X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fanalysis%2FNJTree.js;h=8f3a36749a7cc70c13b1f12c85b06eda321cae94;hp=24a8fc55dd910ce317f5581ff41e82e2e823e237;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/analysis/NJTree.js b/bin/jalview/analysis/NJTree.js
index 24a8fc5..8f3a367 100644
--- a/bin/jalview/analysis/NJTree.js
+++ b/bin/jalview/analysis/NJTree.js
@@ -1,577 +1,577 @@
-Clazz.declarePackage ("jalview.analysis");
-Clazz.load (["java.util.Vector"], ["jalview.analysis.Cluster", "$.NJTree"], ["jalview.analysis.SequenceIdMatcher", "jalview.datamodel.AlignmentView", "$.CigarArray", "$.NodeTransformI", "$.SeqCigar", "$.Sequence", "$.SequenceI", "$.SequenceNode", "jalview.io.NewickFile", "jalview.schemes.ResidueProperties", "jalview.util.Format", "java.lang.StringBuffer"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.$cluster = null;
-this.sequence = null;
-this.seqData = null;
-this.done = null;
-this.noseqs = 0;
-this.noClus = 0;
-this.distance = null;
-this.mini = 0;
-this.minj = 0;
-this.ri = 0;
-this.rj = 0;
-this.groups = null;
-this.maxdist = null;
-this.top = null;
-this.maxDistValue = 0;
-this.maxheight = 0;
-this.ycount = 0;
-this.node = null;
-this.type = null;
-this.pwtype = null;
-this.found = null;
-this.leaves = null;
-this.hasDistances = true;
-this.hasBootstrap = false;
-this.hasRootDistance = true;
-this._lycount = 0;
-this._lylimit = 0;
-Clazz.instantialize (this, arguments);
-}, jalview.analysis, "NJTree");
-Clazz.prepareFields (c$, function () {
-this.groups =  new java.util.Vector ();
-});
-Clazz.makeConstructor (c$, 
-function (seqs, odata, treefile) {
-this.construct (seqs, treefile);
-if (odata != null) {
-this.seqData = odata;
-}}, "~A,jalview.datamodel.AlignmentView,jalview.io.NewickFile");
-Clazz.makeConstructor (c$, 
-function (seqs, treefile) {
-this.sequence = seqs;
-this.top = treefile.getTree ();
-this.hasDistances = treefile.HasDistances ();
-this.hasBootstrap = treefile.HasBootstrap ();
-this.hasRootDistance = treefile.HasRootDistance ();
-this.maxheight = this.findHeight (this.top);
-var algnIds =  new jalview.analysis.SequenceIdMatcher (seqs);
-var leaves =  new java.util.Vector ();
-this.findLeaves (this.top, leaves);
-var i = 0;
-var namesleft = seqs.length;
-var j;
-var nam;
-var realnam;
-var one2many =  new java.util.Vector ();
-var countOne2Many = 0;
-while (i < leaves.size ()) {
-j = leaves.elementAt (i++);
-realnam = j.getName ();
-nam = null;
-if (namesleft > -1) {
-nam = algnIds.findIdMatch (realnam);
-}if (nam != null) {
-j.setElement (nam);
-if (one2many.contains (nam)) {
-countOne2Many++;
-} else {
-one2many.addElement (nam);
-namesleft--;
-}} else {
-j.setElement ( new jalview.datamodel.Sequence (realnam, "THISISAPLACEHLDER"));
-j.setPlaceholder (true);
-}}
-}, "~A,jalview.io.NewickFile");
-Clazz.makeConstructor (c$, 
-function (sequence, seqData, type, pwtype, sm, start, end) {
-this.sequence = sequence;
-this.node =  new java.util.Vector ();
-this.type = type;
-this.pwtype = pwtype;
-if (seqData != null) {
-this.seqData = seqData;
-} else {
-var seqs =  new Array (sequence.length);
-for (var i = 0; i < sequence.length; i++) {
-seqs[i] =  new jalview.datamodel.SeqCigar (sequence[i], start, end);
