-Clazz.declarePackage ("jalview.analysis");
-Clazz.load (null, "jalview.analysis.SecStrConsensus", ["java.util.ArrayList", "$.Hashtable"], function () {
-c$ = Clazz.declareType (jalview.analysis, "SecStrConsensus");
-c$.extractConsensus = Clazz.defineMethod (c$, "extractConsensus",
-function (bps) {
-var maxlength = 0;
-for (var strs, $strs = bps.iterator (); $strs.hasNext () && ((strs = $strs.next ()) || true);) {
-for (var bp, $bp = strs.iterator (); $bp.hasNext () && ((bp = $bp.next ()) || true);) {
-maxlength = Math.max (1 + Math.max (bp.bp5, bp.bp3), maxlength);
-}
-}
-var seq = new java.util.ArrayList ();
-for (var i = 0; i < maxlength; i++) {
-seq.add ( new java.util.Hashtable ());
-}
-for (var strs, $strs = bps.iterator (); $strs.hasNext () && ((strs = $strs.next ()) || true);) {
-for (var bp, $bp = strs.iterator (); $bp.hasNext () && ((bp = $bp.next ()) || true);) {
-var i = bp.bp5;
-var j = bp.bp3;
-var h = seq.get (i);
-if (!h.containsKey (new Integer (j))) {
-h.put (new Integer (j), new Double (0.0));
-}h.put (new Integer (j), new Double ((h.get (new Integer (j))).doubleValue () + 1.));
-}
-}
-var mat = jalview.analysis.SecStrConsensus.fillMatrix (seq);
-var res = jalview.analysis.SecStrConsensus.backtrack (mat, seq);
-var finalres = Clazz.newIntArray (seq.size (), 0);
-for (var i = 0; i < seq.size (); i++) {
-finalres[i] = -1;
-}
-for (var bp, $bp = res.iterator (); $bp.hasNext () && ((bp = $bp.next ()) || true);) {
-finalres[bp.bp5] = bp.bp3;
-finalres[bp.bp3] = bp.bp5;
-}
-return finalres;
-}, "java.util.ArrayList");
-c$.canBasePair = Clazz.defineMethod (c$, "canBasePair",
-($fz = function (seq, i, k) {
-return seq.get (i).containsKey (new Integer (k));
-}, $fz.isPrivate = true, $fz), "java.util.ArrayList,~N,~N");
-c$.basePairScore = Clazz.defineMethod (c$, "basePairScore",
-($fz = function (seq, i, k) {
-return seq.get (i).get (new Integer (k));
-}, $fz.isPrivate = true, $fz), "java.util.ArrayList,~N,~N");
-c$.fillMatrix = Clazz.defineMethod (c$, "fillMatrix",
-($fz = function (seq) {
-var n = seq.size ();
-var tab = Clazz.newDoubleArray (n, n, 0);
-for (var m = 1; m <= n; m++) {
-for (var i = 0; i < n - m + 1; i++) {
-var j = i + m - 1;
-tab[i][j] = 0;
-if (i < j) {
-tab[i][j] = Math.max (tab[i][j], tab[i + 1][j]);
-for (var k = i + 1; k <= j; k++) {
-if (jalview.analysis.SecStrConsensus.canBasePair (seq, i, k)) {
-var fact1 = 0;
-if (k > i + 1) {
-fact1 = tab[i + 1][k - 1];
-}var fact2 = 0;
-if (k < j) {
-fact2 = tab[k + 1][j];
-}tab[i][j] = Math.max (tab[i][j], jalview.analysis.SecStrConsensus.basePairScore (seq, i, k) + fact1 + fact2);
-}}
-}}
-}
-return tab;
-}, $fz.isPrivate = true, $fz), "java.util.ArrayList");
-c$.backtrack = Clazz.defineMethod (c$, "backtrack",
-($fz = function (tab, seq) {
-return jalview.analysis.SecStrConsensus.backtrack (tab, seq, 0, seq.size () - 1);
-}, $fz.isPrivate = true, $fz), "~A,java.util.ArrayList");
-c$.backtrack = Clazz.defineMethod (c$, "backtrack",
-($fz = function (tab, seq, i, j) {
-var result = new java.util.ArrayList ();
-if (i < j) {
-var indices = new java.util.ArrayList ();
-indices.add (new Integer (-1));
-for (var k = i + 1; k <= j; k++) {
-indices.add (new Integer (k));
-}
-for (var k, $k = indices.iterator (); $k.hasNext () && ((k = $k.next ()) || true);) {
-if (k == -1) {
