getScoreMatrix = Clazz.defineMethod (c$, "getScoreMatrix", 
-function (pwtype) {
-var val = jalview.schemes.ResidueProperties.scoreMatrices.get (pwtype);
-if (val != null && Clazz.instanceOf (val, jalview.schemes.ScoreMatrix)) {
-return val;
-}return null;
-}, "~S");
-c$.getScoreModel = Clazz.defineMethod (c$, "getScoreModel", 
-function (pwtype) {
-return jalview.schemes.ResidueProperties.scoreMatrices.get (pwtype);
-}, "~S");
-c$.getPAM250 = Clazz.defineMethod (c$, "getPAM250", 
-function (c, d) {
-var a = jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)];
-var b = jalview.schemes.ResidueProperties.aaIndex[d.charCodeAt (0)];
-var pog = jalview.schemes.ResidueProperties.PAM250[a][b];
-return pog;
-}, "~S,~S");
-c$.getDssp3state = Clazz.defineMethod (c$, "getDssp3state", 
-function (ssstring) {
-if (ssstring == null) {
-return null;
-}var ss =  new StringBuffer ();
-for (var i = 0; i < ssstring.length; i++) {
-var ssc = ssstring.substring (i, i + 1);
-if (jalview.schemes.ResidueProperties.toDssp3State.containsKey (ssc)) {
-ss.append (jalview.schemes.ResidueProperties.toDssp3State.get (ssc));
-} else {
-ss.append (" ");
-}}
-return ss.toString ();
-}, "~S");
-c$.getRNASecStrucState = Clazz.defineMethod (c$, "getRNASecStrucState", 
-function (ssstring) {
-if (ssstring == null) {
-return null;
-}var ss =  new StringBuffer ();
-for (var i = 0; i < ssstring.length; i++) {
-var ssc = ssstring.substring (i, i + 1);
-if (jalview.schemes.ResidueProperties.toRNAssState.containsKey (ssc)) {
-ss.append (ssc);
-} else {
-ss.append (" ");
-}}
-return ss.toString ();
-}, "~S");
-c$.isCloseParenRNA = Clazz.defineMethod (c$, "isCloseParenRNA", 
-function (dc) {
-return jalview.schemes.ResidueProperties.RNAcloseParen[dc.charCodeAt (0)];
-}, "~S");
-c$.getResidues = Clazz.defineMethod (c$, "getResidues", 
-function (nucleotide, includeAmbiguous) {
-var result =  new java.util.ArrayList ();
-if (nucleotide) {
-for (var nuc, $nuc = jalview.schemes.ResidueProperties.nucleotideName.keySet ().iterator (); $nuc.hasNext () && ((nuc = $nuc.next ()) || true);) {
-var val = jalview.schemes.ResidueProperties.nucleotideIndex[nuc.charCodeAt (0)];
-if ((!includeAmbiguous && val > 4) || (val >= 10)) {
-continue;
-}nuc = nuc.toUpperCase ();
-if (!result.contains (nuc)) {
-result.add (nuc);
-}}
-} else {
-for (var res, $res = jalview.schemes.ResidueProperties.aa3Hash.keySet ().iterator (); $res.hasNext () && ((res = $res.next ()) || true);) {
-var index = jalview.schemes.ResidueProperties.aa3Hash.get (res).intValue ();
-if ((!includeAmbiguous && index >= 20) || index >= 23) {
-continue;
-}res = res.toUpperCase ();
-if (!result.contains (res)) {
-result.add (res);
-}}
-}return result;
-}, "~B,~B");
-c$.scoreMatrices = c$.prototype.scoreMatrices =  new java.util.Hashtable ();
-Clazz.defineStatics (c$,
-"aaIndex", null,
-"nucleotideIndex", null,
-"purinepyrimidineIndex", null);
-c$.aa3Hash = c$.prototype.aa3Hash =  new java.util.HashMap ();
-c$.aa2Triplet = c$.prototype.aa2Triplet =  new java.util.HashMap ();
-c$.nucleotideName = c$.prototype.nucleotideName =  new java.util.HashMap ();
-{
-jalview.schemes.ResidueProperties.aaIndex =  Clazz.newIntArray (255, 0);
-for (var i = 0; i < 255; i++) {
-jalview.schemes.ResidueProperties.aaIndex[i] = 23;
-}
-jalview.schemes.ResidueProperties.aaIndex['A'.charCodeAt (0)] = 0;
-jalview.schemes.ResidueProperties.aaIndex['R'.charCodeAt (0)] = 1;
-jalview.schemes.ResidueProperties.aaIndex['N'.charCodeAt (0)] = 2;
-jalview.schemes.ResidueProperties.aaIndex['D'.charCodeAt (0)] = 3;
-jalview.schemes.ResidueProperties.aaIndex['C'.charCodeAt (0)] = 4;
-jalview.schemes.ResidueProperties.aaIndex['Q'.charCodeAt (0)] = 5;
-jalview.schemes.ResidueProperties.aaIndex['E'.charCodeAt (0)] = 6;
-jalview.schemes.ResidueProperties.aaIndex['G'.charCodeAt (0)] = 7;
-jalview.schemes.ResidueProperties.aaIndex['H'.charCodeAt (0)] = 8;
-jalview.schemes.ResidueProperties.aaIndex['I'.charCodeAt (0)] = 9;
-jalview.schemes.ResidueProperties.aaIndex['L'.charCodeAt (0)] = 10;
-jalview.schemes.ResidueProperties.aaIndex['K'.charCodeAt (0)] = 11;
-jalview.schemes.ResidueProperties.aaIndex['M'.charCodeAt (0)] = 12;
-jalview.schemes.ResidueProperties.aaIndex['F'.charCodeAt (0)] = 13;
-jalview.schemes.ResidueProperties.aaIndex['P'.charCodeAt (0)] = 14;
-jalview.schemes.ResidueProperties.aaIndex['S'.charCodeAt (0)] = 15;
-jalview.schemes.ResidueProperties.aaIndex['T'.charCodeAt (0)] = 16;
-jalview.schemes.ResidueProperties.aaIndex['W'.charCodeAt (0)] = 17;
-jalview.schemes.ResidueProperties.aaIndex['Y'.charCodeAt (0)] = 18;
-jalview.schemes.ResidueProperties.aaIndex['V'.charCodeAt (0)] = 19;
-jalview.schemes.ResidueProperties.aaIndex['B'.charCodeAt (0)] = 20;
-jalview.schemes.ResidueProperties.aaIndex['Z'.charCodeAt (0)] = 21;
-jalview.schemes.ResidueProperties.aaIndex['X'.charCodeAt (0)] = 22;
-jalview.schemes.ResidueProperties.aaIndex['U'.charCodeAt (0)] = 22;
-jalview.schemes.ResidueProperties.aaIndex['a'.charCodeAt (0)] = 0;
-jalview.schemes.ResidueProperties.aaIndex['r'.charCodeAt (0)] = 1;
-jalview.schemes.ResidueProperties.aaIndex['n'.charCodeAt (0)] = 2;
-jalview.schemes.ResidueProperties.aaIndex['d'.charCodeAt (0)] = 3;
-jalview.schemes.ResidueProperties.aaIndex['c'.charCodeAt (0)] = 4;
-jalview.schemes.ResidueProperties.aaIndex['q'.charCodeAt (0)] = 5;
-jalview.schemes.ResidueProperties.aaIndex['e'.charCodeAt (0)] = 6;
-jalview.schemes.ResidueProperties.aaIndex['g'.charCodeAt (0)] = 7;
-jalview.schemes.ResidueProperties.aaIndex['h'.charCodeAt (0)] = 8;
-jalview.schemes.ResidueProperties.aaIndex['i'.charCodeAt (0)] = 9;
-jalview.schemes.ResidueProperties.aaIndex['l'.charCodeAt (0)] = 10;
-jalview.schemes.ResidueProperties.aaIndex['k'.charCodeAt (0)] = 11;
-jalview.schemes.ResidueProperties.aaIndex['m'.charCodeAt (0)] = 12;
-jalview.schemes.ResidueProperties.aaIndex['f'.charCodeAt (0)] = 13;
-jalview.schemes.ResidueProperties.aaIndex['p'.charCodeAt (0)] = 14;
-jalview.schemes.ResidueProperties.aaIndex['s'.charCodeAt (0)] = 15;
-jalview.schemes.ResidueProperties.aaIndex['t'.charCodeAt (0)] = 16;
-jalview.schemes.ResidueProperties.aaIndex['w'.charCodeAt (0)] = 17;
-jalview.schemes.ResidueProperties.aaIndex['y'.charCodeAt (0)] = 18;
-jalview.schemes.ResidueProperties.aaIndex['v'.charCodeAt (0)] = 19;
-jalview.schemes.ResidueProperties.aaIndex['b'.charCodeAt (0)] = 20;
-jalview.schemes.ResidueProperties.aaIndex['z'.charCodeAt (0)] = 21;
-jalview.schemes.ResidueProperties.aaIndex['x'.charCodeAt (0)] = 22;
-jalview.schemes.ResidueProperties.aaIndex['u'.charCodeAt (0)] = 22;
-}Clazz.defineStatics (c$,
-"maxProteinIndex", 23,
-"maxNucleotideIndex", 10);
-{
-jalview.schemes.ResidueProperties.nucleotideIndex =  Clazz.newIntArray (255, 0);
-for (var i = 0; i < 255; i++) {
-jalview.schemes.ResidueProperties.nucleotideIndex[i] = 10;
-}
-jalview.schemes.ResidueProperties.nucleotideIndex['A'.charCodeAt (0)] = 0;
-jalview.schemes.ResidueProperties.nucleotideIndex['a'.charCodeAt (0)] = 0;
-jalview.schemes.ResidueProperties.nucleotideIndex['C'.charCodeAt (0)] = 1;
-jalview.schemes.ResidueProperties.nucleotideIndex['c'.charCodeAt (0)] = 1;
-jalview.schemes.ResidueProperties.nucleotideIndex['G'.charCodeAt (0)] = 2;
-jalview.schemes.ResidueProperties.nucleotideIndex['g'.charCodeAt (0)] = 2;
-jalview.schemes.ResidueProperties.nucleotideIndex['T'.charCodeAt (0)] = 3;
-jalview.schemes.ResidueProperties.nucleotideIndex['t'.charCodeAt (0)] = 3;
-jalview.schemes.ResidueProperties.nucleotideIndex['U'.charCodeAt (0)] = 4;
-jalview.schemes.ResidueProperties.nucleotideIndex['u'.charCodeAt (0)] = 4;
-jalview.schemes.ResidueProperties.nucleotideIndex['I'.charCodeAt (0)] = 5;
-jalview.schemes.ResidueProperties.nucleotideIndex['i'.charCodeAt (0)] = 5;
-jalview.schemes.ResidueProperties.nucleotideIndex['X'.charCodeAt (0)] = 6;
-jalview.schemes.ResidueProperties.nucleotideIndex['x'.charCodeAt (0)] = 6;
-jalview.schemes.ResidueProperties.nucleotideIndex['R'.charCodeAt (0)] = 7;
-jalview.schemes.ResidueProperties.nucleotideIndex['r'.charCodeAt (0)] = 7;
-jalview.schemes.ResidueProperties.nucleotideIndex['Y'.charCodeAt (0)] = 8;
-jalview.schemes.ResidueProperties.nucleotideIndex['y'.charCodeAt (0)] = 8;
-jalview.schemes.ResidueProperties.nucleotideIndex['N'.charCodeAt (0)] = 9;
-jalview.schemes.ResidueProperties.nucleotideIndex['n'.charCodeAt (0)] = 9;
-jalview.schemes.ResidueProperties.nucleotideName.put ("A", "Adenine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("a", "Adenine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("G", "Guanine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("g", "Guanine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("C", "Cytosine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("c", "Cytosine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("T", "Thymine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("t", "Thymine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("U", "Uracil");
-jalview.schemes.ResidueProperties.nucleotideName.put ("u", "Uracil");
-jalview.schemes.ResidueProperties.nucleotideName.put ("I", "Inosine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("i", "Inosine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("X", "Xanthine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("x", "Xanthine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("R", "Unknown Purine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("r", "Unknown Purine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("Y", "Unknown Pyrimidine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("y", "Unknown Pyrimidine");
-jalview.schemes.ResidueProperties.nucleotideName.put ("N", "Unknown");
-jalview.schemes.ResidueProperties.nucleotideName.put ("n", "Unknown");
-jalview.schemes.ResidueProperties.nucleotideName.put ("W", "Weak nucleotide (A or T)");
-jalview.schemes.ResidueProperties.nucleotideName.put ("w", "Weak nucleotide (A or T)");
-jalview.schemes.ResidueProperties.nucleotideName.put ("S", "Strong nucleotide (G or C)");
-jalview.schemes.ResidueProperties.nucleotideName.put ("s", "Strong nucleotide (G or C)");
-jalview.schemes.ResidueProperties.nucleotideName.put ("M", "Amino (A or C)");
-jalview.schemes.ResidueProperties.nucleotideName.put ("m", "Amino (A or C)");
-jalview.schemes.ResidueProperties.nucleotideName.put ("K", "Keto (G or T)");
-jalview.schemes.ResidueProperties.nucleotideName.put ("k", "Keto (G or T)");
-jalview.schemes.ResidueProperties.nucleotideName.put ("B", "Not A (G or C or T)");
-jalview.schemes.ResidueProperties.nucleotideName.put ("b", "Not A (G or C or T)");
-jalview.schemes.ResidueProperties.nucleotideName.put ("H", "Not G (A or C or T)");
-jalview.schemes.ResidueProperties.nucleotideName.put ("h", "Not G (A or C or T)");
-jalview.schemes.ResidueProperties.nucleotideName.put ("D", "Not C (A or G or T)");
-jalview.schemes.ResidueProperties.nucleotideName.put ("d", "Not C (A or G or T)");
-jalview.schemes.ResidueProperties.nucleotideName.put ("V", "Not T (A or G or C");
-jalview.schemes.ResidueProperties.nucleotideName.put ("v", "Not T (A or G or C");
-}{
-jalview.schemes.ResidueProperties.purinepyrimidineIndex =  Clazz.newIntArray (255, 0);
-for (var i = 0; i < 255; i++) {
-jalview.schemes.ResidueProperties.purinepyrimidineIndex[i] = 3;
-}
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['A'.charCodeAt (0)] = 0;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['a'.charCodeAt (0)] = 0;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['C'.charCodeAt (0)] = 1;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['c'.charCodeAt (0)] = 1;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['G'.charCodeAt (0)] = 0;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['g'.charCodeAt (0)] = 0;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['T'.charCodeAt (0)] = 1;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['t'.charCodeAt (0)] = 1;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['U'.charCodeAt (0)] = 1;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['u'.charCodeAt (0)] = 1;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['I'.charCodeAt (0)] = 2;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['i'.charCodeAt (0)] = 2;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['X'.charCodeAt (0)] = 2;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['x'.charCodeAt (0)] = 2;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['R'.charCodeAt (0)] = 0;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['r'.charCodeAt (0)] = 0;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['Y'.charCodeAt (0)] = 1;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['y'.charCodeAt (0)] = 1;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['N'.charCodeAt (0)] = 2;
-jalview.schemes.ResidueProperties.purinepyrimidineIndex['n'.charCodeAt (0)] = 2;
-}{
-jalview.schemes.ResidueProperties.aa3Hash.put ("ALA",  new Integer (0));
-jalview.schemes.ResidueProperties.aa3Hash.put ("ARG",  new Integer (1));
-jalview.schemes.ResidueProperties.aa3Hash.put ("ASN",  new Integer (2));
-jalview.schemes.ResidueProperties.aa3Hash.put ("ASP",  new Integer (3));
-jalview.schemes.ResidueProperties.aa3Hash.put ("CYS",  new Integer (4));
-jalview.schemes.ResidueProperties.aa3Hash.put ("GLN",  new Integer (5));
-jalview.schemes.ResidueProperties.aa3Hash.put ("GLU",  new Integer (6));
-jalview.schemes.ResidueProperties.aa3Hash.put ("GLY",  new Integer (7));
-jalview.schemes.ResidueProperties.aa3Hash.put ("HIS",  new Integer (8));
-jalview.schemes.ResidueProperties.aa3Hash.put ("ILE",  new Integer (9));
-jalview.schemes.ResidueProperties.aa3Hash.put ("LEU",  new Integer (10));
-jalview.schemes.ResidueProperties.aa3Hash.put ("LYS",  new Integer (11));
-jalview.schemes.ResidueProperties.aa3Hash.put ("MET",  new Integer (12));
-jalview.schemes.ResidueProperties.aa3Hash.put ("PHE",  new Integer (13));
-jalview.schemes.ResidueProperties.aa3Hash.put ("PRO",  new Integer (14));
-jalview.schemes.ResidueProperties.aa3Hash.put ("SER",  new Integer (15));
-jalview.schemes.ResidueProperties.aa3Hash.put ("THR",  new Integer (16));
-jalview.schemes.ResidueProperties.aa3Hash.put ("TRP",  new Integer (17));
-jalview.schemes.ResidueProperties.aa3Hash.put ("TYR",  new Integer (18));
-jalview.schemes.ResidueProperties.aa3Hash.put ("VAL",  new Integer (19));
-jalview.schemes.ResidueProperties.aa3Hash.put ("ASX",  new Integer (20));
-jalview.schemes.ResidueProperties.aa3Hash.put ("GLX",  new Integer (21));
-jalview.schemes.ResidueProperties.aa3Hash.put ("XAA",  new Integer (22));
-jalview.schemes.ResidueProperties.aa3Hash.put ("-",  new Integer (23));
-jalview.schemes.ResidueProperties.aa3Hash.put ("*",  new Integer (23));
-jalview.schemes.ResidueProperties.aa3Hash.put (".",  new Integer (23));
-jalview.schemes.ResidueProperties.aa3Hash.put (" ",  new Integer (23));
-jalview.schemes.ResidueProperties.aa3Hash.put ("Gap",  new Integer (23));
-}{
-jalview.schemes.ResidueProperties.aa2Triplet.put ("A", "ALA");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("a", "ALA");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("R", "ARG");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("r", "ARG");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("N", "ASN");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("n", "ASN");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("D", "ASP");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("d", "ASP");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("C", "CYS");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("c", "CYS");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("Q", "GLN");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("q", "GLN");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("E", "GLU");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("e", "GLU");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("G", "GLY");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("g", "GLY");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("H", "HIS");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("h", "HIS");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("I", "ILE");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("i", "ILE");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("L", "LEU");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("l", "LEU");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("K", "LYS");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("k", "LYS");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("M", "MET");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("m", "MET");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("F", "PHE");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("f", "PHE");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("P", "PRO");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("p", "PRO");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("S", "SER");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("s", "SER");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("T", "THR");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("t", "THR");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("W", "TRP");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("w", "TRP");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("Y", "TYR");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("y", "TYR");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("V", "VAL");