-}
-var sdata =  new jalview.datamodel.CigarArray (seqs);
-sdata.addOperation ('M', end - start + 1);
-this.seqData =  new jalview.datamodel.AlignmentView (sdata, start);
-}if (!(type.equals ("NJ"))) {
-type = "AV";
-}if (sm == null && !(pwtype.equals ("PID"))) {
-if (jalview.schemes.ResidueProperties.getScoreMatrix (pwtype) == null) {
-pwtype = "BLOSUM62";
-}}var i = 0;
-this.done =  Clazz.newIntArray (sequence.length, 0);
-while ((i < sequence.length) && (sequence[i] != null)) {
-this.done[i] = 0;
-i++;
-}
-this.noseqs = i++;
-this.distance = this.findDistances (sm);
-this.makeLeaves ();
-this.noClus = this.$cluster.size ();
-this.cluster ();
-}, "~A,jalview.datamodel.AlignmentView,~S,~S,jalview.api.analysis.ScoreModelI,~N,~N");
-Clazz.overrideMethod (c$, "toString", 
-function () {
-var fout =  new jalview.io.NewickFile (this.getTopNode ());
-return fout.print (this.isHasBootstrap (), this.isHasDistances (), this.isHasRootDistance ());
-});
-Clazz.defineMethod (c$, "UpdatePlaceHolders", 
-function (list) {
-var leaves =  new java.util.Vector ();
-this.findLeaves (this.top, leaves);
-var sz = leaves.size ();
-var seqmatcher = null;
-var i = 0;
-while (i < sz) {
-var leaf = leaves.elementAt (i++);
-if (list.contains (leaf.element ())) {
-leaf.setPlaceholder (false);
-} else {
-if (seqmatcher == null) {
-var seqs =  new Array (list.size ());
-for (var j = 0; j < seqs.length; j++) {
-seqs[j] = list.get (j);
-}
-seqmatcher =  new jalview.analysis.SequenceIdMatcher (seqs);
-}var nam = seqmatcher.findIdMatch (leaf.getName ());
-if (nam != null) {
-if (!leaf.isPlaceholder ()) {
-}leaf.setPlaceholder (false);
-leaf.setElement (nam);
-} else {
-if (!leaf.isPlaceholder ()) {
-leaf.setElement ( new jalview.datamodel.Sequence (leaf.getName (), "THISISAPLACEHLDER"));
-}leaf.setPlaceholder (true);
-}}}
-}, "java.util.List");
-Clazz.defineMethod (c$, "renameAssociatedNodes", 
-function () {
-this.applyToNodes (((Clazz.isClassDefined ("jalview.analysis.NJTree$1") ? 0 : jalview.analysis.NJTree.$NJTree$1$ ()), Clazz.innerTypeInstance (jalview.analysis.NJTree$1, this, null)));
-});
-Clazz.defineMethod (c$, "cluster", 
-function () {
-while (this.noClus > 2) {
-if (this.type.equals ("NJ")) {
-this.findMinNJDistance ();
-} else {
-this.findMinDistance ();
-}var c = this.joinClusters (this.mini, this.minj);
-this.done[this.minj] = 1;
-this.$cluster.setElementAt (null, this.minj);
-this.$cluster.setElementAt (c, this.mini);
-this.noClus--;
-}
-var onefound = false;
-var one = -1;
-var two = -1;
-for (var i = 0; i < this.noseqs; i++) {
-if (this.done[i] != 1) {
-if (onefound == false) {
-two = i;
-onefound = true;
-} else {
-one = i;
-}}}
-this.joinClusters (one, two);
-this.top = (this.node.elementAt (one));
-this.reCount (this.top);
-this.findHeight (this.top);
-this.findMaxDist (this.top);
-});
-Clazz.defineMethod (c$, "joinClusters", 
-function (i, j) {
-var dist = this.distance[i][j];
-var noi = (this.$cluster.elementAt (i)).value.length;
-var noj = (this.$cluster.elementAt (j)).value.length;
-var value =  Clazz.newIntArray (noi + noj, 0);
-for (var ii = 0; ii < noi; ii++) {
-value[ii] = (this.$cluster.elementAt (i)).value[ii];
-}
