X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fanalysis%2FSecStrConsensus.js;h=f96678ee6f0a0b69d0a620f03de74cb8e45ecf15;hp=44e1009426e8cfcc962e4a2eef345cf14c126e80;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/analysis/SecStrConsensus.js b/bin/jalview/analysis/SecStrConsensus.js
index 44e1009..f96678e 100644
--- a/bin/jalview/analysis/SecStrConsensus.js
+++ b/bin/jalview/analysis/SecStrConsensus.js
@@ -1,139 +1,139 @@
-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");
+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 ();
+});