-jalview.schemes.ResidueProperties.aa2Triplet.put ("v", "VAL");
-}Clazz.defineStatics (c$,
-"aa",  Clazz.newArray (-1, ["A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " "]));
-c$.midBlue = c$.prototype.midBlue =  new java.awt.Color (100, 100, 255);
-c$.scaleColours = c$.prototype.scaleColours =  new java.util.Vector ();
-{
-jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (114, 0, 147));
-jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (156, 0, 98));
-jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (190, 0, 0));
-jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.red);
-jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (255, 125, 0));
-jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.orange);
-jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (255, 194, 85));
-jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.yellow);
-jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (255, 255, 181));
-jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.white);
-}c$.taylor = c$.prototype.taylor =  Clazz.newArray (-1, [ new java.awt.Color (204, 255, 0),  new java.awt.Color (0, 0, 255),  new java.awt.Color (204, 0, 255),  new java.awt.Color (255, 0, 0),  new java.awt.Color (255, 255, 0),  new java.awt.Color (255, 0, 204),  new java.awt.Color (255, 0, 102),  new java.awt.Color (255, 153, 0),  new java.awt.Color (0, 102, 255),  new java.awt.Color (102, 255, 0),  new java.awt.Color (51, 255, 0),  new java.awt.Color (102, 0, 255),  new java.awt.Color (0, 255, 0),  new java.awt.Color (0, 255, 102),  new java.awt.Color (255, 204, 0),  new java.awt.Color (255, 51, 0),  new java.awt.Color (255, 102, 0),  new java.awt.Color (0, 204, 255),  new java.awt.Color (0, 255, 204),  new java.awt.Color (153, 255, 0), java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white]);
-c$.nucleotide = c$.prototype.nucleotide =  Clazz.newArray (-1, [ new java.awt.Color (100, 247, 63),  new java.awt.Color (255, 179, 64),  new java.awt.Color (235, 65, 60),  new java.awt.Color (60, 136, 238),  new java.awt.Color (60, 136, 238), java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white]);
-c$.purinepyrimidine = c$.prototype.purinepyrimidine =  Clazz.newArray (-1, [ new java.awt.Color (255, 131, 250),  new java.awt.Color (64, 224, 208), java.awt.Color.white, java.awt.Color.white]);
-c$.zappo = c$.prototype.zappo =  Clazz.newArray (-1, [java.awt.Color.pink, jalview.schemes.ResidueProperties.midBlue, java.awt.Color.green, java.awt.Color.red, java.awt.Color.yellow, java.awt.Color.green, java.awt.Color.red, java.awt.Color.magenta, jalview.schemes.ResidueProperties.midBlue, java.awt.Color.pink, java.awt.Color.pink, jalview.schemes.ResidueProperties.midBlue, java.awt.Color.pink, java.awt.Color.orange, java.awt.Color.magenta, java.awt.Color.green, java.awt.Color.green, java.awt.Color.orange, java.awt.Color.orange, java.awt.Color.pink, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white]);
-Clazz.defineStatics (c$,
-"hyd2",  Clazz.newDoubleArray (-1, [0.62, 0.29, -0.9, -0.74, 1.19, 0.48, -0.4, 1.38, -1.5, 1.06, 0.64, -0.78, 0.12, -0.85, -2.53, -0.18, -0.05, 1.08, 0.81, 0.0, 0.26, 0.0, 0.0]),
-"helix",  Clazz.newDoubleArray (-1, [1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0]),
-"helixmin", 0.57,
-"helixmax", 1.51,
-"strand",  Clazz.newDoubleArray (-1, [0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74, 1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0]),
-"strandmin", 0.37,
-"strandmax", 1.7,
-"turn",  Clazz.newDoubleArray (-1, [0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01, 0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0]),
-"turnmin", 0.47,
-"turnmax", 1.56,
-"buried",  Clazz.newDoubleArray (-1, [1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2, 0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00]),
-"buriedmin", 0.05,
-"buriedmax", 4.6,
-"hyd",  Clazz.newDoubleArray (-1, [1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9, 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0]),
-"hydmax", 4.5,
-"hydmin", -3.9,
-"BLOSUM62",  Clazz.newArray (-1, [ Clazz.newIntArray (-1, [4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0, -4]),  Clazz.newIntArray (-1, [-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4]),  Clazz.newIntArray (-1, [-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4]),  Clazz.newIntArray (-1, [-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4]),  Clazz.newIntArray (-1, [0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4]),  Clazz.newIntArray (-1, [-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4]),  Clazz.newIntArray (-1, [-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4]),  Clazz.newIntArray (-1, [0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4]),  Clazz.newIntArray (-1, [-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4]),  Clazz.newIntArray (-1, [-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4]),  Clazz.newIntArray (-1, [-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4]),  Clazz.newIntArray (-1, [-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4]),  Clazz.newIntArray (-1, [-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4]),  Clazz.newIntArray (-1, [-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4]),  Clazz.newIntArray (-1, [-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4]),  Clazz.newIntArray (-1, [1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4]),  Clazz.newIntArray (-1, [0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4]),  Clazz.newIntArray (-1, [-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4]),  Clazz.newIntArray (-1, [-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4]),  Clazz.newIntArray (-1, [0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4]),  Clazz.newIntArray (-1, [-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4]),  Clazz.newIntArray (-1, [-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4]),  Clazz.newIntArray (-1, [0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4]),  Clazz.newIntArray (-1, [-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1])]),
-"PAM250",  Clazz.newArray (-1, [ Clazz.newIntArray (-1, [2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0, 0, 0, 0, -8]),  Clazz.newIntArray (-1, [-2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4, -2, -1, 0, -1, -8]),  Clazz.newIntArray (-1, [0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2, 2, 1, 0, -8]),  Clazz.newIntArray (-1, [0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2, 3, 3, -1, -8]),  Clazz.newIntArray (-1, [-2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2, -8, 0, -2, -4, -5, -3, -8]),  Clazz.newIntArray (-1, [0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4, -2, 1, 3, -1, -8]),  Clazz.newIntArray (-1, [0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2, 3, 3, -1, -8]),  Clazz.newIntArray (-1, [1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5, -1, 0, 0, -1, -8]),  Clazz.newIntArray (-1, [-1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0, -2, 1, 2, -1, -8]),  Clazz.newIntArray (-1, [-1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5, -1, 4, -2, -2, -1, -8]),  Clazz.newIntArray (-1, [-2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2, -1, 2, -3, -3, -1, -8]),  Clazz.newIntArray (-1, [-1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2, 1, 0, -1, -8]),  Clazz.newIntArray (-1, [-1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2, 2, -2, -2, -1, -8]),  Clazz.newIntArray (-1, [-3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7, -1, -4, -5, -2, -8]),  Clazz.newIntArray (-1, [1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5, -1, -1, 0, -1, -8]),  Clazz.newIntArray (-1, [1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1, 0, 0, 0, -8]),  Clazz.newIntArray (-1, [1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0, 0, -1, 0, -8]),  Clazz.newIntArray (-1, [-6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17, 0, -6, -5, -6, -4, -8]),  Clazz.newIntArray (-1, [-3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0, 10, -2, -3, -4, -2, -8]),  Clazz.newIntArray (-1, [0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6, -2, 4, -2, -2, -1, -8]),  Clazz.newIntArray (-1, [0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2, 3, 2, -1, -8]),  Clazz.newIntArray (-1, [0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2, 2, 3, -1, -8]),  Clazz.newIntArray (-1, [0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4, -2, -1, -1, -1, -1, -8]),  Clazz.newIntArray (-1, [-8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, 1])]));
-c$.ssHash = c$.prototype.ssHash =  new java.util.Hashtable ();
-{
-jalview.schemes.ResidueProperties.ssHash.put ("H", java.awt.Color.magenta);
-jalview.schemes.ResidueProperties.ssHash.put ("E", java.awt.Color.yellow);
-jalview.schemes.ResidueProperties.ssHash.put ("-", java.awt.Color.white);
-jalview.schemes.ResidueProperties.ssHash.put (".", java.awt.Color.white);
-jalview.schemes.ResidueProperties.ssHash.put ("S", java.awt.Color.cyan);
-jalview.schemes.ResidueProperties.ssHash.put ("T", java.awt.Color.blue);
-jalview.schemes.ResidueProperties.ssHash.put ("G", java.awt.Color.pink);
-jalview.schemes.ResidueProperties.ssHash.put ("I", java.awt.Color.pink);
-jalview.schemes.ResidueProperties.ssHash.put ("B", java.awt.Color.yellow);
-}Clazz.defineStatics (c$,
-"DNA",  Clazz.newArray (-1, [ Clazz.newIntArray (-1, [10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1]),  Clazz.newIntArray (-1, [-8, 10, -8, -8, -8, 1, 1, -8, 1, 1, 1]),  Clazz.newIntArray (-1, [-8, -8, 10, -8, -8, 1, 1, 1, -8, 1, 1]),  Clazz.newIntArray (-1, [-8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1]),  Clazz.newIntArray (-1, [-8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1]),  Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 10, 0, 0, 0, 1, 1]),  Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 0, 10, 0, 0, 1, 1]),  Clazz.newIntArray (-1, [1, -8, 1, -8, -8, 0, 0, 10, -8, 1, 1]),  Clazz.newIntArray (-1, [-8, 1, -8, 1, 1, 0, 0, -8, 10, 1, 1]),  Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 1]),  Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1])]));
-{
-jalview.schemes.ResidueProperties.scoreMatrices.put ("BLOSUM62",  new jalview.schemes.ScoreMatrix ("BLOSUM62", jalview.schemes.ResidueProperties.BLOSUM62, 0));
-jalview.schemes.ResidueProperties.scoreMatrices.put ("PAM250",  new jalview.schemes.ScoreMatrix ("PAM250", jalview.schemes.ResidueProperties.PAM250, 0));
-jalview.schemes.ResidueProperties.scoreMatrices.put ("DNA",  new jalview.schemes.ScoreMatrix ("DNA", jalview.schemes.ResidueProperties.DNA, 1));
-}c$.pidColours = c$.prototype.pidColours =  Clazz.newArray (-1, [jalview.schemes.ResidueProperties.midBlue,  new java.awt.Color (153, 153, 255),  new java.awt.Color (204, 204, 255)]);
-Clazz.defineStatics (c$,
-"pidThresholds",  Clazz.newFloatArray (-1, [80, 60, 40]));
-c$.codonHash = c$.prototype.codonHash =  new java.util.HashMap ();
-c$.Lys = c$.prototype.Lys =  new java.util.ArrayList ();
-c$.Asn = c$.prototype.Asn =  new java.util.ArrayList ();
-c$.Gln = c$.prototype.Gln =  new java.util.ArrayList ();
-c$.His = c$.prototype.His =  new java.util.ArrayList ();
-c$.Glu = c$.prototype.Glu =  new java.util.ArrayList ();
-c$.Asp = c$.prototype.Asp =  new java.util.ArrayList ();
-c$.Tyr = c$.prototype.Tyr =  new java.util.ArrayList ();
-c$.Thr = c$.prototype.Thr =  new java.util.ArrayList ();
-c$.Pro = c$.prototype.Pro =  new java.util.ArrayList ();
-c$.Ala = c$.prototype.Ala =  new java.util.ArrayList ();
-c$.Ser = c$.prototype.Ser =  new java.util.ArrayList ();
-c$.Arg = c$.prototype.Arg =  new java.util.ArrayList ();
-c$.Gly = c$.prototype.Gly =  new java.util.ArrayList ();
-c$.Trp = c$.prototype.Trp =  new java.util.ArrayList ();
-c$.Cys = c$.prototype.Cys =  new java.util.ArrayList ();
-c$.Ile = c$.prototype.Ile =  new java.util.ArrayList ();
-c$.Met = c$.prototype.Met =  new java.util.ArrayList ();
-c$.Leu = c$.prototype.Leu =  new java.util.ArrayList ();
-c$.Val = c$.prototype.Val =  new java.util.ArrayList ();
-c$.Phe = c$.prototype.Phe =  new java.util.ArrayList ();
-c$.STOP = c$.prototype.STOP =  new java.util.ArrayList ();
-Clazz.defineStatics (c$,
-"START", "ATG");
-{
-jalview.schemes.ResidueProperties.codonHash.put ("K", jalview.schemes.ResidueProperties.Lys);
-jalview.schemes.ResidueProperties.codonHash.put ("N", jalview.schemes.ResidueProperties.Asn);
-jalview.schemes.ResidueProperties.codonHash.put ("Q", jalview.schemes.ResidueProperties.Gln);
-jalview.schemes.ResidueProperties.codonHash.put ("H", jalview.schemes.ResidueProperties.His);
-jalview.schemes.ResidueProperties.codonHash.put ("E", jalview.schemes.ResidueProperties.Glu);
-jalview.schemes.ResidueProperties.codonHash.put ("D", jalview.schemes.ResidueProperties.Asp);
-jalview.schemes.ResidueProperties.codonHash.put ("Y", jalview.schemes.ResidueProperties.Tyr);
-jalview.schemes.ResidueProperties.codonHash.put ("T", jalview.schemes.ResidueProperties.Thr);
-jalview.schemes.ResidueProperties.codonHash.put ("P", jalview.schemes.ResidueProperties.Pro);
-jalview.schemes.ResidueProperties.codonHash.put ("A", jalview.schemes.ResidueProperties.Ala);
-jalview.schemes.ResidueProperties.codonHash.put ("S", jalview.schemes.ResidueProperties.Ser);
-jalview.schemes.ResidueProperties.codonHash.put ("R", jalview.schemes.ResidueProperties.Arg);
-jalview.schemes.ResidueProperties.codonHash.put ("G", jalview.schemes.ResidueProperties.Gly);
-jalview.schemes.ResidueProperties.codonHash.put ("W", jalview.schemes.ResidueProperties.Trp);
-jalview.schemes.ResidueProperties.codonHash.put ("C", jalview.schemes.ResidueProperties.Cys);
-jalview.schemes.ResidueProperties.codonHash.put ("I", jalview.schemes.ResidueProperties.Ile);
-jalview.schemes.ResidueProperties.codonHash.put ("M", jalview.schemes.ResidueProperties.Met);
-jalview.schemes.ResidueProperties.codonHash.put ("L", jalview.schemes.ResidueProperties.Leu);
-jalview.schemes.ResidueProperties.codonHash.put ("V", jalview.schemes.ResidueProperties.Val);
-jalview.schemes.ResidueProperties.codonHash.put ("F", jalview.schemes.ResidueProperties.Phe);
-jalview.schemes.ResidueProperties.codonHash.put ("STOP", jalview.schemes.ResidueProperties.STOP);
-}c$.ambiguityCodes = c$.prototype.ambiguityCodes =  new java.util.Hashtable ();
-c$.codonHash2 = c$.prototype.codonHash2 =  new java.util.Hashtable ();
-c$._ambiguityCodes = c$.prototype._ambiguityCodes =  new java.util.Hashtable ();
-{
-jalview.schemes.ResidueProperties.ambiguityCodes.put ("R",  Clazz.newArray (-1, ["A", "G"]));
-jalview.schemes.ResidueProperties.ambiguityCodes.put ("Y",  Clazz.newArray (-1, ["T", "C"]));
-jalview.schemes.ResidueProperties.ambiguityCodes.put ("W",  Clazz.newArray (-1, ["A", "T"]));
-jalview.schemes.ResidueProperties.ambiguityCodes.put ("S",  Clazz.newArray (-1, ["G", "C"]));
-jalview.schemes.ResidueProperties.ambiguityCodes.put ("M",  Clazz.newArray (-1, ["A", "C"]));
-jalview.schemes.ResidueProperties.ambiguityCodes.put ("K",  Clazz.newArray (-1, ["G", "T"]));
-jalview.schemes.ResidueProperties.ambiguityCodes.put ("H",  Clazz.newArray (-1, ["A", "T", "C"]));
-jalview.schemes.ResidueProperties.ambiguityCodes.put ("B",  Clazz.newArray (-1, ["G", "T", "C"]));
-jalview.schemes.ResidueProperties.ambiguityCodes.put ("V",  Clazz.newArray (-1, ["G", "A", "C"]));
-jalview.schemes.ResidueProperties.ambiguityCodes.put ("D",  Clazz.newArray (-1, ["G", "A", "T"]));
-jalview.schemes.ResidueProperties.ambiguityCodes.put ("N",  Clazz.newArray (-1, ["G", "A", "T", "C"]));
-jalview.schemes.ResidueProperties.codonHash2.put ("AAA", "K");
-jalview.schemes.ResidueProperties.codonHash2.put ("AAG", "K");
-jalview.schemes.ResidueProperties.codonHash2.put ("AAC", "N");
-jalview.schemes.ResidueProperties.codonHash2.put ("AAT", "N");
-jalview.schemes.ResidueProperties.codonHash2.put ("CAA", "Q");
-jalview.schemes.ResidueProperties.codonHash2.put ("CAG", "Q");
-jalview.schemes.ResidueProperties.codonHash2.put ("CAC", "H");