-for (var ii = noi; ii < (noi + noj); ii++) {
-value[ii] = (this.$cluster.elementAt (j)).value[ii - noi];
-}
-var c =  new jalview.analysis.Cluster (value);
-this.ri = this.findr (i, j);
-this.rj = this.findr (j, i);
-if (this.type.equals ("NJ")) {
-this.findClusterNJDistance (i, j);
-} else {
-this.findClusterDistance (i, j);
-}var sn =  new jalview.datamodel.SequenceNode ();
-sn.setLeft ((this.node.elementAt (i)));
-sn.setRight ((this.node.elementAt (j)));
-var tmpi = (this.node.elementAt (i));
-var tmpj = (this.node.elementAt (j));
-if (this.type.equals ("NJ")) {
-this.findNewNJDistances (tmpi, tmpj, dist);
-} else {
-this.findNewDistances (tmpi, tmpj, dist);
-}tmpi.setParent (sn);
-tmpj.setParent (sn);
-this.node.setElementAt (sn, i);
-return c;
-}, "~N,~N");
-Clazz.defineMethod (c$, "findNewNJDistances", 
-function (tmpi, tmpj, dist) {
-tmpi.dist = ((dist + this.ri) - this.rj) / 2;
-tmpj.dist = (dist - tmpi.dist);
-if (tmpi.dist < 0) {
-tmpi.dist = 0;
-}if (tmpj.dist < 0) {
-tmpj.dist = 0;
-}}, "jalview.datamodel.SequenceNode,jalview.datamodel.SequenceNode,~N");
-Clazz.defineMethod (c$, "findNewDistances", 
-function (tmpi, tmpj, dist) {
-var ih = 0;
-var jh = 0;
-var sni = tmpi;
-var snj = tmpj;
-while (sni != null) {
-ih = ih + sni.dist;
-sni = sni.left ();
-}
-while (snj != null) {
-jh = jh + snj.dist;
-snj = snj.left ();
-}
-tmpi.dist = ((dist / 2) - ih);
-tmpj.dist = ((dist / 2) - jh);
-}, "jalview.datamodel.SequenceNode,jalview.datamodel.SequenceNode,~N");
-Clazz.defineMethod (c$, "findClusterDistance", 
-function (i, j) {
-var noi = (this.$cluster.elementAt (i)).value.length;
-var noj = (this.$cluster.elementAt (j)).value.length;
-var newdist =  Clazz.newFloatArray (this.noseqs, 0);
-for (var l = 0; l < this.noseqs; l++) {
-if ((l != i) && (l != j)) {
-newdist[l] = ((this.distance[i][l] * noi) + (this.distance[j][l] * noj)) / (noi + noj);
-} else {
-newdist[l] = 0;
-}}
-for (var ii = 0; ii < this.noseqs; ii++) {
-this.distance[i][ii] = newdist[ii];
-this.distance[ii][i] = newdist[ii];
-}
-}, "~N,~N");
-Clazz.defineMethod (c$, "findClusterNJDistance", 
-function (i, j) {
-var newdist =  Clazz.newFloatArray (this.noseqs, 0);
-for (var l = 0; l < this.noseqs; l++) {
-if ((l != i) && (l != j)) {
-newdist[l] = ((this.distance[i][l] + this.distance[j][l]) - this.distance[i][j]) / 2;
-} else {
-newdist[l] = 0;
-}}
-for (var ii = 0; ii < this.noseqs; ii++) {
-this.distance[i][ii] = newdist[ii];
-this.distance[ii][i] = newdist[ii];
-}
-}, "~N,~N");
-Clazz.defineMethod (c$, "findr", 
-function (i, j) {
-var tmp = 1;
-for (var k = 0; k < this.noseqs; k++) {
-if ((k != i) && (k != j) && (this.done[k] != 1)) {
-tmp = tmp + this.distance[i][k];
-}}
-if (this.noClus > 2) {
-tmp = tmp / (this.noClus - 2);
-}return tmp;
-}, "~N,~N");
-Clazz.defineMethod (c$, "findMinNJDistance", 
-function () {
-var min = 100000;
-for (var i = 0; i < (this.noseqs - 1); i++) {
-for (var j = i + 1; j < this.noseqs; j++) {
-if ((this.done[i] != 1) && (this.done[j] != 1)) {
-var tmp = this.distance[i][j] - (this.findr (i, j) + this.findr (j, i));
-if (tmp < min) {
-this.mini = i;
-this.minj = j;
-min = tmp;
-}}}
-}
-return min;
-});
-Clazz.defineMethod (c$, "findMinDistance", 
-function () {
