-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
+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 ();
+});
git://source.jalview.org / jalviewjs.git / blobdiff