-jalview.schemes.ResidueProperties.codonHash2.put ("CAT", "H");
-jalview.schemes.ResidueProperties.codonHash2.put ("GAA", "E");
-jalview.schemes.ResidueProperties.codonHash2.put ("GAG", "E");
-jalview.schemes.ResidueProperties.codonHash2.put ("GAC", "D");
-jalview.schemes.ResidueProperties.codonHash2.put ("GAT", "D");
-jalview.schemes.ResidueProperties.codonHash2.put ("TAC", "Y");
-jalview.schemes.ResidueProperties.codonHash2.put ("TAT", "Y");
-jalview.schemes.ResidueProperties.codonHash2.put ("ACA", "T");
-jalview.schemes.ResidueProperties.codonHash2.put ("ACC", "T");
-jalview.schemes.ResidueProperties.codonHash2.put ("ACT", "T");
-jalview.schemes.ResidueProperties.codonHash2.put ("ACG", "T");
-jalview.schemes.ResidueProperties.codonHash2.put ("CCA", "P");
-jalview.schemes.ResidueProperties.codonHash2.put ("CCG", "P");
-jalview.schemes.ResidueProperties.codonHash2.put ("CCC", "P");
-jalview.schemes.ResidueProperties.codonHash2.put ("CCT", "P");
-jalview.schemes.ResidueProperties.codonHash2.put ("GCA", "A");
-jalview.schemes.ResidueProperties.codonHash2.put ("GCG", "A");
-jalview.schemes.ResidueProperties.codonHash2.put ("GCC", "A");
-jalview.schemes.ResidueProperties.codonHash2.put ("GCT", "A");
-jalview.schemes.ResidueProperties.codonHash2.put ("TCA", "S");
-jalview.schemes.ResidueProperties.codonHash2.put ("TCG", "S");
-jalview.schemes.ResidueProperties.codonHash2.put ("TCC", "S");
-jalview.schemes.ResidueProperties.codonHash2.put ("TCT", "S");
-jalview.schemes.ResidueProperties.codonHash2.put ("AGC", "S");
-jalview.schemes.ResidueProperties.codonHash2.put ("AGT", "S");
-jalview.schemes.ResidueProperties.codonHash2.put ("AGA", "R");
-jalview.schemes.ResidueProperties.codonHash2.put ("AGG", "R");
-jalview.schemes.ResidueProperties.codonHash2.put ("CGA", "R");
-jalview.schemes.ResidueProperties.codonHash2.put ("CGG", "R");
-jalview.schemes.ResidueProperties.codonHash2.put ("CGC", "R");
-jalview.schemes.ResidueProperties.codonHash2.put ("CGT", "R");
-jalview.schemes.ResidueProperties.codonHash2.put ("GGA", "G");
-jalview.schemes.ResidueProperties.codonHash2.put ("GGG", "G");
-jalview.schemes.ResidueProperties.codonHash2.put ("GGC", "G");
-jalview.schemes.ResidueProperties.codonHash2.put ("GGT", "G");
-jalview.schemes.ResidueProperties.codonHash2.put ("TGA", "*");
-jalview.schemes.ResidueProperties.codonHash2.put ("TAA", "*");
-jalview.schemes.ResidueProperties.codonHash2.put ("TAG", "*");
-jalview.schemes.ResidueProperties.codonHash2.put ("TGG", "W");
-jalview.schemes.ResidueProperties.codonHash2.put ("TGC", "C");
-jalview.schemes.ResidueProperties.codonHash2.put ("TGT", "C");
-jalview.schemes.ResidueProperties.codonHash2.put ("ATA", "I");
-jalview.schemes.ResidueProperties.codonHash2.put ("ATC", "I");
-jalview.schemes.ResidueProperties.codonHash2.put ("ATT", "I");
-jalview.schemes.ResidueProperties.codonHash2.put ("ATG", "M");
-jalview.schemes.ResidueProperties.codonHash2.put ("CTA", "L");
-jalview.schemes.ResidueProperties.codonHash2.put ("CTG", "L");
-jalview.schemes.ResidueProperties.codonHash2.put ("CTC", "L");
-jalview.schemes.ResidueProperties.codonHash2.put ("CTT", "L");
-jalview.schemes.ResidueProperties.codonHash2.put ("TTA", "L");
-jalview.schemes.ResidueProperties.codonHash2.put ("TTG", "L");
-jalview.schemes.ResidueProperties.codonHash2.put ("GTA", "V");
-jalview.schemes.ResidueProperties.codonHash2.put ("GTG", "V");
-jalview.schemes.ResidueProperties.codonHash2.put ("GTC", "V");
-jalview.schemes.ResidueProperties.codonHash2.put ("GTT", "V");
-jalview.schemes.ResidueProperties.codonHash2.put ("TTC", "F");
-jalview.schemes.ResidueProperties.codonHash2.put ("TTT", "F");
-jalview.schemes.ResidueProperties.buildAmbiguityCodonSet ();
-}{
-jalview.schemes.ResidueProperties.Lys.add ("AAA");
-jalview.schemes.ResidueProperties.Lys.add ("AAG");
-jalview.schemes.ResidueProperties.Asn.add ("AAC");
-jalview.schemes.ResidueProperties.Asn.add ("AAT");
-jalview.schemes.ResidueProperties.Gln.add ("CAA");
-jalview.schemes.ResidueProperties.Gln.add ("CAG");
-jalview.schemes.ResidueProperties.His.add ("CAC");
-jalview.schemes.ResidueProperties.His.add ("CAT");
-jalview.schemes.ResidueProperties.Glu.add ("GAA");
-jalview.schemes.ResidueProperties.Glu.add ("GAG");
-jalview.schemes.ResidueProperties.Asp.add ("GAC");
-jalview.schemes.ResidueProperties.Asp.add ("GAT");
-jalview.schemes.ResidueProperties.Tyr.add ("TAC");
-jalview.schemes.ResidueProperties.Tyr.add ("TAT");
-jalview.schemes.ResidueProperties.Thr.add ("ACA");
-jalview.schemes.ResidueProperties.Thr.add ("ACG");
-jalview.schemes.ResidueProperties.Thr.add ("ACC");
-jalview.schemes.ResidueProperties.Thr.add ("ACT");
-jalview.schemes.ResidueProperties.Pro.add ("CCA");
-jalview.schemes.ResidueProperties.Pro.add ("CCG");
-jalview.schemes.ResidueProperties.Pro.add ("CCC");
-jalview.schemes.ResidueProperties.Pro.add ("CCT");
-jalview.schemes.ResidueProperties.Ala.add ("GCA");
-jalview.schemes.ResidueProperties.Ala.add ("GCG");
-jalview.schemes.ResidueProperties.Ala.add ("GCC");
-jalview.schemes.ResidueProperties.Ala.add ("GCT");
-jalview.schemes.ResidueProperties.Ser.add ("TCA");
-jalview.schemes.ResidueProperties.Ser.add ("TCG");
-jalview.schemes.ResidueProperties.Ser.add ("TCC");
-jalview.schemes.ResidueProperties.Ser.add ("TCT");
-jalview.schemes.ResidueProperties.Ser.add ("AGC");
-jalview.schemes.ResidueProperties.Ser.add ("AGT");
-jalview.schemes.ResidueProperties.Arg.add ("AGA");
-jalview.schemes.ResidueProperties.Arg.add ("AGG");
-jalview.schemes.ResidueProperties.Arg.add ("CGA");
-jalview.schemes.ResidueProperties.Arg.add ("CGG");
-jalview.schemes.ResidueProperties.Arg.add ("CGC");
-jalview.schemes.ResidueProperties.Arg.add ("CGT");
-jalview.schemes.ResidueProperties.Gly.add ("GGA");
-jalview.schemes.ResidueProperties.Gly.add ("GGG");
-jalview.schemes.ResidueProperties.Gly.add ("GGC");
-jalview.schemes.ResidueProperties.Gly.add ("GGT");
-jalview.schemes.ResidueProperties.STOP.add ("TGA");
-jalview.schemes.ResidueProperties.STOP.add ("TAA");
-jalview.schemes.ResidueProperties.STOP.add ("TAG");
-jalview.schemes.ResidueProperties.Trp.add ("TGG");
-jalview.schemes.ResidueProperties.Cys.add ("TGC");
-jalview.schemes.ResidueProperties.Cys.add ("TGT");
-jalview.schemes.ResidueProperties.Ile.add ("ATA");
-jalview.schemes.ResidueProperties.Ile.add ("ATC");
-jalview.schemes.ResidueProperties.Ile.add ("ATT");
-jalview.schemes.ResidueProperties.Met.add ("ATG");
-jalview.schemes.ResidueProperties.Leu.add ("CTA");
-jalview.schemes.ResidueProperties.Leu.add ("CTG");
-jalview.schemes.ResidueProperties.Leu.add ("CTC");
-jalview.schemes.ResidueProperties.Leu.add ("CTT");
-jalview.schemes.ResidueProperties.Leu.add ("TTA");
-jalview.schemes.ResidueProperties.Leu.add ("TTG");
-jalview.schemes.ResidueProperties.Val.add ("GTA");
-jalview.schemes.ResidueProperties.Val.add ("GTG");
-jalview.schemes.ResidueProperties.Val.add ("GTC");
-jalview.schemes.ResidueProperties.Val.add ("GTT");
-jalview.schemes.ResidueProperties.Phe.add ("TTC");
-jalview.schemes.ResidueProperties.Phe.add ("TTT");
-}c$.propHash = c$.prototype.propHash =  new java.util.Hashtable ();
-c$.hydrophobic = c$.prototype.hydrophobic =  new java.util.Hashtable ();
-c$.polar = c$.prototype.polar =  new java.util.Hashtable ();
-c$.small = c$.prototype.small =  new java.util.Hashtable ();
-c$.positive = c$.prototype.positive =  new java.util.Hashtable ();
-c$.negative = c$.prototype.negative =  new java.util.Hashtable ();
-c$.charged = c$.prototype.charged =  new java.util.Hashtable ();
-c$.aromatic = c$.prototype.aromatic =  new java.util.Hashtable ();
-c$.aliphatic = c$.prototype.aliphatic =  new java.util.Hashtable ();
-c$.tiny = c$.prototype.tiny =  new java.util.Hashtable ();
-c$.proline = c$.prototype.proline =  new java.util.Hashtable ();
-{
-jalview.schemes.ResidueProperties.hydrophobic.put ("I",  new Integer (1));
-jalview.schemes.ResidueProperties.hydrophobic.put ("L",  new Integer (1));
-jalview.schemes.ResidueProperties.hydrophobic.put ("V",  new Integer (1));
-jalview.schemes.ResidueProperties.hydrophobic.put ("C",  new Integer (1));
-jalview.schemes.ResidueProperties.hydrophobic.put ("A",  new Integer (1));
-jalview.schemes.ResidueProperties.hydrophobic.put ("G",  new Integer (1));
-jalview.schemes.ResidueProperties.hydrophobic.put ("M",  new Integer (1));
-jalview.schemes.ResidueProperties.hydrophobic.put ("F",  new Integer (1));
-jalview.schemes.ResidueProperties.hydrophobic.put ("Y",  new Integer (1));
-jalview.schemes.ResidueProperties.hydrophobic.put ("W",  new Integer (1));
-jalview.schemes.ResidueProperties.hydrophobic.put ("H",  new Integer (1));
-jalview.schemes.ResidueProperties.hydrophobic.put ("K",  new Integer (1));
-jalview.schemes.ResidueProperties.hydrophobic.put ("X",  new Integer (1));
-jalview.schemes.ResidueProperties.hydrophobic.put ("-",  new Integer (1));
-jalview.schemes.ResidueProperties.hydrophobic.put ("*",  new Integer (1));
-jalview.schemes.ResidueProperties.hydrophobic.put ("R",  new Integer (0));
-jalview.schemes.ResidueProperties.hydrophobic.put ("E",  new Integer (0));
-jalview.schemes.ResidueProperties.hydrophobic.put ("Q",  new Integer (0));
-jalview.schemes.ResidueProperties.hydrophobic.put ("D",  new Integer (0));
-jalview.schemes.ResidueProperties.hydrophobic.put ("N",  new Integer (0));
-jalview.schemes.ResidueProperties.hydrophobic.put ("S",  new Integer (0));
-jalview.schemes.ResidueProperties.hydrophobic.put ("T",  new Integer (0));
-jalview.schemes.ResidueProperties.hydrophobic.put ("P",  new Integer (0));
-}{
-jalview.schemes.ResidueProperties.polar.put ("Y",  new Integer (1));
-jalview.schemes.ResidueProperties.polar.put ("W",  new Integer (1));
-jalview.schemes.ResidueProperties.polar.put ("H",  new Integer (1));
-jalview.schemes.ResidueProperties.polar.put ("K",  new Integer (1));
-jalview.schemes.ResidueProperties.polar.put ("R",  new Integer (1));
-jalview.schemes.ResidueProperties.polar.put ("E",  new Integer (1));
-jalview.schemes.ResidueProperties.polar.put ("Q",  new Integer (1));
-jalview.schemes.ResidueProperties.polar.put ("D",  new Integer (1));
-jalview.schemes.ResidueProperties.polar.put ("N",  new Integer (1));
-jalview.schemes.ResidueProperties.polar.put ("S",  new Integer (1));
-jalview.schemes.ResidueProperties.polar.put ("T",  new Integer (1));
-jalview.schemes.ResidueProperties.polar.put ("X",  new Integer (1));
-jalview.schemes.ResidueProperties.polar.put ("-",  new Integer (1));
-jalview.schemes.ResidueProperties.polar.put ("*",  new Integer (1));
-jalview.schemes.ResidueProperties.polar.put ("I",  new Integer (0));
-jalview.schemes.ResidueProperties.polar.put ("L",  new Integer (0));
-jalview.schemes.ResidueProperties.polar.put ("V",  new Integer (0));
-jalview.schemes.ResidueProperties.polar.put ("C",  new Integer (0));
-jalview.schemes.ResidueProperties.polar.put ("A",  new Integer (0));
-jalview.schemes.ResidueProperties.polar.put ("G",  new Integer (0));
-jalview.schemes.ResidueProperties.polar.put ("M",  new Integer (0));
-jalview.schemes.ResidueProperties.polar.put ("F",  new Integer (0));
-jalview.schemes.ResidueProperties.polar.put ("P",  new Integer (0));
-}{
-jalview.schemes.ResidueProperties.small.put ("I",  new Integer (0));
-jalview.schemes.ResidueProperties.small.put ("L",  new Integer (0));
-jalview.schemes.ResidueProperties.small.put ("V",  new Integer (1));
-jalview.schemes.ResidueProperties.small.put ("C",  new Integer (1));
-jalview.schemes.ResidueProperties.small.put ("A",  new Integer (1));
-jalview.schemes.ResidueProperties.small.put ("G",  new Integer (1));
-jalview.schemes.ResidueProperties.small.put ("M",  new Integer (0));
-jalview.schemes.ResidueProperties.small.put ("F",  new Integer (0));
-jalview.schemes.ResidueProperties.small.put ("Y",  new Integer (0));
-jalview.schemes.ResidueProperties.small.put ("W",  new Integer (0));
-jalview.schemes.ResidueProperties.small.put ("H",  new Integer (0));
-jalview.schemes.ResidueProperties.small.put ("K",  new Integer (0));
-jalview.schemes.ResidueProperties.small.put ("R",  new Integer (0));
-jalview.schemes.ResidueProperties.small.put ("E",  new Integer (0));
-jalview.schemes.ResidueProperties.small.put ("Q",  new Integer (0));
-jalview.schemes.ResidueProperties.small.put ("D",  new Integer (1));
-jalview.schemes.ResidueProperties.small.put ("N",  new Integer (1));
-jalview.schemes.ResidueProperties.small.put ("S",  new Integer (1));
-jalview.schemes.ResidueProperties.small.put ("T",  new Integer (1));
-jalview.schemes.ResidueProperties.small.put ("P",  new Integer (1));
-jalview.schemes.ResidueProperties.small.put ("-",  new Integer (1));
-jalview.schemes.ResidueProperties.small.put ("*",  new Integer (1));
-}{
-jalview.schemes.ResidueProperties.positive.put ("I",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("L",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("V",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("C",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("A",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("G",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("M",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("F",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("Y",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("W",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("H",  new Integer (1));
-jalview.schemes.ResidueProperties.positive.put ("K",  new Integer (1));
-jalview.schemes.ResidueProperties.positive.put ("R",  new Integer (1));
-jalview.schemes.ResidueProperties.positive.put ("E",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("Q",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("D",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("N",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("S",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("T",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("P",  new Integer (0));
-jalview.schemes.ResidueProperties.positive.put ("-",  new Integer (1));
-jalview.schemes.ResidueProperties.positive.put ("*",  new Integer (1));
-}{
-jalview.schemes.ResidueProperties.negative.put ("I",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("L",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("V",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("C",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("A",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("G",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("M",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("F",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("Y",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("W",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("H",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("K",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("R",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("E",  new Integer (1));
-jalview.schemes.ResidueProperties.negative.put ("Q",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("D",  new Integer (1));
-jalview.schemes.ResidueProperties.negative.put ("N",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("S",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("T",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("P",  new Integer (0));
-jalview.schemes.ResidueProperties.negative.put ("-",  new Integer (1));
-jalview.schemes.ResidueProperties.negative.put ("*",  new Integer (1));
-}{
-jalview.schemes.ResidueProperties.charged.put ("I",  new Integer (0));
-jalview.schemes.ResidueProperties.charged.put ("L",  new Integer (0));
-jalview.schemes.ResidueProperties.charged.put ("V",  new Integer (0));
-jalview.schemes.ResidueProperties.charged.put ("C",  new Integer (0));
-jalview.schemes.ResidueProperties.charged.put ("A",  new Integer (0));
-jalview.schemes.ResidueProperties.charged.put ("G",  new Integer (0));
-jalview.schemes.ResidueProperties.charged.put ("M",  new Integer (0));
-jalview.schemes.ResidueProperties.charged.put ("F",  new Integer (0));
-jalview.schemes.ResidueProperties.charged.put ("Y",  new Integer (0));
-jalview.schemes.ResidueProperties.charged.put ("W",  new Integer (0));
-jalview.schemes.ResidueProperties.charged.put ("H",  new Integer (1));
-jalview.schemes.ResidueProperties.charged.put ("K",  new Integer (1));
-jalview.schemes.ResidueProperties.charged.put ("R",  new Integer (1));
-jalview.schemes.ResidueProperties.charged.put ("E",  new Integer (1));
-jalview.schemes.ResidueProperties.charged.put ("Q",  new Integer (0));
-jalview.schemes.ResidueProperties.charged.put ("D",  new Integer (1));
-jalview.schemes.ResidueProperties.charged.put ("N",  new Integer (0));
-jalview.schemes.ResidueProperties.charged.put ("S",  new Integer (0));
-jalview.schemes.ResidueProperties.charged.put ("T",  new Integer (0));