-var min = 100000;
-for (var i = 0; i < (this.noseqs - 1); i++) {
-for (var j = i + 1; j < this.noseqs; j++) {
-if ((this.done[i] != 1) && (this.done[j] != 1)) {
-if (this.distance[i][j] < min) {
-this.mini = i;
-this.minj = j;
-min = this.distance[i][j];
-}}}
-}
-return min;
-});
-Clazz.defineMethod (c$, "findDistances", 
-function (_pwmatrix) {
-var distance =  Clazz.newFloatArray (this.noseqs, this.noseqs, 0);
-if (_pwmatrix == null) {
-_pwmatrix = jalview.schemes.ResidueProperties.getScoreModel (this.pwtype);
-if (_pwmatrix == null) {
-_pwmatrix = jalview.schemes.ResidueProperties.getScoreMatrix ("BLOSUM62");
-}}distance = _pwmatrix.findDistances (this.seqData);
-return distance;
-}, "jalview.api.analysis.ScoreModelI");
-Clazz.defineMethod (c$, "makeLeaves", 
-function () {
-this.$cluster =  new java.util.Vector ();
-for (var i = 0; i < this.noseqs; i++) {
-var sn =  new jalview.datamodel.SequenceNode ();
-sn.setElement (this.sequence[i]);
-sn.setName (this.sequence[i].getName ());
-this.node.addElement (sn);
-var value =  Clazz.newIntArray (1, 0);
-value[0] = i;
-var c =  new jalview.analysis.Cluster (value);
-this.$cluster.addElement (c);
-}
-});
-Clazz.defineMethod (c$, "findLeaves", 
-function (node, leaves) {
-if (node == null) {
-return leaves;
-}if ((node.left () == null) && (node.right () == null)) {
-leaves.addElement (node);
-return leaves;
-} else {
-this.findLeaves (node.left (), leaves);
-this.findLeaves (node.right (), leaves);
-}return leaves;
-}, "jalview.datamodel.SequenceNode,java.util.Vector");
-Clazz.defineMethod (c$, "findLeaf", 
-function (node, count) {
-this.found = this._findLeaf (node, count);
-return this.found;
-}, "jalview.datamodel.SequenceNode,~N");
-Clazz.defineMethod (c$, "_findLeaf", 
-function (node, count) {
-if (node == null) {
-return null;
-}if (node.ycount == count) {
-this.found = node.element ();
-return this.found;
-} else {
-this._findLeaf (node.left (), count);
-this._findLeaf (node.right (), count);
-}return this.found;
-}, "jalview.datamodel.SequenceNode,~N");
-Clazz.defineMethod (c$, "printNode", 
-function (node) {
-if (node == null) {
-return;
-}if ((node.left () == null) && (node.right () == null)) {
-System.out.println ("Leaf = " + (node.element ()).getName ());
-System.out.println ("Dist " + node.dist);
-System.out.println ("Boot " + node.getBootstrap ());
-} else {
-System.out.println ("Dist " + node.dist);
-this.printNode (node.left ());
-this.printNode (node.right ());
-}}, "jalview.datamodel.SequenceNode");
-Clazz.defineMethod (c$, "findMaxDist", 
-function (node) {
-if (node == null) {
-return;
-}if ((node.left () == null) && (node.right () == null)) {
-var dist = node.dist;
-if (dist > this.maxDistValue) {
-this.maxdist = node;
-this.maxDistValue = dist;
-}} else {
-this.findMaxDist (node.left ());
-this.findMaxDist (node.right ());
-}}, "jalview.datamodel.SequenceNode");
-Clazz.defineMethod (c$, "getGroups", 
-function () {
-return this.groups;
-});
-Clazz.defineMethod (c$, "getMaxHeight", 
-function () {
-return this.maxheight;
-});
-Clazz.defineMethod (c$, "groupNodes", 
-function (node, threshold) {
-if (node == null) {
-return;
-}if ((node.height / this.maxheight) > threshold) {