-if (tab[i][j] == tab[i + 1][j]) {
-result = jalview.analysis.SecStrConsensus.backtrack (tab, seq, i + 1, j);
-}} else {
-if (jalview.analysis.SecStrConsensus.canBasePair (seq, i, k)) {
-var fact1 = 0;
-if (k > i + 1) {
-fact1 = tab[i + 1][k - 1];
-}var fact2 = 0;
-if (k < j) {
-fact2 = tab[k + 1][j];
-}if (tab[i][j] == jalview.analysis.SecStrConsensus.basePairScore (seq, i, k) + fact1 + fact2) {
-result = jalview.analysis.SecStrConsensus.backtrack (tab, seq, i + 1, k - 1);
-result.addAll (jalview.analysis.SecStrConsensus.backtrack (tab, seq, k + 1, j));
-result.add ( new jalview.analysis.SecStrConsensus.SimpleBP (i, k));
-}}}}
-} else if (i == j) {
-} else {
-}return result;
-}, $fz.isPrivate = true, $fz), "~A,java.util.ArrayList,~N,~N");
-Clazz.pu$h ();
-c$ = Clazz.decorateAsClass (function () {
-this.bp5 = 0;
-this.bp3 = 0;
-Clazz.instantialize (this, arguments);
-}, jalview.analysis.SecStrConsensus, "SimpleBP");
-Clazz.makeConstructor (c$,
-function () {
-});
-Clazz.makeConstructor (c$,
-function (a, b) {
-this.bp5 = a;
-this.bp3 = b;
-}, "~N,~N");
-Clazz.defineMethod (c$, "setBP5",
-function (a) {
-this.bp5 = a;
-}, "~N");
-Clazz.defineMethod (c$, "setBP3",
-function (a) {
-this.bp3 = a;
-}, "~N");
-Clazz.defineMethod (c$, "getBP5",
-function () {
-return this.bp5;
-});
-Clazz.defineMethod (c$, "getBP3",
-function () {
-return this.bp3;
-});
-Clazz.overrideMethod (c$, "toString",
-function () {
-return "(" + this.bp5 + "," + this.bp3 + ")";
-});
-c$ = Clazz.p0p ();
-});
+Clazz.declarePackage ("jalview.analysis");\r
+Clazz.load (null, "jalview.analysis.SecStrConsensus", ["java.util.ArrayList", "$.Hashtable"], function () {\r
+c$ = Clazz.declareType (jalview.analysis, "SecStrConsensus");\r
+c$.extractConsensus = Clazz.defineMethod (c$, "extractConsensus", \r
+function (bps) {\r
+var maxlength = 0;\r
+for (var strs, $strs = bps.iterator (); $strs.hasNext () && ((strs = $strs.next ()) || true);) {\r
+for (var bp, $bp = strs.iterator (); $bp.hasNext () && ((bp = $bp.next ()) || true);) {\r
+maxlength = Math.max (1 + Math.max (bp.bp5, bp.bp3), maxlength);\r
+}\r
+}\r
+var seq = new java.util.ArrayList ();\r
+for (var i = 0; i < maxlength; i++) {\r
+seq.add ( new java.util.Hashtable ());\r
+}\r
+for (var strs, $strs = bps.iterator (); $strs.hasNext () && ((strs = $strs.next ()) || true);) {\r
+for (var bp, $bp = strs.iterator (); $bp.hasNext () && ((bp = $bp.next ()) || true);) {\r
+var i = bp.bp5;\r
+var j = bp.bp3;\r
+var h = seq.get (i);\r
+if (!h.containsKey (new Integer (j))) {\r
+h.put (new Integer (j), new Double (0.0));\r
+}h.put (new Integer (j), new Double ((h.get (new Integer (j))).doubleValue () + 1.));\r
+}\r
+}\r
+var mat = jalview.analysis.SecStrConsensus.fillMatrix (seq);\r
+var res = jalview.analysis.SecStrConsensus.backtrack (mat, seq);\r
+var finalres = Clazz.newIntArray (seq.size (), 0);\r
+for (var i = 0; i < seq.size (); i++) {\r
+finalres[i] = -1;\r
+}\r
+for (var bp, $bp = res.iterator (); $bp.hasNext () && ((bp = $bp.next ()) || true);) {\r
+finalres[bp.bp5] = bp.bp3;\r
+finalres[bp.bp3] = bp.bp5;\r
+}\r
+return finalres;\r
+}, "java.util.ArrayList");\r
+c$.canBasePair = Clazz.defineMethod (c$, "canBasePair", \r
+($fz = function (seq, i, k) {\r
+return seq.get (i).containsKey (new Integer (k));\r
+}, $fz.isPrivate = true, $fz), "java.util.ArrayList,~N,~N");\r