-jalview.schemes.ResidueProperties.charged.put ("P",  new Integer (0));
-jalview.schemes.ResidueProperties.charged.put ("-",  new Integer (1));
-jalview.schemes.ResidueProperties.charged.put ("*",  new Integer (1));
-}{
-jalview.schemes.ResidueProperties.aromatic.put ("I",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("L",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("V",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("C",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("A",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("G",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("M",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("F",  new Integer (1));
-jalview.schemes.ResidueProperties.aromatic.put ("Y",  new Integer (1));
-jalview.schemes.ResidueProperties.aromatic.put ("W",  new Integer (1));
-jalview.schemes.ResidueProperties.aromatic.put ("H",  new Integer (1));
-jalview.schemes.ResidueProperties.aromatic.put ("K",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("R",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("E",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("Q",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("D",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("N",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("S",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("T",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("P",  new Integer (0));
-jalview.schemes.ResidueProperties.aromatic.put ("-",  new Integer (1));
-jalview.schemes.ResidueProperties.aromatic.put ("*",  new Integer (1));
-}{
-jalview.schemes.ResidueProperties.aliphatic.put ("I",  new Integer (1));
-jalview.schemes.ResidueProperties.aliphatic.put ("L",  new Integer (1));
-jalview.schemes.ResidueProperties.aliphatic.put ("V",  new Integer (1));
-jalview.schemes.ResidueProperties.aliphatic.put ("C",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("A",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("G",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("M",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("F",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("Y",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("W",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("H",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("K",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("R",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("E",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("Q",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("D",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("N",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("S",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("T",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("P",  new Integer (0));
-jalview.schemes.ResidueProperties.aliphatic.put ("-",  new Integer (1));
-jalview.schemes.ResidueProperties.aliphatic.put ("*",  new Integer (1));
-}{
-jalview.schemes.ResidueProperties.tiny.put ("I",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("L",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("V",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("C",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("A",  new Integer (1));
-jalview.schemes.ResidueProperties.tiny.put ("G",  new Integer (1));
-jalview.schemes.ResidueProperties.tiny.put ("M",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("F",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("Y",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("W",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("H",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("K",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("R",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("E",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("Q",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("D",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("N",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("S",  new Integer (1));
-jalview.schemes.ResidueProperties.tiny.put ("T",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("P",  new Integer (0));
-jalview.schemes.ResidueProperties.tiny.put ("-",  new Integer (1));
-jalview.schemes.ResidueProperties.tiny.put ("*",  new Integer (1));
-}{
-jalview.schemes.ResidueProperties.proline.put ("I",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("L",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("V",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("C",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("A",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("G",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("M",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("F",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("Y",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("W",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("H",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("K",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("R",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("E",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("Q",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("D",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("N",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("S",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("T",  new Integer (0));
-jalview.schemes.ResidueProperties.proline.put ("P",  new Integer (1));
-jalview.schemes.ResidueProperties.proline.put ("-",  new Integer (1));
-jalview.schemes.ResidueProperties.proline.put ("*",  new Integer (1));
-}{
-jalview.schemes.ResidueProperties.propHash.put ("hydrophobic", jalview.schemes.ResidueProperties.hydrophobic);
-jalview.schemes.ResidueProperties.propHash.put ("small", jalview.schemes.ResidueProperties.small);
-jalview.schemes.ResidueProperties.propHash.put ("positive", jalview.schemes.ResidueProperties.positive);
-jalview.schemes.ResidueProperties.propHash.put ("negative", jalview.schemes.ResidueProperties.negative);
-jalview.schemes.ResidueProperties.propHash.put ("charged", jalview.schemes.ResidueProperties.charged);
-jalview.schemes.ResidueProperties.propHash.put ("aromatic", jalview.schemes.ResidueProperties.aromatic);
-jalview.schemes.ResidueProperties.propHash.put ("aliphatic", jalview.schemes.ResidueProperties.aliphatic);
-jalview.schemes.ResidueProperties.propHash.put ("tiny", jalview.schemes.ResidueProperties.tiny);
-jalview.schemes.ResidueProperties.propHash.put ("proline", jalview.schemes.ResidueProperties.proline);
-jalview.schemes.ResidueProperties.propHash.put ("polar", jalview.schemes.ResidueProperties.polar);
-}{
-var propMatrixF =  Clazz.newIntArray (23, 23, 0);
-var propMatrixPos =  Clazz.newIntArray (23, 23, 0);
-var propMatrixEpos =  Clazz.newIntArray (23, 23, 0);
-for (var i = 0; i < 23; i++) {
-var maxF = 0;
-var maxP = 0;
-var maxEP = 0;
-var ic = "";
-if (jalview.schemes.ResidueProperties.aa.length > i) {
-ic += jalview.schemes.ResidueProperties.aa[i];
-} else {
-ic = "-";
-}for (var j = i + 1; j < 23; j++) {
-var jc = "";
-if (jalview.schemes.ResidueProperties.aa.length > j) {
-jc += jalview.schemes.ResidueProperties.aa[j];
-} else {
-jc = "-";
-}propMatrixF[i][j] = 0;
-propMatrixPos[i][j] = 0;
-propMatrixEpos[i][j] = 0;
-for (var en = jalview.schemes.ResidueProperties.propHash.keys (); en.hasMoreElements (); ) {
-var ph = en.nextElement ();
-var pph = jalview.schemes.ResidueProperties.propHash.get (ph);
-if (pph.get (ic) != null && pph.get (jc) != null) {
-var icp = pph.get (ic).intValue ();
-var jcp = pph.get (jc).intValue ();
-propMatrixPos[i][j] += icp == jcp && icp > 0 ? 2 : 0;
-propMatrixPos[j][i] += icp == jcp && icp > 0 ? 2 : 0;
-propMatrixF[i][j] += icp == jcp ? 2 : 0;
-propMatrixF[j][i] += icp == jcp ? 2 : 0;
-propMatrixEpos[i][j] += icp == jcp ? (1 + icp * 2) : 0;
-propMatrixEpos[j][i] += icp == jcp ? (1 + icp * 2) : 0;
-}}
-if (maxF < propMatrixF[i][j]) {
-maxF = propMatrixF[i][j];
-}if (maxP < propMatrixPos[i][j]) {
-maxP = propMatrixPos[i][j];
-}if (maxEP < propMatrixEpos[i][j]) {
-maxEP = propMatrixEpos[i][j];
-}}
-propMatrixF[i][i] = maxF;
-propMatrixPos[i][i] = maxP;
-propMatrixEpos[i][i] = maxEP;
-}
-jalview.schemes.ResidueProperties.scoreMatrices.put ("PID",  new jalview.analysis.scoremodels.PIDScoreModel ());
-jalview.schemes.ResidueProperties.scoreMatrices.put ("Displayed Features",  new jalview.analysis.scoremodels.FeatureScoreModel ());
-}Clazz.defineStatics (c$,
-"toDssp3State", null);
-{
-jalview.schemes.ResidueProperties.toDssp3State =  new java.util.Hashtable ();
-jalview.schemes.ResidueProperties.toDssp3State.put ("H", "H");
-jalview.schemes.ResidueProperties.toDssp3State.put ("E", "E");
-jalview.schemes.ResidueProperties.toDssp3State.put ("C", " ");
-jalview.schemes.ResidueProperties.toDssp3State.put (" ", " ");
-jalview.schemes.ResidueProperties.toDssp3State.put ("T", " ");
-jalview.schemes.ResidueProperties.toDssp3State.put ("B", "E");
-jalview.schemes.ResidueProperties.toDssp3State.put ("G", "H");
-jalview.schemes.ResidueProperties.toDssp3State.put ("I", "H");
-jalview.schemes.ResidueProperties.toDssp3State.put ("X", " ");
-}Clazz.defineStatics (c$,
-"toRNAssState", null,
-"RNAcloseParen",  Clazz.newBooleanArray (255, false));
-{
-jalview.schemes.ResidueProperties.toRNAssState =  new java.util.Hashtable ();
-jalview.schemes.ResidueProperties.toRNAssState.put (")", "(");
-jalview.schemes.ResidueProperties.toRNAssState.put ("(", "(");
-jalview.schemes.ResidueProperties.toRNAssState.put ("]", "[");
-jalview.schemes.ResidueProperties.toRNAssState.put ("[", "[");
-jalview.schemes.ResidueProperties.toRNAssState.put ("{", "{");
-jalview.schemes.ResidueProperties.toRNAssState.put ("}", "{");
-jalview.schemes.ResidueProperties.toRNAssState.put (">", ">");
-jalview.schemes.ResidueProperties.toRNAssState.put ("<", ">");
-jalview.schemes.ResidueProperties.toRNAssState.put ("A", "A");
-jalview.schemes.ResidueProperties.toRNAssState.put ("a", "A");
-jalview.schemes.ResidueProperties.toRNAssState.put ("B", "B");
-jalview.schemes.ResidueProperties.toRNAssState.put ("b", "B");
-jalview.schemes.ResidueProperties.toRNAssState.put ("C", "C");
-jalview.schemes.ResidueProperties.toRNAssState.put ("c", "C");
-jalview.schemes.ResidueProperties.toRNAssState.put ("D", "D");
-jalview.schemes.ResidueProperties.toRNAssState.put ("d", "D");
-jalview.schemes.ResidueProperties.toRNAssState.put ("E", "E");
-jalview.schemes.ResidueProperties.toRNAssState.put ("e", "E");
-jalview.schemes.ResidueProperties.toRNAssState.put ("F", "F");
-jalview.schemes.ResidueProperties.toRNAssState.put ("f", "F");
-jalview.schemes.ResidueProperties.toRNAssState.put ("G", "G");
-jalview.schemes.ResidueProperties.toRNAssState.put ("g", "G");
-jalview.schemes.ResidueProperties.toRNAssState.put ("H", "H");
-jalview.schemes.ResidueProperties.toRNAssState.put ("h", "H");
-jalview.schemes.ResidueProperties.toRNAssState.put ("I", "I");
-jalview.schemes.ResidueProperties.toRNAssState.put ("i", "I");
-jalview.schemes.ResidueProperties.toRNAssState.put ("J", "J");
-jalview.schemes.ResidueProperties.toRNAssState.put ("j", "J");
-jalview.schemes.ResidueProperties.toRNAssState.put ("K", "K");
-jalview.schemes.ResidueProperties.toRNAssState.put ("k", "K");
-jalview.schemes.ResidueProperties.toRNAssState.put ("L", "L");
-jalview.schemes.ResidueProperties.toRNAssState.put ("l", "L");
-jalview.schemes.ResidueProperties.toRNAssState.put ("M", "M");
-jalview.schemes.ResidueProperties.toRNAssState.put ("m", "M");
-jalview.schemes.ResidueProperties.toRNAssState.put ("N", "N");
-jalview.schemes.ResidueProperties.toRNAssState.put ("n", "N");
-jalview.schemes.ResidueProperties.toRNAssState.put ("O", "O");
-jalview.schemes.ResidueProperties.toRNAssState.put ("o", "O");
-jalview.schemes.ResidueProperties.toRNAssState.put ("P", "P");
-jalview.schemes.ResidueProperties.toRNAssState.put ("p", "P");
-jalview.schemes.ResidueProperties.toRNAssState.put ("Q", "Q");
-jalview.schemes.ResidueProperties.toRNAssState.put ("q", "Q");
-jalview.schemes.ResidueProperties.toRNAssState.put ("R", "R");
-jalview.schemes.ResidueProperties.toRNAssState.put ("r", "R");
-jalview.schemes.ResidueProperties.toRNAssState.put ("S", "S");
-jalview.schemes.ResidueProperties.toRNAssState.put ("s", "S");
-jalview.schemes.ResidueProperties.toRNAssState.put ("T", "T");
-jalview.schemes.ResidueProperties.toRNAssState.put ("t", "T");
-jalview.schemes.ResidueProperties.toRNAssState.put ("U", "U");
-jalview.schemes.ResidueProperties.toRNAssState.put ("u", "U");
-jalview.schemes.ResidueProperties.toRNAssState.put ("V", "V");
-jalview.schemes.ResidueProperties.toRNAssState.put ("v", "V");
-jalview.schemes.ResidueProperties.toRNAssState.put ("W", "W");
-jalview.schemes.ResidueProperties.toRNAssState.put ("w", "W");
-jalview.schemes.ResidueProperties.toRNAssState.put ("X", "X");
-jalview.schemes.ResidueProperties.toRNAssState.put ("x", "X");
-jalview.schemes.ResidueProperties.toRNAssState.put ("Y", "Y");
-jalview.schemes.ResidueProperties.toRNAssState.put ("y", "Y");
-jalview.schemes.ResidueProperties.toRNAssState.put ("Z", "Z");
-jalview.schemes.ResidueProperties.toRNAssState.put ("z", "Z");
-for (var p = 0; p < jalview.schemes.ResidueProperties.RNAcloseParen.length; p++) {
-jalview.schemes.ResidueProperties.RNAcloseParen[p] = false;
-}
-for (var k, $k = jalview.schemes.ResidueProperties.toRNAssState.keySet ().iterator (); $k.hasNext () && ((k = $k.next ()) || true);) {
-jalview.schemes.ResidueProperties.RNAcloseParen[k.charCodeAt (0)] = k.charAt (0) != jalview.schemes.ResidueProperties.toRNAssState.get (k).charAt (0);
-}
-}});
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (["jalview.analysis.scoremodels.FeatureScoreModel", "$.PIDScoreModel", "jalview.schemes.ScoreMatrix", "java.awt.Color", "java.util.ArrayList", "$.HashMap", "$.Hashtable", "$.Vector"], "jalview.schemes.ResidueProperties", ["java.lang.StringBuffer"], function () {
+c$ = Clazz.declareType (jalview.schemes, "ResidueProperties");
+c$.buildAmbiguityCodonSet = Clazz.defineMethod (c$, "buildAmbiguityCodonSet", 
+function () {
+if (jalview.schemes.ResidueProperties._ambiguityCodes.size () > 0) {
+System.err.println ("Ignoring multiple calls to buildAmbiguityCodonSet");
+return;
+}for (var acode, $acode = jalview.schemes.ResidueProperties.ambiguityCodes.entrySet ().iterator (); $acode.hasNext () && ((acode = $acode.next ()) || true);) {
+for (var r, $r = 0, $$r = acode.getValue (); $r < $$r.length && ((r = $$r[$r]) || true); $r++) {
+var codesfor = jalview.schemes.ResidueProperties._ambiguityCodes.get (r);
+if (codesfor == null) {
+jalview.schemes.ResidueProperties._ambiguityCodes.put (r, codesfor =  new java.util.ArrayList ());
+}if (!codesfor.contains (acode.getKey ())) {
+codesfor.add (acode.getKey ());
+} else {
+System.err.println ("Inconsistency in the IUBMB ambiguity code nomenclature table: collision for " + acode.getKey () + " in residue " + r);
+}}
+}
+var unambcodons = jalview.schemes.ResidueProperties.codonHash2.keySet ().toArray ( new Array (jalview.schemes.ResidueProperties.codonHash2.size ()));
+for (var codon, $codon = 0, $$codon = unambcodons; $codon < $$codon.length && ((codon = $$codon[$codon]) || true); $codon++) {
+var residue = jalview.schemes.ResidueProperties.codonHash2.get (codon);
+var acodon =  new Array (codon.length);
+for (var i = 0, iSize = codon.length; i < iSize; i++) {
+var _ac = "" + codon.charAt (i);
+var acodes = jalview.schemes.ResidueProperties._ambiguityCodes.get (_ac);
+if (acodes != null) {
+acodon[i] = acodes.toArray ( new Array (acodes.size ()));
+} else {
+acodon[i] =  Clazz.newArray (-1, []);
+}}
+var tpos =  Clazz.newIntArray (codon.length, 0);
+var cpos =  Clazz.newIntArray (codon.length, 0);
+for (var i = 0; i < tpos.length; i++) {
+tpos[i] = -1;
+}
+tpos[acodon.length - 1] = 0;
+var ipos;
+var j;
+while (tpos[0] < acodon[0].length) {
+var allres =  Clazz.newCharArray (tpos.length, '\0');
+var _acodon = "";
+var _anuc;
+for (ipos = 0; ipos < tpos.length; ipos++) {
+if (acodon[ipos].length == 0 || tpos[ipos] < 0) {
+_acodon += codon.charAt (ipos);
+allres[ipos] =  Clazz.newCharArray (-1, [codon.charAt (ipos)]);
+} else {
+_acodon += acodon[ipos][tpos[ipos]];
+var altbase = jalview.schemes.ResidueProperties.ambiguityCodes.get (acodon[ipos][tpos[ipos]]);
+allres[ipos] =  Clazz.newCharArray (altbase.length, '\0');
+j = 0;
+for (var ab, $ab = 0, $$ab = altbase; $ab < $$ab.length && ((ab = $$ab[$ab]) || true); $ab++) {
+allres[ipos][j++] = ab.charAt (0);
+}
+}}
+for (ipos = 0; ipos < cpos.length; ipos++) {
+cpos[ipos] = 0;
+}
+var valid = true;
+do {
+var _codon = "";
+for (j = 0; j < cpos.length; j++) {
+_codon += allres[j][cpos[j]];
+}
+var tr = jalview.schemes.ResidueProperties.codonHash2.get (_codon);