-this.groups.addElement (node);
-} else {
-this.groupNodes (node.left (), threshold);
-this.groupNodes (node.right (), threshold);
-}}, "jalview.datamodel.SequenceNode,~N");
-Clazz.defineMethod (c$, "findHeight", 
-function (node) {
-if (node == null) {
-return this.maxheight;
-}if ((node.left () == null) && (node.right () == null)) {
-node.height = (node.parent ()).height + node.dist;
-if (node.height > this.maxheight) {
-return node.height;
-} else {
-return this.maxheight;
-}} else {
-if (node.parent () != null) {
-node.height = (node.parent ()).height + node.dist;
-} else {
-this.maxheight = 0;
-node.height = 0.0;
-}this.maxheight = this.findHeight ((node.left ()));
-this.maxheight = this.findHeight ((node.right ()));
-}return this.maxheight;
-}, "jalview.datamodel.SequenceNode");
-Clazz.defineMethod (c$, "reRoot", 
-function () {
-if (this.maxdist != null) {
-this.ycount = 0;
-var tmpdist = this.maxdist.dist;
-var sn =  new jalview.datamodel.SequenceNode ();
-sn.setParent (null);
-var snr = this.maxdist.parent ();
-this.changeDirection (snr, this.maxdist);
-System.out.println ("Printing reversed tree");
-this.printN (snr);
-snr.dist = tmpdist / 2;
-this.maxdist.dist = tmpdist / 2;
-snr.setParent (sn);
-this.maxdist.setParent (sn);
-sn.setRight (snr);
-sn.setLeft (this.maxdist);
-this.top = sn;
-this.ycount = 0;
-this.reCount (this.top);
-this.findHeight (this.top);
-}return this.top;
-});
-Clazz.defineMethod (c$, "hasOriginalSequenceData", 
-function () {
-return this.seqData != null;
-});
-Clazz.defineMethod (c$, "printOriginalSequenceData", 
-function (gapChar) {
-if (this.seqData == null) {
-return null;
-}var sb =  new StringBuffer ();
-var seqdatas = this.seqData.getSequenceStrings (gapChar);
-for (var i = 0; i < seqdatas.length; i++) {
-sb.append ( new jalview.util.Format ("%-15s").form (this.sequence[i].getName ()));
-sb.append (" " + seqdatas[i] + "\n");
-}
-return sb.toString ();
-}, "~S");
-Clazz.defineMethod (c$, "printN", 
-function (node) {
-if (node == null) {
-return;
-}if ((node.left () != null) && (node.right () != null)) {
-this.printN (node.left ());
-this.printN (node.right ());
-} else {
-System.out.println (" name = " + (node.element ()).getName ());
-}System.out.println (" dist = " + node.dist + " " + node.count + " " + node.height);
-}, "jalview.datamodel.SequenceNode");
-Clazz.defineMethod (c$, "reCount", 
-function (node) {
-this.ycount = 0;
-this._lycount = 0;
-this._reCount (node);
-}, "jalview.datamodel.SequenceNode");
-Clazz.defineMethod (c$, "_reCount", 
-function (node) {
-if (node == null) {
-return;
-}this._lycount++;
-if ((node.left () != null) && (node.right () != null)) {
-this._reCount (node.left ());
-this._reCount (node.right ());
-var l = node.left ();
-var r = node.right ();
-node.count = l.count + r.count;
-node.ycount = (l.ycount + r.ycount) / 2;
-} else {
-node.count = 1;
-node.ycount = this.ycount++;
-}this._lycount--;
-}, "jalview.datamodel.SequenceNode");
-Clazz.defineMethod (c$, "swapNodes", 
-function (node) {
-if (node == null) {
-return;
-}var tmp = node.left ();
-node.setLeft (node.right ());
-node.setRight (tmp);
-}, "jalview.datamodel.SequenceNode");
-Clazz.defineMethod (c$, "changeDirection", 