+c$.basePairScore = Clazz.defineMethod (c$, "basePairScore", \r
+($fz = function (seq, i, k) {\r
+return seq.get (i).get (new Integer (k));\r
+}, $fz.isPrivate = true, $fz), "java.util.ArrayList,~N,~N");\r
+c$.fillMatrix = Clazz.defineMethod (c$, "fillMatrix", \r
+($fz = function (seq) {\r
+var n = seq.size ();\r
+var tab = Clazz.newDoubleArray (n, n, 0);\r
+for (var m = 1; m <= n; m++) {\r
+for (var i = 0; i < n - m + 1; i++) {\r
+var j = i + m - 1;\r
+tab[i][j] = 0;\r
+if (i < j) {\r
+tab[i][j] = Math.max (tab[i][j], tab[i + 1][j]);\r
+for (var k = i + 1; k <= j; k++) {\r
+if (jalview.analysis.SecStrConsensus.canBasePair (seq, i, k)) {\r
+var fact1 = 0;\r
+if (k > i + 1) {\r
+fact1 = tab[i + 1][k - 1];\r
+}var fact2 = 0;\r
+if (k < j) {\r
+fact2 = tab[k + 1][j];\r
+}tab[i][j] = Math.max (tab[i][j], jalview.analysis.SecStrConsensus.basePairScore (seq, i, k) + fact1 + fact2);\r
+}}\r
+}}\r
+}\r
+return tab;\r
+}, $fz.isPrivate = true, $fz), "java.util.ArrayList");\r
+c$.backtrack = Clazz.defineMethod (c$, "backtrack", \r
+($fz = function (tab, seq) {\r
+return jalview.analysis.SecStrConsensus.backtrack (tab, seq, 0, seq.size () - 1);\r
+}, $fz.isPrivate = true, $fz), "~A,java.util.ArrayList");\r
+c$.backtrack = Clazz.defineMethod (c$, "backtrack", \r
+($fz = function (tab, seq, i, j) {\r
+var result = new java.util.ArrayList ();\r
+if (i < j) {\r
+var indices = new java.util.ArrayList ();\r
+indices.add (new Integer (-1));\r
+for (var k = i + 1; k <= j; k++) {\r
+indices.add (new Integer (k));\r
+}\r
+for (var k, $k = indices.iterator (); $k.hasNext () && ((k = $k.next ()) || true);) {\r
+if (k == -1) {\r
+if (tab[i][j] == tab[i + 1][j]) {\r
+result = jalview.analysis.SecStrConsensus.backtrack (tab, seq, i + 1, j);\r
+}} else {\r
+if (jalview.analysis.SecStrConsensus.canBasePair (seq, i, k)) {\r
+var fact1 = 0;\r
+if (k > i + 1) {\r
+fact1 = tab[i + 1][k - 1];\r
+}var fact2 = 0;\r
+if (k < j) {\r
+fact2 = tab[k + 1][j];\r
+}if (tab[i][j] == jalview.analysis.SecStrConsensus.basePairScore (seq, i, k) + fact1 + fact2) {\r
+result = jalview.analysis.SecStrConsensus.backtrack (tab, seq, i + 1, k - 1);\r
+result.addAll (jalview.analysis.SecStrConsensus.backtrack (tab, seq, k + 1, j));\r
+result.add ( new jalview.analysis.SecStrConsensus.SimpleBP (i, k));\r
+}}}}\r
+} else if (i == j) {\r
+} else {\r
+}return result;\r
+}, $fz.isPrivate = true, $fz), "~A,java.util.ArrayList,~N,~N");\r
+Clazz.pu$h ();\r
+c$ = Clazz.decorateAsClass (function () {\r
+this.bp5 = 0;\r
+this.bp3 = 0;\r
+Clazz.instantialize (this, arguments);\r
+}, jalview.analysis.SecStrConsensus, "SimpleBP");\r
+Clazz.makeConstructor (c$, \r
+function () {\r
+});\r
+Clazz.makeConstructor (c$, \r
+function (a, b) {\r
+this.bp5 = a;\r
+this.bp3 = b;\r
+}, "~N,~N");\r
+Clazz.defineMethod (c$, "setBP5", \r
+function (a) {\r
+this.bp5 = a;\r
+}, "~N");\r
+Clazz.defineMethod (c$, "setBP3", \r
+function (a) {\r
+this.bp3 = a;\r
+}, "~N");\r
+Clazz.defineMethod (c$, "getBP5", \r
+function () {\r
+return this.bp5;\r
+});\r
+Clazz.defineMethod (c$, "getBP3", \r
+function () {\r
+return this.bp3;\r
+});\r
+Clazz.overrideMethod (c$, "toString", \r
+function () {\r
+return "(" + this.bp5 + "," + this.bp3 + ")";\r
+});\r
+c$ = Clazz.p0p ();\r
+});\r
git://source.jalview.org / jalviewjs.git / blobdiff