+if (valid = (tr != null && tr.equals (residue))) {
+ipos = acodon.length - 1;
+while (++cpos[ipos] >= allres[ipos].length && ipos > 0) {
+cpos[ipos] = 0;
+ipos--;
+}
+}} while (valid && cpos[0] < allres[0].length);
+if (valid) {
+jalview.schemes.ResidueProperties.codonHash2.put (_acodon, residue);
+} else {
+}ipos = acodon.length - 1;
+while (++tpos[ipos] >= acodon[ipos].length && ipos > 0) {
+tpos[ipos] = -1;
+ipos--;
+}
+}
+}
+});
+c$.getHydmax = Clazz.defineMethod (c$, "getHydmax", 
+function () {
+return 4.5;
+});
+c$.getHydmin = Clazz.defineMethod (c$, "getHydmin", 
+function () {
+return -3.9;
+});
+c$.getHyd = Clazz.defineMethod (c$, "getHyd", 
+function () {
+return jalview.schemes.ResidueProperties.hyd;
+});
+c$.getAA3Hash = Clazz.defineMethod (c$, "getAA3Hash", 
+function () {
+return jalview.schemes.ResidueProperties.aa3Hash;
+});
+c$.getDNA = Clazz.defineMethod (c$, "getDNA", 
+function () {
+return jalview.schemes.ResidueProperties.DNA;
+});
+c$.getBLOSUM62 = Clazz.defineMethod (c$, "getBLOSUM62", 
+function () {
+return jalview.schemes.ResidueProperties.BLOSUM62;
+});
+c$.getPAM250 = Clazz.defineMethod (c$, "getPAM250", 
+function (A1, A2) {
+return jalview.schemes.ResidueProperties.getPAM250 (A1.charAt (0), A2.charAt (0));
+}, "~S,~S");
+c$.getBLOSUM62 = Clazz.defineMethod (c$, "getBLOSUM62", 
+function (c1, c2) {
+var pog = 0;
+try {
+var a = jalview.schemes.ResidueProperties.aaIndex[c1.charCodeAt (0)];
+var b = jalview.schemes.ResidueProperties.aaIndex[c2.charCodeAt (0)];
+pog = jalview.schemes.ResidueProperties.BLOSUM62[a][b];
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+} else {
+throw e;
+}
+}
+return pog;
+}, "~S,~S");
+c$.getCodons = Clazz.defineMethod (c$, "getCodons", 
+function (res) {
+if (jalview.schemes.ResidueProperties.codonHash.containsKey (res)) {
+return jalview.schemes.ResidueProperties.codonHash.get (res);
+}return null;
+}, "~S");
+c$.codonTranslate = Clazz.defineMethod (c$, "codonTranslate", 
+function (lccodon) {
+if (false) {
+return jalview.schemes.ResidueProperties._codonTranslate (lccodon);
+}var cdn = jalview.schemes.ResidueProperties.codonHash2.get (lccodon.toUpperCase ());
+if (cdn != null && cdn.equals ("*")) {
+return "STOP";
+}return cdn;
+}, "~S");
+c$._codonTranslate = Clazz.defineMethod (c$, "_codonTranslate", 
+function (lccodon) {
+var codon = lccodon.toUpperCase ();
+if (codon.indexOf ('X') > -1 || codon.indexOf ('N') > -1) {
+return "X";
+}for (var key, $key = jalview.schemes.ResidueProperties.codonHash.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) {
+if (jalview.schemes.ResidueProperties.codonHash.get (key).contains (codon)) {
+return key;
+}}
+return null;
+}, "~S");
+c$.getDefaultPeptideMatrix = Clazz.defineMethod (c$, "getDefaultPeptideMatrix", 
+function () {
+return jalview.schemes.ResidueProperties.getBLOSUM62 ();
+});
+c$.getDefaultDnaMatrix = Clazz.defineMethod (c$, "getDefaultDnaMatrix", 
+function () {
+return jalview.schemes.ResidueProperties.getDNA ();
+});
+c$.getScoreMatrix = Clazz.defineMethod (c$, "getScoreMatrix", 
+function (pwtype) {
+var val = jalview.schemes.ResidueProperties.scoreMatrices.get (pwtype);
+if (val != null && Clazz.instanceOf (val, jalview.schemes.ScoreMatrix)) {
+return val;
+}return null;
+}, "~S");
+c$.getScoreModel = Clazz.defineMethod (c$, "getScoreModel", 
+function (pwtype) {
+return jalview.schemes.ResidueProperties.scoreMatrices.get (pwtype);
+}, "~S");
+c$.getPAM250 = Clazz.defineMethod (c$, "getPAM250", 
+function (c, d) {
+var a = jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt (0)];
+var b = jalview.schemes.ResidueProperties.aaIndex[d.charCodeAt (0)];
+var pog = jalview.schemes.ResidueProperties.PAM250[a][b];
+return pog;
+}, "~S,~S");
+c$.getDssp3state = Clazz.defineMethod (c$, "getDssp3state", 
+function (ssstring) {
+if (ssstring == null) {
+return null;
+}var ss =  new StringBuffer ();
+for (var i = 0; i < ssstring.length; i++) {
+var ssc = ssstring.substring (i, i + 1);
+if (jalview.schemes.ResidueProperties.toDssp3State.containsKey (ssc)) {
+ss.append (jalview.schemes.ResidueProperties.toDssp3State.get (ssc));
+} else {
+ss.append (" ");
+}}
+return ss.toString ();
+}, "~S");
+c$.getRNASecStrucState = Clazz.defineMethod (c$, "getRNASecStrucState", 
+function (ssstring) {
+if (ssstring == null) {
+return null;
+}var ss =  new StringBuffer ();
+for (var i = 0; i < ssstring.length; i++) {
+var ssc = ssstring.substring (i, i + 1);
+if (jalview.schemes.ResidueProperties.toRNAssState.containsKey (ssc)) {
+ss.append (ssc);
+} else {
+ss.append (" ");
+}}
+return ss.toString ();
+}, "~S");
+c$.isCloseParenRNA = Clazz.defineMethod (c$, "isCloseParenRNA", 
+function (dc) {
+return jalview.schemes.ResidueProperties.RNAcloseParen[dc.charCodeAt (0)];
+}, "~S");
+c$.getResidues = Clazz.defineMethod (c$, "getResidues", 
+function (nucleotide, includeAmbiguous) {
+var result =  new java.util.ArrayList ();
+if (nucleotide) {
+for (var nuc, $nuc = jalview.schemes.ResidueProperties.nucleotideName.keySet ().iterator (); $nuc.hasNext () && ((nuc = $nuc.next ()) || true);) {
+var val = jalview.schemes.ResidueProperties.nucleotideIndex[nuc.charCodeAt (0)];
+if ((!includeAmbiguous && val > 4) || (val >= 10)) {
+continue;
+}nuc = nuc.toUpperCase ();
+if (!result.contains (nuc)) {
+result.add (nuc);
+}}
+} else {
+for (var res, $res = jalview.schemes.ResidueProperties.aa3Hash.keySet ().iterator (); $res.hasNext () && ((res = $res.next ()) || true);) {
+var index = jalview.schemes.ResidueProperties.aa3Hash.get (res).intValue ();
+if ((!includeAmbiguous && index >= 20) || index >= 23) {
+continue;
+}res = res.toUpperCase ();
+if (!result.contains (res)) {
+result.add (res);
+}}
+}return result;
+}, "~B,~B");
+c$.scoreMatrices = c$.prototype.scoreMatrices =  new java.util.Hashtable ();
+Clazz.defineStatics (c$,
+"aaIndex", null,
+"nucleotideIndex", null,
+"purinepyrimidineIndex", null);
+c$.aa3Hash = c$.prototype.aa3Hash =  new java.util.HashMap ();
+c$.aa2Triplet = c$.prototype.aa2Triplet =  new java.util.HashMap ();
+c$.nucleotideName = c$.prototype.nucleotideName =  new java.util.HashMap ();
+{
+jalview.schemes.ResidueProperties.aaIndex =  Clazz.newIntArray (255, 0);
+for (var i = 0; i < 255; i++) {
+jalview.schemes.ResidueProperties.aaIndex[i] = 23;
+}
+jalview.schemes.ResidueProperties.aaIndex['A'.charCodeAt (0)] = 0;
+jalview.schemes.ResidueProperties.aaIndex['R'.charCodeAt (0)] = 1;
+jalview.schemes.ResidueProperties.aaIndex['N'.charCodeAt (0)] = 2;
+jalview.schemes.ResidueProperties.aaIndex['D'.charCodeAt (0)] = 3;
+jalview.schemes.ResidueProperties.aaIndex['C'.charCodeAt (0)] = 4;
+jalview.schemes.ResidueProperties.aaIndex['Q'.charCodeAt (0)] = 5;
+jalview.schemes.ResidueProperties.aaIndex['E'.charCodeAt (0)] = 6;
+jalview.schemes.ResidueProperties.aaIndex['G'.charCodeAt (0)] = 7;
+jalview.schemes.ResidueProperties.aaIndex['H'.charCodeAt (0)] = 8;
+jalview.schemes.ResidueProperties.aaIndex['I'.charCodeAt (0)] = 9;
+jalview.schemes.ResidueProperties.aaIndex['L'.charCodeAt (0)] = 10;
+jalview.schemes.ResidueProperties.aaIndex['K'.charCodeAt (0)] = 11;
+jalview.schemes.ResidueProperties.aaIndex['M'.charCodeAt (0)] = 12;
+jalview.schemes.ResidueProperties.aaIndex['F'.charCodeAt (0)] = 13;
+jalview.schemes.ResidueProperties.aaIndex['P'.charCodeAt (0)] = 14;
+jalview.schemes.ResidueProperties.aaIndex['S'.charCodeAt (0)] = 15;
+jalview.schemes.ResidueProperties.aaIndex['T'.charCodeAt (0)] = 16;
+jalview.schemes.ResidueProperties.aaIndex['W'.charCodeAt (0)] = 17;
+jalview.schemes.ResidueProperties.aaIndex['Y'.charCodeAt (0)] = 18;
+jalview.schemes.ResidueProperties.aaIndex['V'.charCodeAt (0)] = 19;
+jalview.schemes.ResidueProperties.aaIndex['B'.charCodeAt (0)] = 20;
+jalview.schemes.ResidueProperties.aaIndex['Z'.charCodeAt (0)] = 21;
+jalview.schemes.ResidueProperties.aaIndex['X'.charCodeAt (0)] = 22;
+jalview.schemes.ResidueProperties.aaIndex['U'.charCodeAt (0)] = 22;
+jalview.schemes.ResidueProperties.aaIndex['a'.charCodeAt (0)] = 0;
+jalview.schemes.ResidueProperties.aaIndex['r'.charCodeAt (0)] = 1;
+jalview.schemes.ResidueProperties.aaIndex['n'.charCodeAt (0)] = 2;
+jalview.schemes.ResidueProperties.aaIndex['d'.charCodeAt (0)] = 3;
+jalview.schemes.ResidueProperties.aaIndex['c'.charCodeAt (0)] = 4;
+jalview.schemes.ResidueProperties.aaIndex['q'.charCodeAt (0)] = 5;
+jalview.schemes.ResidueProperties.aaIndex['e'.charCodeAt (0)] = 6;
+jalview.schemes.ResidueProperties.aaIndex['g'.charCodeAt (0)] = 7;
+jalview.schemes.ResidueProperties.aaIndex['h'.charCodeAt (0)] = 8;
+jalview.schemes.ResidueProperties.aaIndex['i'.charCodeAt (0)] = 9;
+jalview.schemes.ResidueProperties.aaIndex['l'.charCodeAt (0)] = 10;
+jalview.schemes.ResidueProperties.aaIndex['k'.charCodeAt (0)] = 11;
+jalview.schemes.ResidueProperties.aaIndex['m'.charCodeAt (0)] = 12;
+jalview.schemes.ResidueProperties.aaIndex['f'.charCodeAt (0)] = 13;
+jalview.schemes.ResidueProperties.aaIndex['p'.charCodeAt (0)] = 14;
+jalview.schemes.ResidueProperties.aaIndex['s'.charCodeAt (0)] = 15;
+jalview.schemes.ResidueProperties.aaIndex['t'.charCodeAt (0)] = 16;
+jalview.schemes.ResidueProperties.aaIndex['w'.charCodeAt (0)] = 17;
+jalview.schemes.ResidueProperties.aaIndex['y'.charCodeAt (0)] = 18;
+jalview.schemes.ResidueProperties.aaIndex['v'.charCodeAt (0)] = 19;
+jalview.schemes.ResidueProperties.aaIndex['b'.charCodeAt (0)] = 20;
+jalview.schemes.ResidueProperties.aaIndex['z'.charCodeAt (0)] = 21;
+jalview.schemes.ResidueProperties.aaIndex['x'.charCodeAt (0)] = 22;
+jalview.schemes.ResidueProperties.aaIndex['u'.charCodeAt (0)] = 22;
+}Clazz.defineStatics (c$,
+"maxProteinIndex", 23,
+"maxNucleotideIndex", 10);
+{
+jalview.schemes.ResidueProperties.nucleotideIndex =  Clazz.newIntArray (255, 0);
+for (var i = 0; i < 255; i++) {
+jalview.schemes.ResidueProperties.nucleotideIndex[i] = 10;
+}
+jalview.schemes.ResidueProperties.nucleotideIndex['A'.charCodeAt (0)] = 0;
+jalview.schemes.ResidueProperties.nucleotideIndex['a'.charCodeAt (0)] = 0;
+jalview.schemes.ResidueProperties.nucleotideIndex['C'.charCodeAt (0)] = 1;
+jalview.schemes.ResidueProperties.nucleotideIndex['c'.charCodeAt (0)] = 1;
+jalview.schemes.ResidueProperties.nucleotideIndex['G'.charCodeAt (0)] = 2;
+jalview.schemes.ResidueProperties.nucleotideIndex['g'.charCodeAt (0)] = 2;
+jalview.schemes.ResidueProperties.nucleotideIndex['T'.charCodeAt (0)] = 3;
+jalview.schemes.ResidueProperties.nucleotideIndex['t'.charCodeAt (0)] = 3;
+jalview.schemes.ResidueProperties.nucleotideIndex['U'.charCodeAt (0)] = 4;
+jalview.schemes.ResidueProperties.nucleotideIndex['u'.charCodeAt (0)] = 4;
+jalview.schemes.ResidueProperties.nucleotideIndex['I'.charCodeAt (0)] = 5;
+jalview.schemes.ResidueProperties.nucleotideIndex['i'.charCodeAt (0)] = 5;
+jalview.schemes.ResidueProperties.nucleotideIndex['X'.charCodeAt (0)] = 6;
+jalview.schemes.ResidueProperties.nucleotideIndex['x'.charCodeAt (0)] = 6;
+jalview.schemes.ResidueProperties.nucleotideIndex['R'.charCodeAt (0)] = 7;
+jalview.schemes.ResidueProperties.nucleotideIndex['r'.charCodeAt (0)] = 7;
+jalview.schemes.ResidueProperties.nucleotideIndex['Y'.charCodeAt (0)] = 8;
+jalview.schemes.ResidueProperties.nucleotideIndex['y'.charCodeAt (0)] = 8;
+jalview.schemes.ResidueProperties.nucleotideIndex['N'.charCodeAt (0)] = 9;
+jalview.schemes.ResidueProperties.nucleotideIndex['n'.charCodeAt (0)] = 9;
+jalview.schemes.ResidueProperties.nucleotideName.put ("A", "Adenine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("a", "Adenine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("G", "Guanine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("g", "Guanine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("C", "Cytosine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("c", "Cytosine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("T", "Thymine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("t", "Thymine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("U", "Uracil");
+jalview.schemes.ResidueProperties.nucleotideName.put ("u", "Uracil");
+jalview.schemes.ResidueProperties.nucleotideName.put ("I", "Inosine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("i", "Inosine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("X", "Xanthine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("x", "Xanthine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("R", "Unknown Purine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("r", "Unknown Purine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("Y", "Unknown Pyrimidine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("y", "Unknown Pyrimidine");
+jalview.schemes.ResidueProperties.nucleotideName.put ("N", "Unknown");
+jalview.schemes.ResidueProperties.nucleotideName.put ("n", "Unknown");
+jalview.schemes.ResidueProperties.nucleotideName.put ("W", "Weak nucleotide (A or T)");
+jalview.schemes.ResidueProperties.nucleotideName.put ("w", "Weak nucleotide (A or T)");
+jalview.schemes.ResidueProperties.nucleotideName.put ("S", "Strong nucleotide (G or C)");
+jalview.schemes.ResidueProperties.nucleotideName.put ("s", "Strong nucleotide (G or C)");
+jalview.schemes.ResidueProperties.nucleotideName.put ("M", "Amino (A or C)");
+jalview.schemes.ResidueProperties.nucleotideName.put ("m", "Amino (A or C)");
+jalview.schemes.ResidueProperties.nucleotideName.put ("K", "Keto (G or T)");
+jalview.schemes.ResidueProperties.nucleotideName.put ("k", "Keto (G or T)");
+jalview.schemes.ResidueProperties.nucleotideName.put ("B", "Not A (G or C or T)");
+jalview.schemes.ResidueProperties.nucleotideName.put ("b", "Not A (G or C or T)");
+jalview.schemes.ResidueProperties.nucleotideName.put ("H", "Not G (A or C or T)");
+jalview.schemes.ResidueProperties.nucleotideName.put ("h", "Not G (A or C or T)");
+jalview.schemes.ResidueProperties.nucleotideName.put ("D", "Not C (A or G or T)");
+jalview.schemes.ResidueProperties.nucleotideName.put ("d", "Not C (A or G or T)");
+jalview.schemes.ResidueProperties.nucleotideName.put ("V", "Not T (A or G or C");
+jalview.schemes.ResidueProperties.nucleotideName.put ("v", "Not T (A or G or C");
+}{
+jalview.schemes.ResidueProperties.purinepyrimidineIndex =  Clazz.newIntArray (255, 0);
+for (var i = 0; i < 255; i++) {
+jalview.schemes.ResidueProperties.purinepyrimidineIndex[i] = 3;
+}
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['A'.charCodeAt (0)] = 0;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['a'.charCodeAt (0)] = 0;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['C'.charCodeAt (0)] = 1;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['c'.charCodeAt (0)] = 1;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['G'.charCodeAt (0)] = 0;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['g'.charCodeAt (0)] = 0;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['T'.charCodeAt (0)] = 1;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['t'.charCodeAt (0)] = 1;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['U'.charCodeAt (0)] = 1;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['u'.charCodeAt (0)] = 1;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['I'.charCodeAt (0)] = 2;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['i'.charCodeAt (0)] = 2;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['X'.charCodeAt (0)] = 2;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['x'.charCodeAt (0)] = 2;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['R'.charCodeAt (0)] = 0;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['r'.charCodeAt (0)] = 0;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['Y'.charCodeAt (0)] = 1;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['y'.charCodeAt (0)] = 1;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['N'.charCodeAt (0)] = 2;
+jalview.schemes.ResidueProperties.purinepyrimidineIndex['n'.charCodeAt (0)] = 2;
+}{
+jalview.schemes.ResidueProperties.aa3Hash.put ("ALA",  new Integer (0));
+jalview.schemes.ResidueProperties.aa3Hash.put ("ARG",  new Integer (1));
+jalview.schemes.ResidueProperties.aa3Hash.put ("ASN",  new Integer (2));
+jalview.schemes.ResidueProperties.aa3Hash.put ("ASP",  new Integer (3));
+jalview.schemes.ResidueProperties.aa3Hash.put ("CYS",  new Integer (4));
+jalview.schemes.ResidueProperties.aa3Hash.put ("GLN",  new Integer (5));
+jalview.schemes.ResidueProperties.aa3Hash.put ("GLU",  new Integer (6));
+jalview.schemes.ResidueProperties.aa3Hash.put ("GLY",  new Integer (7));
+jalview.schemes.ResidueProperties.aa3Hash.put ("HIS",  new Integer (8));
+jalview.schemes.ResidueProperties.aa3Hash.put ("ILE",  new Integer (9));
+jalview.schemes.ResidueProperties.aa3Hash.put ("LEU",  new Integer (10));
+jalview.schemes.ResidueProperties.aa3Hash.put ("LYS",  new Integer (11));