-function (node, dir) {
-if (node == null) {
-return;
-}if (node.parent () !== this.top) {
-this.changeDirection (node.parent (), node);
-var tmp = node.parent ();
-if (dir === node.left ()) {
-node.setParent (dir);
-node.setLeft (tmp);
-} else if (dir === node.right ()) {
-node.setParent (dir);
-node.setRight (tmp);
-}} else {
-if (dir === node.left ()) {
-node.setParent (node.left ());
-if (this.top.left () === node) {
-node.setRight (this.top.right ());
-} else {
-node.setRight (this.top.left ());
-}} else {
-node.setParent (node.right ());
-if (this.top.left () === node) {
-node.setLeft (this.top.right ());
-} else {
-node.setLeft (this.top.left ());
-}}}}, "jalview.datamodel.SequenceNode,jalview.datamodel.SequenceNode");
-Clazz.defineMethod (c$, "getMaxDist", 
-function () {
-return this.maxdist;
-});
-Clazz.defineMethod (c$, "getTopNode", 
-function () {
-return this.top;
-});
-Clazz.defineMethod (c$, "isHasDistances", 
-function () {
-return this.hasDistances;
-});
-Clazz.defineMethod (c$, "isHasBootstrap", 
-function () {
-return this.hasBootstrap;
-});
-Clazz.defineMethod (c$, "isHasRootDistance", 
-function () {
-return this.hasRootDistance;
-});
-Clazz.defineMethod (c$, "applyToNodes", 
-function (nodeTransformI) {
-for (var nodes = this.node.elements (); nodes.hasMoreElements (); nodeTransformI.transform (nodes.nextElement ())) {
-;}
-}, "jalview.datamodel.NodeTransformI");
-c$.$NJTree$1$ = function () {
-Clazz.pu$h ();
-c$ = Clazz.declareAnonymous (jalview.analysis, "NJTree$1", null, jalview.datamodel.NodeTransformI);
-Clazz.defineMethod (c$, "transform", 
-function (node) {
-var el = node.element ();
-if (el != null && Clazz.instanceOf (el, jalview.datamodel.SequenceI)) {
-node.setName ((el).getName ());
-}}, "jalview.datamodel.BinaryNode");
-c$ = Clazz.p0p ();
-};
-c$ = Clazz.decorateAsClass (function () {
-this.value = null;
-Clazz.instantialize (this, arguments);
-}, jalview.analysis, "Cluster");
-Clazz.makeConstructor (c$, 
-function (value) {
-this.value = value;
-}, "~A");
-});
+Clazz.declarePackage ("jalview.analysis");
+Clazz.load (["java.util.Vector"], ["jalview.analysis.Cluster", "$.NJTree"], ["jalview.analysis.SequenceIdMatcher", "jalview.datamodel.AlignmentView", "$.CigarArray", "$.NodeTransformI", "$.SeqCigar", "$.Sequence", "$.SequenceI", "$.SequenceNode", "jalview.io.NewickFile", "jalview.schemes.ResidueProperties", "jalview.util.Format", "java.lang.StringBuffer"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.$cluster = null;
+this.sequence = null;
+this.seqData = null;
+this.done = null;
+this.noseqs = 0;
+this.noClus = 0;
+this.distance = null;
+this.mini = 0;
+this.minj = 0;
+this.ri = 0;
+this.rj = 0;
+this.groups = null;
+this.maxdist = null;
+this.top = null;
+this.maxDistValue = 0;
+this.maxheight = 0;
+this.ycount = 0;
+this.node = null;
+this.type = null;
+this.pwtype = null;
+this.found = null;
+this.leaves = null;
+this.hasDistances = true;
+this.hasBootstrap = false;
+this.hasRootDistance = true;
+this._lycount = 0;
+this._lylimit = 0;
+Clazz.instantialize (this, arguments);
+}, jalview.analysis, "NJTree");
+Clazz.prepareFields (c$, function () {
+this.groups =  new java.util.Vector ();
+});
+Clazz.makeConstructor (c$, 