+jalview.schemes.ResidueProperties.aa3Hash.put ("MET",  new Integer (12));
+jalview.schemes.ResidueProperties.aa3Hash.put ("PHE",  new Integer (13));
+jalview.schemes.ResidueProperties.aa3Hash.put ("PRO",  new Integer (14));
+jalview.schemes.ResidueProperties.aa3Hash.put ("SER",  new Integer (15));
+jalview.schemes.ResidueProperties.aa3Hash.put ("THR",  new Integer (16));
+jalview.schemes.ResidueProperties.aa3Hash.put ("TRP",  new Integer (17));
+jalview.schemes.ResidueProperties.aa3Hash.put ("TYR",  new Integer (18));
+jalview.schemes.ResidueProperties.aa3Hash.put ("VAL",  new Integer (19));
+jalview.schemes.ResidueProperties.aa3Hash.put ("ASX",  new Integer (20));
+jalview.schemes.ResidueProperties.aa3Hash.put ("GLX",  new Integer (21));
+jalview.schemes.ResidueProperties.aa3Hash.put ("XAA",  new Integer (22));
+jalview.schemes.ResidueProperties.aa3Hash.put ("-",  new Integer (23));
+jalview.schemes.ResidueProperties.aa3Hash.put ("*",  new Integer (23));
+jalview.schemes.ResidueProperties.aa3Hash.put (".",  new Integer (23));
+jalview.schemes.ResidueProperties.aa3Hash.put (" ",  new Integer (23));
+jalview.schemes.ResidueProperties.aa3Hash.put ("Gap",  new Integer (23));
+}{
+jalview.schemes.ResidueProperties.aa2Triplet.put ("A", "ALA");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("a", "ALA");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("R", "ARG");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("r", "ARG");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("N", "ASN");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("n", "ASN");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("D", "ASP");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("d", "ASP");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("C", "CYS");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("c", "CYS");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("Q", "GLN");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("q", "GLN");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("E", "GLU");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("e", "GLU");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("G", "GLY");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("g", "GLY");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("H", "HIS");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("h", "HIS");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("I", "ILE");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("i", "ILE");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("L", "LEU");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("l", "LEU");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("K", "LYS");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("k", "LYS");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("M", "MET");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("m", "MET");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("F", "PHE");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("f", "PHE");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("P", "PRO");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("p", "PRO");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("S", "SER");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("s", "SER");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("T", "THR");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("t", "THR");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("W", "TRP");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("w", "TRP");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("Y", "TYR");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("y", "TYR");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("V", "VAL");
+jalview.schemes.ResidueProperties.aa2Triplet.put ("v", "VAL");
+}Clazz.defineStatics (c$,
+"aa",  Clazz.newArray (-1, ["A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " "]));
+c$.midBlue = c$.prototype.midBlue =  new java.awt.Color (100, 100, 255);
+c$.scaleColours = c$.prototype.scaleColours =  new java.util.Vector ();
+{
+jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (114, 0, 147));
+jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (156, 0, 98));
+jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (190, 0, 0));
+jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.red);
+jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (255, 125, 0));
+jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.orange);
+jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (255, 194, 85));
+jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.yellow);
+jalview.schemes.ResidueProperties.scaleColours.addElement ( new java.awt.Color (255, 255, 181));
+jalview.schemes.ResidueProperties.scaleColours.addElement (java.awt.Color.white);
+}c$.taylor = c$.prototype.taylor =  Clazz.newArray (-1, [ new java.awt.Color (204, 255, 0),  new java.awt.Color (0, 0, 255),  new java.awt.Color (204, 0, 255),  new java.awt.Color (255, 0, 0),  new java.awt.Color (255, 255, 0),  new java.awt.Color (255, 0, 204),  new java.awt.Color (255, 0, 102),  new java.awt.Color (255, 153, 0),  new java.awt.Color (0, 102, 255),  new java.awt.Color (102, 255, 0),  new java.awt.Color (51, 255, 0),  new java.awt.Color (102, 0, 255),  new java.awt.Color (0, 255, 0),  new java.awt.Color (0, 255, 102),  new java.awt.Color (255, 204, 0),  new java.awt.Color (255, 51, 0),  new java.awt.Color (255, 102, 0),  new java.awt.Color (0, 204, 255),  new java.awt.Color (0, 255, 204),  new java.awt.Color (153, 255, 0), java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white]);
+c$.nucleotide = c$.prototype.nucleotide =  Clazz.newArray (-1, [ new java.awt.Color (100, 247, 63),  new java.awt.Color (255, 179, 64),  new java.awt.Color (235, 65, 60),  new java.awt.Color (60, 136, 238),  new java.awt.Color (60, 136, 238), java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white]);
+c$.purinepyrimidine = c$.prototype.purinepyrimidine =  Clazz.newArray (-1, [ new java.awt.Color (255, 131, 250),  new java.awt.Color (64, 224, 208), java.awt.Color.white, java.awt.Color.white]);
+c$.zappo = c$.prototype.zappo =  Clazz.newArray (-1, [java.awt.Color.pink, jalview.schemes.ResidueProperties.midBlue, java.awt.Color.green, java.awt.Color.red, java.awt.Color.yellow, java.awt.Color.green, java.awt.Color.red, java.awt.Color.magenta, jalview.schemes.ResidueProperties.midBlue, java.awt.Color.pink, java.awt.Color.pink, jalview.schemes.ResidueProperties.midBlue, java.awt.Color.pink, java.awt.Color.orange, java.awt.Color.magenta, java.awt.Color.green, java.awt.Color.green, java.awt.Color.orange, java.awt.Color.orange, java.awt.Color.pink, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white, java.awt.Color.white]);
+Clazz.defineStatics (c$,
+"hyd2",  Clazz.newDoubleArray (-1, [0.62, 0.29, -0.9, -0.74, 1.19, 0.48, -0.4, 1.38, -1.5, 1.06, 0.64, -0.78, 0.12, -0.85, -2.53, -0.18, -0.05, 1.08, 0.81, 0.0, 0.26, 0.0, 0.0]),
+"helix",  Clazz.newDoubleArray (-1, [1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0]),
+"helixmin", 0.57,
+"helixmax", 1.51,
+"strand",  Clazz.newDoubleArray (-1, [0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74, 1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0]),
+"strandmin", 0.37,
+"strandmax", 1.7,
+"turn",  Clazz.newDoubleArray (-1, [0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01, 0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0]),
+"turnmin", 0.47,
+"turnmax", 1.56,
+"buried",  Clazz.newDoubleArray (-1, [1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2, 0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00]),
+"buriedmin", 0.05,
+"buriedmax", 4.6,
+"hyd",  Clazz.newDoubleArray (-1, [1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9, 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0]),
+"hydmax", 4.5,
+"hydmin", -3.9,
+"BLOSUM62",  Clazz.newArray (-1, [ Clazz.newIntArray (-1, [4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0, -4]),  Clazz.newIntArray (-1, [-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4]),  Clazz.newIntArray (-1, [-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4]),  Clazz.newIntArray (-1, [-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4]),  Clazz.newIntArray (-1, [0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4]),  Clazz.newIntArray (-1, [-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4]),  Clazz.newIntArray (-1, [-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4]),  Clazz.newIntArray (-1, [0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4]),  Clazz.newIntArray (-1, [-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4]),  Clazz.newIntArray (-1, [-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4]),  Clazz.newIntArray (-1, [-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4]),  Clazz.newIntArray (-1, [-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4]),  Clazz.newIntArray (-1, [-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4]),  Clazz.newIntArray (-1, [-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4]),  Clazz.newIntArray (-1, [-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4]),  Clazz.newIntArray (-1, [1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4]),  Clazz.newIntArray (-1, [0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4]),  Clazz.newIntArray (-1, [-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4]),  Clazz.newIntArray (-1, [-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4]),  Clazz.newIntArray (-1, [0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4]),  Clazz.newIntArray (-1, [-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4]),  Clazz.newIntArray (-1, [-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4]),  Clazz.newIntArray (-1, [0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4]),  Clazz.newIntArray (-1, [-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1])]),
+"PAM250",  Clazz.newArray (-1, [ Clazz.newIntArray (-1, [2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0, 0, 0, 0, -8]),  Clazz.newIntArray (-1, [-2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4, -2, -1, 0, -1, -8]),  Clazz.newIntArray (-1, [0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2, 2, 1, 0, -8]),  Clazz.newIntArray (-1, [0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2, 3, 3, -1, -8]),  Clazz.newIntArray (-1, [-2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2, -8, 0, -2, -4, -5, -3, -8]),  Clazz.newIntArray (-1, [0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4, -2, 1, 3, -1, -8]),  Clazz.newIntArray (-1, [0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2, 3, 3, -1, -8]),  Clazz.newIntArray (-1, [1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5, -1, 0, 0, -1, -8]),  Clazz.newIntArray (-1, [-1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0, -2, 1, 2, -1, -8]),  Clazz.newIntArray (-1, [-1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5, -1, 4, -2, -2, -1, -8]),  Clazz.newIntArray (-1, [-2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2, -1, 2, -3, -3, -1, -8]),  Clazz.newIntArray (-1, [-1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2, 1, 0, -1, -8]),  Clazz.newIntArray (-1, [-1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2, 2, -2, -2, -1, -8]),  Clazz.newIntArray (-1, [-3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7, -1, -4, -5, -2, -8]),  Clazz.newIntArray (-1, [1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5, -1, -1, 0, -1, -8]),  Clazz.newIntArray (-1, [1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1, 0, 0, 0, -8]),  Clazz.newIntArray (-1, [1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0, 0, -1, 0, -8]),  Clazz.newIntArray (-1, [-6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17, 0, -6, -5, -6, -4, -8]),  Clazz.newIntArray (-1, [-3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0, 10, -2, -3, -4, -2, -8]),  Clazz.newIntArray (-1, [0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6, -2, 4, -2, -2, -1, -8]),  Clazz.newIntArray (-1, [0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2, 3, 2, -1, -8]),  Clazz.newIntArray (-1, [0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2, 2, 3, -1, -8]),  Clazz.newIntArray (-1, [0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4, -2, -1, -1, -1, -1, -8]),  Clazz.newIntArray (-1, [-8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, 1])]));
+c$.ssHash = c$.prototype.ssHash =  new java.util.Hashtable ();
+{
+jalview.schemes.ResidueProperties.ssHash.put ("H", java.awt.Color.magenta);
+jalview.schemes.ResidueProperties.ssHash.put ("E", java.awt.Color.yellow);
+jalview.schemes.ResidueProperties.ssHash.put ("-", java.awt.Color.white);
+jalview.schemes.ResidueProperties.ssHash.put (".", java.awt.Color.white);
+jalview.schemes.ResidueProperties.ssHash.put ("S", java.awt.Color.cyan);
+jalview.schemes.ResidueProperties.ssHash.put ("T", java.awt.Color.blue);
+jalview.schemes.ResidueProperties.ssHash.put ("G", java.awt.Color.pink);
+jalview.schemes.ResidueProperties.ssHash.put ("I", java.awt.Color.pink);
+jalview.schemes.ResidueProperties.ssHash.put ("B", java.awt.Color.yellow);
+}Clazz.defineStatics (c$,
+"DNA",  Clazz.newArray (-1, [ Clazz.newIntArray (-1, [10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1]),  Clazz.newIntArray (-1, [-8, 10, -8, -8, -8, 1, 1, -8, 1, 1, 1]),  Clazz.newIntArray (-1, [-8, -8, 10, -8, -8, 1, 1, 1, -8, 1, 1]),  Clazz.newIntArray (-1, [-8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1]),  Clazz.newIntArray (-1, [-8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1]),  Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 10, 0, 0, 0, 1, 1]),  Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 0, 10, 0, 0, 1, 1]),  Clazz.newIntArray (-1, [1, -8, 1, -8, -8, 0, 0, 10, -8, 1, 1]),  Clazz.newIntArray (-1, [-8, 1, -8, 1, 1, 0, 0, -8, 10, 1, 1]),  Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 1]),  Clazz.newIntArray (-1, [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1])]));
+{
+jalview.schemes.ResidueProperties.scoreMatrices.put ("BLOSUM62",  new jalview.schemes.ScoreMatrix ("BLOSUM62", jalview.schemes.ResidueProperties.BLOSUM62, 0));
+jalview.schemes.ResidueProperties.scoreMatrices.put ("PAM250",  new jalview.schemes.ScoreMatrix ("PAM250", jalview.schemes.ResidueProperties.PAM250, 0));
+jalview.schemes.ResidueProperties.scoreMatrices.put ("DNA",  new jalview.schemes.ScoreMatrix ("DNA", jalview.schemes.ResidueProperties.DNA, 1));
+}c$.pidColours = c$.prototype.pidColours =  Clazz.newArray (-1, [jalview.schemes.ResidueProperties.midBlue,  new java.awt.Color (153, 153, 255),  new java.awt.Color (204, 204, 255)]);
+Clazz.defineStatics (c$,
+"pidThresholds",  Clazz.newFloatArray (-1, [80, 60, 40]));
+c$.codonHash = c$.prototype.codonHash =  new java.util.HashMap ();
+c$.Lys = c$.prototype.Lys =  new java.util.ArrayList ();
+c$.Asn = c$.prototype.Asn =  new java.util.ArrayList ();
+c$.Gln = c$.prototype.Gln =  new java.util.ArrayList ();
+c$.His = c$.prototype.His =  new java.util.ArrayList ();
+c$.Glu = c$.prototype.Glu =  new java.util.ArrayList ();
+c$.Asp = c$.prototype.Asp =  new java.util.ArrayList ();
+c$.Tyr = c$.prototype.Tyr =  new java.util.ArrayList ();
+c$.Thr = c$.prototype.Thr =  new java.util.ArrayList ();
+c$.Pro = c$.prototype.Pro =  new java.util.ArrayList ();
+c$.Ala = c$.prototype.Ala =  new java.util.ArrayList ();
+c$.Ser = c$.prototype.Ser =  new java.util.ArrayList ();
+c$.Arg = c$.prototype.Arg =  new java.util.ArrayList ();
+c$.Gly = c$.prototype.Gly =  new java.util.ArrayList ();
+c$.Trp = c$.prototype.Trp =  new java.util.ArrayList ();
+c$.Cys = c$.prototype.Cys =  new java.util.ArrayList ();
+c$.Ile = c$.prototype.Ile =  new java.util.ArrayList ();
+c$.Met = c$.prototype.Met =  new java.util.ArrayList ();
+c$.Leu = c$.prototype.Leu =  new java.util.ArrayList ();
+c$.Val = c$.prototype.Val =  new java.util.ArrayList ();
+c$.Phe = c$.prototype.Phe =  new java.util.ArrayList ();
+c$.STOP = c$.prototype.STOP =  new java.util.ArrayList ();
+Clazz.defineStatics (c$,
+"START", "ATG");
+{
+jalview.schemes.ResidueProperties.codonHash.put ("K", jalview.schemes.ResidueProperties.Lys);
+jalview.schemes.ResidueProperties.codonHash.put ("N", jalview.schemes.ResidueProperties.Asn);
+jalview.schemes.ResidueProperties.codonHash.put ("Q", jalview.schemes.ResidueProperties.Gln);
+jalview.schemes.ResidueProperties.codonHash.put ("H", jalview.schemes.ResidueProperties.His);
+jalview.schemes.ResidueProperties.codonHash.put ("E", jalview.schemes.ResidueProperties.Glu);
+jalview.schemes.ResidueProperties.codonHash.put ("D", jalview.schemes.ResidueProperties.Asp);
+jalview.schemes.ResidueProperties.codonHash.put ("Y", jalview.schemes.ResidueProperties.Tyr);
+jalview.schemes.ResidueProperties.codonHash.put ("T", jalview.schemes.ResidueProperties.Thr);
+jalview.schemes.ResidueProperties.codonHash.put ("P", jalview.schemes.ResidueProperties.Pro);
+jalview.schemes.ResidueProperties.codonHash.put ("A", jalview.schemes.ResidueProperties.Ala);
+jalview.schemes.ResidueProperties.codonHash.put ("S", jalview.schemes.ResidueProperties.Ser);
+jalview.schemes.ResidueProperties.codonHash.put ("R", jalview.schemes.ResidueProperties.Arg);
+jalview.schemes.ResidueProperties.codonHash.put ("G", jalview.schemes.ResidueProperties.Gly);
+jalview.schemes.ResidueProperties.codonHash.put ("W", jalview.schemes.ResidueProperties.Trp);
+jalview.schemes.ResidueProperties.codonHash.put ("C", jalview.schemes.ResidueProperties.Cys);
+jalview.schemes.ResidueProperties.codonHash.put ("I", jalview.schemes.ResidueProperties.Ile);
+jalview.schemes.ResidueProperties.codonHash.put ("M", jalview.schemes.ResidueProperties.Met);
+jalview.schemes.ResidueProperties.codonHash.put ("L", jalview.schemes.ResidueProperties.Leu);
+jalview.schemes.ResidueProperties.codonHash.put ("V", jalview.schemes.ResidueProperties.Val);
+jalview.schemes.ResidueProperties.codonHash.put ("F", jalview.schemes.ResidueProperties.Phe);
+jalview.schemes.ResidueProperties.codonHash.put ("STOP", jalview.schemes.ResidueProperties.STOP);
+}c$.ambiguityCodes = c$.prototype.ambiguityCodes =  new java.util.Hashtable ();
+c$.codonHash2 = c$.prototype.codonHash2 =  new java.util.Hashtable ();
+c$._ambiguityCodes = c$.prototype._ambiguityCodes =  new java.util.Hashtable ();
+{
+jalview.schemes.ResidueProperties.ambiguityCodes.put ("R",  Clazz.newArray (-1, ["A", "G"]));
+jalview.schemes.ResidueProperties.ambiguityCodes.put ("Y",  Clazz.newArray (-1, ["T", "C"]));
+jalview.schemes.ResidueProperties.ambiguityCodes.put ("W",  Clazz.newArray (-1, ["A", "T"]));
+jalview.schemes.ResidueProperties.ambiguityCodes.put ("S",  Clazz.newArray (-1, ["G", "C"]));
+jalview.schemes.ResidueProperties.ambiguityCodes.put ("M",  Clazz.newArray (-1, ["A", "C"]));
+jalview.schemes.ResidueProperties.ambiguityCodes.put ("K",  Clazz.newArray (-1, ["G", "T"]));
+jalview.schemes.ResidueProperties.ambiguityCodes.put ("H",  Clazz.newArray (-1, ["A", "T", "C"]));
+jalview.schemes.ResidueProperties.ambiguityCodes.put ("B",  Clazz.newArray (-1, ["G", "T", "C"]));
+jalview.schemes.ResidueProperties.ambiguityCodes.put ("V",  Clazz.newArray (-1, ["G", "A", "C"]));
+jalview.schemes.ResidueProperties.ambiguityCodes.put ("D",  Clazz.newArray (-1, ["G", "A", "T"]));
+jalview.schemes.ResidueProperties.ambiguityCodes.put ("N",  Clazz.newArray (-1, ["G", "A", "T", "C"]));
+jalview.schemes.ResidueProperties.codonHash2.put ("AAA", "K");
+jalview.schemes.ResidueProperties.codonHash2.put ("AAG", "K");
+jalview.schemes.ResidueProperties.codonHash2.put ("AAC", "N");
+jalview.schemes.ResidueProperties.codonHash2.put ("AAT", "N");
+jalview.schemes.ResidueProperties.codonHash2.put ("CAA", "Q");
+jalview.schemes.ResidueProperties.codonHash2.put ("CAG", "Q");
+jalview.schemes.ResidueProperties.codonHash2.put ("CAC", "H");
+jalview.schemes.ResidueProperties.codonHash2.put ("CAT", "H");
+jalview.schemes.ResidueProperties.codonHash2.put ("GAA", "E");
+jalview.schemes.ResidueProperties.codonHash2.put ("GAG", "E");
+jalview.schemes.ResidueProperties.codonHash2.put ("GAC", "D");
+jalview.schemes.ResidueProperties.codonHash2.put ("GAT", "D");
+jalview.schemes.ResidueProperties.codonHash2.put ("TAC", "Y");
+jalview.schemes.ResidueProperties.codonHash2.put ("TAT", "Y");
+jalview.schemes.ResidueProperties.codonHash2.put ("ACA", "T");
+jalview.schemes.ResidueProperties.codonHash2.put ("ACC", "T");
+jalview.schemes.ResidueProperties.codonHash2.put ("ACT", "T");
+jalview.schemes.ResidueProperties.codonHash2.put ("ACG", "T");
+jalview.schemes.ResidueProperties.codonHash2.put ("CCA", "P");
+jalview.schemes.ResidueProperties.codonHash2.put ("CCG", "P");
+jalview.schemes.ResidueProperties.codonHash2.put ("CCC", "P");
+jalview.schemes.ResidueProperties.codonHash2.put ("CCT", "P");
+jalview.schemes.ResidueProperties.codonHash2.put ("GCA", "A");
+jalview.schemes.ResidueProperties.codonHash2.put ("GCG", "A");
+jalview.schemes.ResidueProperties.codonHash2.put ("GCC", "A");
+jalview.schemes.ResidueProperties.codonHash2.put ("GCT", "A");
+jalview.schemes.ResidueProperties.codonHash2.put ("TCA", "S");
+jalview.schemes.ResidueProperties.codonHash2.put ("TCG", "S");
+jalview.schemes.ResidueProperties.codonHash2.put ("TCC", "S");
+jalview.schemes.ResidueProperties.codonHash2.put ("TCT", "S");
+jalview.schemes.ResidueProperties.codonHash2.put ("AGC", "S");
+jalview.schemes.ResidueProperties.codonHash2.put ("AGT", "S");
+jalview.schemes.ResidueProperties.codonHash2.put ("AGA", "R");
+jalview.schemes.ResidueProperties.codonHash2.put ("AGG", "R");
+jalview.schemes.ResidueProperties.codonHash2.put ("CGA", "R");
+jalview.schemes.ResidueProperties.codonHash2.put ("CGG", "R");
+jalview.schemes.ResidueProperties.codonHash2.put ("CGC", "R");
+jalview.schemes.ResidueProperties.codonHash2.put ("CGT", "R");
+jalview.schemes.ResidueProperties.codonHash2.put ("GGA", "G");
+jalview.schemes.ResidueProperties.codonHash2.put ("GGG", "G");
+jalview.schemes.ResidueProperties.codonHash2.put ("GGC", "G");
+jalview.schemes.ResidueProperties.codonHash2.put ("GGT", "G");
+jalview.schemes.ResidueProperties.codonHash2.put ("TGA", "*");
+jalview.schemes.ResidueProperties.codonHash2.put ("TAA", "*");
+jalview.schemes.ResidueProperties.codonHash2.put ("TAG", "*");
+jalview.schemes.ResidueProperties.codonHash2.put ("TGG", "W");
+jalview.schemes.ResidueProperties.codonHash2.put ("TGC", "C");
+jalview.schemes.ResidueProperties.codonHash2.put ("TGT", "C");
+jalview.schemes.ResidueProperties.codonHash2.put ("ATA", "I");
+jalview.schemes.ResidueProperties.codonHash2.put ("ATC", "I");
+jalview.schemes.ResidueProperties.codonHash2.put ("ATT", "I");
+jalview.schemes.ResidueProperties.codonHash2.put ("ATG", "M");
+jalview.schemes.ResidueProperties.codonHash2.put ("CTA", "L");
+jalview.schemes.ResidueProperties.codonHash2.put ("CTG", "L");
+jalview.schemes.ResidueProperties.codonHash2.put ("CTC", "L");
+jalview.schemes.ResidueProperties.codonHash2.put ("CTT", "L");
+jalview.schemes.ResidueProperties.codonHash2.put ("TTA", "L");
+jalview.schemes.ResidueProperties.codonHash2.put ("TTG", "L");
+jalview.schemes.ResidueProperties.codonHash2.put ("GTA", "V");
+jalview.schemes.ResidueProperties.codonHash2.put ("GTG", "V");
+jalview.schemes.ResidueProperties.codonHash2.put ("GTC", "V");
+jalview.schemes.ResidueProperties.codonHash2.put ("GTT", "V");
+jalview.schemes.ResidueProperties.codonHash2.put ("TTC", "F");
+jalview.schemes.ResidueProperties.codonHash2.put ("TTT", "F");
+jalview.schemes.ResidueProperties.buildAmbiguityCodonSet ();
+}{
+jalview.schemes.ResidueProperties.Lys.add ("AAA");
+jalview.schemes.ResidueProperties.Lys.add ("AAG");
+jalview.schemes.ResidueProperties.Asn.add ("AAC");
+jalview.schemes.ResidueProperties.Asn.add ("AAT");
+jalview.schemes.ResidueProperties.Gln.add ("CAA");
+jalview.schemes.ResidueProperties.Gln.add ("CAG");
+jalview.schemes.ResidueProperties.His.add ("CAC");
+jalview.schemes.ResidueProperties.His.add ("CAT");
+jalview.schemes.ResidueProperties.Glu.add ("GAA");
+jalview.schemes.ResidueProperties.Glu.add ("GAG");
+jalview.schemes.ResidueProperties.Asp.add ("GAC");
+jalview.schemes.ResidueProperties.Asp.add ("GAT");
+jalview.schemes.ResidueProperties.Tyr.add ("TAC");
+jalview.schemes.ResidueProperties.Tyr.add ("TAT");
+jalview.schemes.ResidueProperties.Thr.add ("ACA");
+jalview.schemes.ResidueProperties.Thr.add ("ACG");
+jalview.schemes.ResidueProperties.Thr.add ("ACC");
+jalview.schemes.ResidueProperties.Thr.add ("ACT");
+jalview.schemes.ResidueProperties.Pro.add ("CCA");
+jalview.schemes.ResidueProperties.Pro.add ("CCG");
+jalview.schemes.ResidueProperties.Pro.add ("CCC");
+jalview.schemes.ResidueProperties.Pro.add ("CCT");
+jalview.schemes.ResidueProperties.Ala.add ("GCA");
+jalview.schemes.ResidueProperties.Ala.add ("GCG");
+jalview.schemes.ResidueProperties.Ala.add ("GCC");
+jalview.schemes.ResidueProperties.Ala.add ("GCT");
+jalview.schemes.ResidueProperties.Ser.add ("TCA");
+jalview.schemes.ResidueProperties.Ser.add ("TCG");
+jalview.schemes.ResidueProperties.Ser.add ("TCC");
+jalview.schemes.ResidueProperties.Ser.add ("TCT");
+jalview.schemes.ResidueProperties.Ser.add ("AGC");
+jalview.schemes.ResidueProperties.Ser.add ("AGT");
+jalview.schemes.ResidueProperties.Arg.add ("AGA");
+jalview.schemes.ResidueProperties.Arg.add ("AGG");
+jalview.schemes.ResidueProperties.Arg.add ("CGA");
+jalview.schemes.ResidueProperties.Arg.add ("CGG");
+jalview.schemes.ResidueProperties.Arg.add ("CGC");
+jalview.schemes.ResidueProperties.Arg.add ("CGT");
+jalview.schemes.ResidueProperties.Gly.add ("GGA");
+jalview.schemes.ResidueProperties.Gly.add ("GGG");
+jalview.schemes.ResidueProperties.Gly.add ("GGC");
+jalview.schemes.ResidueProperties.Gly.add ("GGT");
+jalview.schemes.ResidueProperties.STOP.add ("TGA");
+jalview.schemes.ResidueProperties.STOP.add ("TAA");
+jalview.schemes.ResidueProperties.STOP.add ("TAG");
+jalview.schemes.ResidueProperties.Trp.add ("TGG");
+jalview.schemes.ResidueProperties.Cys.add ("TGC");
+jalview.schemes.ResidueProperties.Cys.add ("TGT");
+jalview.schemes.ResidueProperties.Ile.add ("ATA");
+jalview.schemes.ResidueProperties.Ile.add ("ATC");
+jalview.schemes.ResidueProperties.Ile.add ("ATT");
+jalview.schemes.ResidueProperties.Met.add ("ATG");
+jalview.schemes.ResidueProperties.Leu.add ("CTA");
+jalview.schemes.ResidueProperties.Leu.add ("CTG");
+jalview.schemes.ResidueProperties.Leu.add ("CTC");
+jalview.schemes.ResidueProperties.Leu.add ("CTT");
+jalview.schemes.ResidueProperties.Leu.add ("TTA");
+jalview.schemes.ResidueProperties.Leu.add ("TTG");
+jalview.schemes.ResidueProperties.Val.add ("GTA");
+jalview.schemes.ResidueProperties.Val.add ("GTG");
+jalview.schemes.ResidueProperties.Val.add ("GTC");
+jalview.schemes.ResidueProperties.Val.add ("GTT");
+jalview.schemes.ResidueProperties.Phe.add ("TTC");
+jalview.schemes.ResidueProperties.Phe.add ("TTT");
+}c$.propHash = c$.prototype.propHash =  new java.util.Hashtable ();
+c$.hydrophobic = c$.prototype.hydrophobic =  new java.util.Hashtable ();
+c$.polar = c$.prototype.polar =  new java.util.Hashtable ();
+c$.small = c$.prototype.small =  new java.util.Hashtable ();
+c$.positive = c$.prototype.positive =  new java.util.Hashtable ();
+c$.negative = c$.prototype.negative =  new java.util.Hashtable ();
+c$.charged = c$.prototype.charged =  new java.util.Hashtable ();
+c$.aromatic = c$.prototype.aromatic =  new java.util.Hashtable ();
+c$.aliphatic = c$.prototype.aliphatic =  new java.util.Hashtable ();
+c$.tiny = c$.prototype.tiny =  new java.util.Hashtable ();
+c$.proline = c$.prototype.proline =  new java.util.Hashtable ();
+{
+jalview.schemes.ResidueProperties.hydrophobic.put ("I",  new Integer (1));
+jalview.schemes.ResidueProperties.hydrophobic.put ("L",  new Integer (1));
+jalview.schemes.ResidueProperties.hydrophobic.put ("V",  new Integer (1));
+jalview.schemes.ResidueProperties.hydrophobic.put ("C",  new Integer (1));
+jalview.schemes.ResidueProperties.hydrophobic.put ("A",  new Integer (1));
+jalview.schemes.ResidueProperties.hydrophobic.put ("G",  new Integer (1));
+jalview.schemes.ResidueProperties.hydrophobic.put ("M",  new Integer (1));
+jalview.schemes.ResidueProperties.hydrophobic.put ("F",  new Integer (1));
+jalview.schemes.ResidueProperties.hydrophobic.put ("Y",  new Integer (1));
+jalview.schemes.ResidueProperties.hydrophobic.put ("W",  new Integer (1));
+jalview.schemes.ResidueProperties.hydrophobic.put ("H",  new Integer (1));
+jalview.schemes.ResidueProperties.hydrophobic.put ("K",  new Integer (1));
+jalview.schemes.ResidueProperties.hydrophobic.put ("X",  new Integer (1));
+jalview.schemes.ResidueProperties.hydrophobic.put ("-",  new Integer (1));
+jalview.schemes.ResidueProperties.hydrophobic.put ("*",  new Integer (1));
+jalview.schemes.ResidueProperties.hydrophobic.put ("R",  new Integer (0));
+jalview.schemes.ResidueProperties.hydrophobic.put ("E",  new Integer (0));
+jalview.schemes.ResidueProperties.hydrophobic.put ("Q",  new Integer (0));
+jalview.schemes.ResidueProperties.hydrophobic.put ("D",  new Integer (0));
+jalview.schemes.ResidueProperties.hydrophobic.put ("N",  new Integer (0));
+jalview.schemes.ResidueProperties.hydrophobic.put ("S",  new Integer (0));
+jalview.schemes.ResidueProperties.hydrophobic.put ("T",  new Integer (0));
+jalview.schemes.ResidueProperties.hydrophobic.put ("P",  new Integer (0));
+}{
+jalview.schemes.ResidueProperties.polar.put ("Y",  new Integer (1));
+jalview.schemes.ResidueProperties.polar.put ("W",  new Integer (1));
+jalview.schemes.ResidueProperties.polar.put ("H",  new Integer (1));
+jalview.schemes.ResidueProperties.polar.put ("K",  new Integer (1));
+jalview.schemes.ResidueProperties.polar.put ("R",  new Integer (1));
+jalview.schemes.ResidueProperties.polar.put ("E",  new Integer (1));
+jalview.schemes.ResidueProperties.polar.put ("Q",  new Integer (1));
+jalview.schemes.ResidueProperties.polar.put ("D",  new Integer (1));
+jalview.schemes.ResidueProperties.polar.put ("N",  new Integer (1));
+jalview.schemes.ResidueProperties.polar.put ("S",  new Integer (1));
+jalview.schemes.ResidueProperties.polar.put ("T",  new Integer (1));
+jalview.schemes.ResidueProperties.polar.put ("X",  new Integer (1));
+jalview.schemes.ResidueProperties.polar.put ("-",  new Integer (1));
+jalview.schemes.ResidueProperties.polar.put ("*",  new Integer (1));
+jalview.schemes.ResidueProperties.polar.put ("I",  new Integer (0));
+jalview.schemes.ResidueProperties.polar.put ("L",  new Integer (0));
+jalview.schemes.ResidueProperties.polar.put ("V",  new Integer (0));
+jalview.schemes.ResidueProperties.polar.put ("C",  new Integer (0));
+jalview.schemes.ResidueProperties.polar.put ("A",  new Integer (0));
+jalview.schemes.ResidueProperties.polar.put ("G",  new Integer (0));
+jalview.schemes.ResidueProperties.polar.put ("M",  new Integer (0));
+jalview.schemes.ResidueProperties.polar.put ("F",  new Integer (0));
+jalview.schemes.ResidueProperties.polar.put ("P",  new Integer (0));
+}{
+jalview.schemes.ResidueProperties.small.put ("I",  new Integer (0));
+jalview.schemes.ResidueProperties.small.put ("L",  new Integer (0));
+jalview.schemes.ResidueProperties.small.put ("V",  new Integer (1));
+jalview.schemes.ResidueProperties.small.put ("C",  new Integer (1));
+jalview.schemes.ResidueProperties.small.put ("A",  new Integer (1));
+jalview.schemes.ResidueProperties.small.put ("G",  new Integer (1));
+jalview.schemes.ResidueProperties.small.put ("M",  new Integer (0));
+jalview.schemes.ResidueProperties.small.put ("F",  new Integer (0));
+jalview.schemes.ResidueProperties.small.put ("Y",  new Integer (0));
+jalview.schemes.ResidueProperties.small.put ("W",  new Integer (0));
+jalview.schemes.ResidueProperties.small.put ("H",  new Integer (0));
+jalview.schemes.ResidueProperties.small.put ("K",  new Integer (0));
+jalview.schemes.ResidueProperties.small.put ("R",  new Integer (0));
+jalview.schemes.ResidueProperties.small.put ("E",  new Integer (0));
+jalview.schemes.ResidueProperties.small.put ("Q",  new Integer (0));
+jalview.schemes.ResidueProperties.small.put ("D",  new Integer (1));
+jalview.schemes.ResidueProperties.small.put ("N",  new Integer (1));
+jalview.schemes.ResidueProperties.small.put ("S",  new Integer (1));
+jalview.schemes.ResidueProperties.small.put ("T",  new Integer (1));
+jalview.schemes.ResidueProperties.small.put ("P",  new Integer (1));
+jalview.schemes.ResidueProperties.small.put ("-",  new Integer (1));
+jalview.schemes.ResidueProperties.small.put ("*",  new Integer (1));
+}{
+jalview.schemes.ResidueProperties.positive.put ("I",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("L",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("V",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("C",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("A",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("G",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("M",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("F",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("Y",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("W",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("H",  new Integer (1));
+jalview.schemes.ResidueProperties.positive.put ("K",  new Integer (1));
+jalview.schemes.ResidueProperties.positive.put ("R",  new Integer (1));
+jalview.schemes.ResidueProperties.positive.put ("E",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("Q",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("D",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("N",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("S",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("T",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("P",  new Integer (0));
+jalview.schemes.ResidueProperties.positive.put ("-",  new Integer (1));
+jalview.schemes.ResidueProperties.positive.put ("*",  new Integer (1));
+}{
+jalview.schemes.ResidueProperties.negative.put ("I",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("L",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("V",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("C",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("A",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("G",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("M",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("F",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("Y",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("W",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("H",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("K",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("R",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("E",  new Integer (1));
+jalview.schemes.ResidueProperties.negative.put ("Q",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("D",  new Integer (1));
+jalview.schemes.ResidueProperties.negative.put ("N",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("S",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("T",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("P",  new Integer (0));
+jalview.schemes.ResidueProperties.negative.put ("-",  new Integer (1));
+jalview.schemes.ResidueProperties.negative.put ("*",  new Integer (1));
+}{
+jalview.schemes.ResidueProperties.charged.put ("I",  new Integer (0));
+jalview.schemes.ResidueProperties.charged.put ("L",  new Integer (0));
+jalview.schemes.ResidueProperties.charged.put ("V",  new Integer (0));
+jalview.schemes.ResidueProperties.charged.put ("C",  new Integer (0));
+jalview.schemes.ResidueProperties.charged.put ("A",  new Integer (0));
+jalview.schemes.ResidueProperties.charged.put ("G",  new Integer (0));
+jalview.schemes.ResidueProperties.charged.put ("M",  new Integer (0));
+jalview.schemes.ResidueProperties.charged.put ("F",  new Integer (0));
+jalview.schemes.ResidueProperties.charged.put ("Y",  new Integer (0));
+jalview.schemes.ResidueProperties.charged.put ("W",  new Integer (0));
+jalview.schemes.ResidueProperties.charged.put ("H",  new Integer (1));
+jalview.schemes.ResidueProperties.charged.put ("K",  new Integer (1));
+jalview.schemes.ResidueProperties.charged.put ("R",  new Integer (1));
+jalview.schemes.ResidueProperties.charged.put ("E",  new Integer (1));
+jalview.schemes.ResidueProperties.charged.put ("Q",  new Integer (0));
+jalview.schemes.ResidueProperties.charged.put ("D",  new Integer (1));
+jalview.schemes.ResidueProperties.charged.put ("N",  new Integer (0));
+jalview.schemes.ResidueProperties.charged.put ("S",  new Integer (0));
+jalview.schemes.ResidueProperties.charged.put ("T",  new Integer (0));
+jalview.schemes.ResidueProperties.charged.put ("P",  new Integer (0));
+jalview.schemes.ResidueProperties.charged.put ("-",  new Integer (1));
+jalview.schemes.ResidueProperties.charged.put ("*",  new Integer (1));
+}{
+jalview.schemes.ResidueProperties.aromatic.put ("I",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("L",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("V",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("C",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("A",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("G",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("M",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("F",  new Integer (1));
+jalview.schemes.ResidueProperties.aromatic.put ("Y",  new Integer (1));
+jalview.schemes.ResidueProperties.aromatic.put ("W",  new Integer (1));
+jalview.schemes.ResidueProperties.aromatic.put ("H",  new Integer (1));
+jalview.schemes.ResidueProperties.aromatic.put ("K",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("R",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("E",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("Q",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("D",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("N",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("S",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("T",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("P",  new Integer (0));
+jalview.schemes.ResidueProperties.aromatic.put ("-",  new Integer (1));
+jalview.schemes.ResidueProperties.aromatic.put ("*",  new Integer (1));
+}{
+jalview.schemes.ResidueProperties.aliphatic.put ("I",  new Integer (1));
+jalview.schemes.ResidueProperties.aliphatic.put ("L",  new Integer (1));
+jalview.schemes.ResidueProperties.aliphatic.put ("V",  new Integer (1));
+jalview.schemes.ResidueProperties.aliphatic.put ("C",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("A",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("G",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("M",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("F",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("Y",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("W",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("H",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("K",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("R",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("E",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("Q",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("D",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("N",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("S",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("T",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("P",  new Integer (0));
+jalview.schemes.ResidueProperties.aliphatic.put ("-",  new Integer (1));
+jalview.schemes.ResidueProperties.aliphatic.put ("*",  new Integer (1));
+}{
+jalview.schemes.ResidueProperties.tiny.put ("I",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("L",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("V",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("C",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("A",  new Integer (1));
+jalview.schemes.ResidueProperties.tiny.put ("G",  new Integer (1));
+jalview.schemes.ResidueProperties.tiny.put ("M",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("F",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("Y",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("W",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("H",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("K",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("R",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("E",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("Q",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("D",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("N",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("S",  new Integer (1));
+jalview.schemes.ResidueProperties.tiny.put ("T",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("P",  new Integer (0));
+jalview.schemes.ResidueProperties.tiny.put ("-",  new Integer (1));
+jalview.schemes.ResidueProperties.tiny.put ("*",  new Integer (1));
+}{
+jalview.schemes.ResidueProperties.proline.put ("I",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("L",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("V",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("C",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("A",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("G",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("M",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("F",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("Y",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("W",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("H",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("K",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("R",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("E",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("Q",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("D",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("N",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("S",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("T",  new Integer (0));
+jalview.schemes.ResidueProperties.proline.put ("P",  new Integer (1));
+jalview.schemes.ResidueProperties.proline.put ("-",  new Integer (1));
+jalview.schemes.ResidueProperties.proline.put ("*",  new Integer (1));
+}{
+jalview.schemes.ResidueProperties.propHash.put ("hydrophobic", jalview.schemes.ResidueProperties.hydrophobic);
+jalview.schemes.ResidueProperties.propHash.put ("small", jalview.schemes.ResidueProperties.small);
+jalview.schemes.ResidueProperties.propHash.put ("positive", jalview.schemes.ResidueProperties.positive);
+jalview.schemes.ResidueProperties.propHash.put ("negative", jalview.schemes.ResidueProperties.negative);
+jalview.schemes.ResidueProperties.propHash.put ("charged", jalview.schemes.ResidueProperties.charged);
+jalview.schemes.ResidueProperties.propHash.put ("aromatic", jalview.schemes.ResidueProperties.aromatic);
+jalview.schemes.ResidueProperties.propHash.put ("aliphatic", jalview.schemes.ResidueProperties.aliphatic);
+jalview.schemes.ResidueProperties.propHash.put ("tiny", jalview.schemes.ResidueProperties.tiny);
+jalview.schemes.ResidueProperties.propHash.put ("proline", jalview.schemes.ResidueProperties.proline);
+jalview.schemes.ResidueProperties.propHash.put ("polar", jalview.schemes.ResidueProperties.polar);
+}{
+var propMatrixF =  Clazz.newIntArray (23, 23, 0);
+var propMatrixPos =  Clazz.newIntArray (23, 23, 0);
+var propMatrixEpos =  Clazz.newIntArray (23, 23, 0);
+for (var i = 0; i < 23; i++) {
+var maxF = 0;
+var maxP = 0;
+var maxEP = 0;
+var ic = "";
+if (jalview.schemes.ResidueProperties.aa.length > i) {
+ic += jalview.schemes.ResidueProperties.aa[i];
+} else {
+ic = "-";
+}for (var j = i + 1; j < 23; j++) {
+var jc = "";
+if (jalview.schemes.ResidueProperties.aa.length > j) {
+jc += jalview.schemes.ResidueProperties.aa[j];
+} else {
+jc = "-";
+}propMatrixF[i][j] = 0;
+propMatrixPos[i][j] = 0;
+propMatrixEpos[i][j] = 0;
+for (var en = jalview.schemes.ResidueProperties.propHash.keys (); en.hasMoreElements (); ) {
+var ph = en.nextElement ();
+var pph = jalview.schemes.ResidueProperties.propHash.get (ph);
+if (pph.get (ic) != null && pph.get (jc) != null) {
+var icp = pph.get (ic).intValue ();
+var jcp = pph.get (jc).intValue ();
+propMatrixPos[i][j] += icp == jcp && icp > 0 ? 2 : 0;
+propMatrixPos[j][i] += icp == jcp && icp > 0 ? 2 : 0;
+propMatrixF[i][j] += icp == jcp ? 2 : 0;
+propMatrixF[j][i] += icp == jcp ? 2 : 0;
+propMatrixEpos[i][j] += icp == jcp ? (1 + icp * 2) : 0;
+propMatrixEpos[j][i] += icp == jcp ? (1 + icp * 2) : 0;
+}}
+if (maxF < propMatrixF[i][j]) {
+maxF = propMatrixF[i][j];
+}if (maxP < propMatrixPos[i][j]) {
+maxP = propMatrixPos[i][j];
+}if (maxEP < propMatrixEpos[i][j]) {
+maxEP = propMatrixEpos[i][j];
+}}
+propMatrixF[i][i] = maxF;
+propMatrixPos[i][i] = maxP;
+propMatrixEpos[i][i] = maxEP;
+}
+jalview.schemes.ResidueProperties.scoreMatrices.put ("PID",  new jalview.analysis.scoremodels.PIDScoreModel ());
+jalview.schemes.ResidueProperties.scoreMatrices.put ("Displayed Features",  new jalview.analysis.scoremodels.FeatureScoreModel ());
+}Clazz.defineStatics (c$,
+"toDssp3State", null);
+{
+jalview.schemes.ResidueProperties.toDssp3State =  new java.util.Hashtable ();
+jalview.schemes.ResidueProperties.toDssp3State.put ("H", "H");
+jalview.schemes.ResidueProperties.toDssp3State.put ("E", "E");
+jalview.schemes.ResidueProperties.toDssp3State.put ("C", " ");
+jalview.schemes.ResidueProperties.toDssp3State.put (" ", " ");
+jalview.schemes.ResidueProperties.toDssp3State.put ("T", " ");
+jalview.schemes.ResidueProperties.toDssp3State.put ("B", "E");
+jalview.schemes.ResidueProperties.toDssp3State.put ("G", "H");
+jalview.schemes.ResidueProperties.toDssp3State.put ("I", "H");
+jalview.schemes.ResidueProperties.toDssp3State.put ("X", " ");
+}Clazz.defineStatics (c$,
+"toRNAssState", null,
+"RNAcloseParen",  Clazz.newBooleanArray (255, false));
+{
+jalview.schemes.ResidueProperties.toRNAssState =  new java.util.Hashtable ();
+jalview.schemes.ResidueProperties.toRNAssState.put (")", "(");
+jalview.schemes.ResidueProperties.toRNAssState.put ("(", "(");
+jalview.schemes.ResidueProperties.toRNAssState.put ("]", "[");
+jalview.schemes.ResidueProperties.toRNAssState.put ("[", "[");
+jalview.schemes.ResidueProperties.toRNAssState.put ("{", "{");
+jalview.schemes.ResidueProperties.toRNAssState.put ("}", "{");
+jalview.schemes.ResidueProperties.toRNAssState.put (">", ">");
+jalview.schemes.ResidueProperties.toRNAssState.put ("<", ">");
+jalview.schemes.ResidueProperties.toRNAssState.put ("A", "A");
+jalview.schemes.ResidueProperties.toRNAssState.put ("a", "A");
+jalview.schemes.ResidueProperties.toRNAssState.put ("B", "B");
+jalview.schemes.ResidueProperties.toRNAssState.put ("b", "B");
+jalview.schemes.ResidueProperties.toRNAssState.put ("C", "C");
+jalview.schemes.ResidueProperties.toRNAssState.put ("c", "C");
+jalview.schemes.ResidueProperties.toRNAssState.put ("D", "D");
+jalview.schemes.ResidueProperties.toRNAssState.put ("d", "D");
+jalview.schemes.ResidueProperties.toRNAssState.put ("E", "E");
+jalview.schemes.ResidueProperties.toRNAssState.put ("e", "E");
+jalview.schemes.ResidueProperties.toRNAssState.put ("F", "F");
+jalview.schemes.ResidueProperties.toRNAssState.put ("f", "F");
+jalview.schemes.ResidueProperties.toRNAssState.put ("G", "G");
+jalview.schemes.ResidueProperties.toRNAssState.put ("g", "G");
+jalview.schemes.ResidueProperties.toRNAssState.put ("H", "H");
+jalview.schemes.ResidueProperties.toRNAssState.put ("h", "H");
+jalview.schemes.ResidueProperties.toRNAssState.put ("I", "I");
+jalview.schemes.ResidueProperties.toRNAssState.put ("i", "I");
+jalview.schemes.ResidueProperties.toRNAssState.put ("J", "J");
+jalview.schemes.ResidueProperties.toRNAssState.put ("j", "J");
+jalview.schemes.ResidueProperties.toRNAssState.put ("K", "K");
+jalview.schemes.ResidueProperties.toRNAssState.put ("k", "K");
+jalview.schemes.ResidueProperties.toRNAssState.put ("L", "L");
+jalview.schemes.ResidueProperties.toRNAssState.put ("l", "L");
+jalview.schemes.ResidueProperties.toRNAssState.put ("M", "M");
+jalview.schemes.ResidueProperties.toRNAssState.put ("m", "M");
+jalview.schemes.ResidueProperties.toRNAssState.put ("N", "N");
+jalview.schemes.ResidueProperties.toRNAssState.put ("n", "N");
+jalview.schemes.ResidueProperties.toRNAssState.put ("O", "O");
+jalview.schemes.ResidueProperties.toRNAssState.put ("o", "O");
+jalview.schemes.ResidueProperties.toRNAssState.put ("P", "P");
+jalview.schemes.ResidueProperties.toRNAssState.put ("p", "P");
+jalview.schemes.ResidueProperties.toRNAssState.put ("Q", "Q");
+jalview.schemes.ResidueProperties.toRNAssState.put ("q", "Q");
+jalview.schemes.ResidueProperties.toRNAssState.put ("R", "R");
+jalview.schemes.ResidueProperties.toRNAssState.put ("r", "R");
+jalview.schemes.ResidueProperties.toRNAssState.put ("S", "S");
+jalview.schemes.ResidueProperties.toRNAssState.put ("s", "S");
+jalview.schemes.ResidueProperties.toRNAssState.put ("T", "T");
+jalview.schemes.ResidueProperties.toRNAssState.put ("t", "T");
+jalview.schemes.ResidueProperties.toRNAssState.put ("U", "U");
+jalview.schemes.ResidueProperties.toRNAssState.put ("u", "U");
+jalview.schemes.ResidueProperties.toRNAssState.put ("V", "V");
+jalview.schemes.ResidueProperties.toRNAssState.put ("v", "V");
+jalview.schemes.ResidueProperties.toRNAssState.put ("W", "W");
+jalview.schemes.ResidueProperties.toRNAssState.put ("w", "W");
+jalview.schemes.ResidueProperties.toRNAssState.put ("X", "X");
+jalview.schemes.ResidueProperties.toRNAssState.put ("x", "X");
+jalview.schemes.ResidueProperties.toRNAssState.put ("Y", "Y");
+jalview.schemes.ResidueProperties.toRNAssState.put ("y", "Y");
+jalview.schemes.ResidueProperties.toRNAssState.put ("Z", "Z");
+jalview.schemes.ResidueProperties.toRNAssState.put ("z", "Z");
+for (var p = 0; p < jalview.schemes.ResidueProperties.RNAcloseParen.length; p++) {
+jalview.schemes.ResidueProperties.RNAcloseParen[p] = false;
+}
+for (var k, $k = jalview.schemes.ResidueProperties.toRNAssState.keySet ().iterator (); $k.hasNext () && ((k = $k.next ()) || true);) {
+jalview.schemes.ResidueProperties.RNAcloseParen[k.charCodeAt (0)] = k.charAt (0) != jalview.schemes.ResidueProperties.toRNAssState.get (k).charAt (0);
+}
+}});