+function (seqs, odata, treefile) {
+this.construct (seqs, treefile);
+if (odata != null) {
+this.seqData = odata;
+}}, "~A,jalview.datamodel.AlignmentView,jalview.io.NewickFile");
+Clazz.makeConstructor (c$, 
+function (seqs, treefile) {
+this.sequence = seqs;
+this.top = treefile.getTree ();
+this.hasDistances = treefile.HasDistances ();
+this.hasBootstrap = treefile.HasBootstrap ();
+this.hasRootDistance = treefile.HasRootDistance ();
+this.maxheight = this.findHeight (this.top);
+var algnIds =  new jalview.analysis.SequenceIdMatcher (seqs);
+var leaves =  new java.util.Vector ();
+this.findLeaves (this.top, leaves);
+var i = 0;
+var namesleft = seqs.length;
+var j;
+var nam;
+var realnam;
+var one2many =  new java.util.Vector ();
+var countOne2Many = 0;
+while (i < leaves.size ()) {
+j = leaves.elementAt (i++);
+realnam = j.getName ();
+nam = null;
+if (namesleft > -1) {
+nam = algnIds.findIdMatch (realnam);
+}if (nam != null) {
+j.setElement (nam);
+if (one2many.contains (nam)) {
+countOne2Many++;
+} else {
+one2many.addElement (nam);
+namesleft--;
+}} else {
+j.setElement ( new jalview.datamodel.Sequence (realnam, "THISISAPLACEHLDER"));
+j.setPlaceholder (true);
+}}
+}, "~A,jalview.io.NewickFile");
+Clazz.makeConstructor (c$, 
+function (sequence, seqData, type, pwtype, sm, start, end) {
+this.sequence = sequence;
+this.node =  new java.util.Vector ();
+this.type = type;
+this.pwtype = pwtype;
+if (seqData != null) {
+this.seqData = seqData;
+} else {
+var seqs =  new Array (sequence.length);
+for (var i = 0; i < sequence.length; i++) {
+seqs[i] =  new jalview.datamodel.SeqCigar (sequence[i], start, end);
+}
+var sdata =  new jalview.datamodel.CigarArray (seqs);
+sdata.addOperation ('M', end - start + 1);
+this.seqData =  new jalview.datamodel.AlignmentView (sdata, start);
+}if (!(type.equals ("NJ"))) {
+type = "AV";
+}if (sm == null && !(pwtype.equals ("PID"))) {
+if (jalview.schemes.ResidueProperties.getScoreMatrix (pwtype) == null) {
+pwtype = "BLOSUM62";
+}}var i = 0;
+this.done =  Clazz.newIntArray (sequence.length, 0);
+while ((i < sequence.length) && (sequence[i] != null)) {
+this.done[i] = 0;
+i++;
+}
+this.noseqs = i++;
+this.distance = this.findDistances (sm);
+this.makeLeaves ();
+this.noClus = this.$cluster.size ();
+this.cluster ();
+}, "~A,jalview.datamodel.AlignmentView,~S,~S,jalview.api.analysis.ScoreModelI,~N,~N");
+Clazz.overrideMethod (c$, "toString", 
+function () {
+var fout =  new jalview.io.NewickFile (this.getTopNode ());
+return fout.print (this.isHasBootstrap (), this.isHasDistances (), this.isHasRootDistance ());
+});
+Clazz.defineMethod (c$, "UpdatePlaceHolders", 
+function (list) {
+var leaves =  new java.util.Vector ();
+this.findLeaves (this.top, leaves);
+var sz = leaves.size ();
+var seqmatcher = null;
+var i = 0;
+while (i < sz) {
+var leaf = leaves.elementAt (i++);
+if (list.contains (leaf.element ())) {
+leaf.setPlaceholder (false);
+} else {
+if (seqmatcher == null) {
+var seqs =  new Array (list.size ());
+for (var j = 0; j < seqs.length; j++) {
+seqs[j] = list.get (j);
+}
+seqmatcher =  new jalview.analysis.SequenceIdMatcher (seqs);
+}var nam = seqmatcher.findIdMatch (leaf.getName ());
+if (nam != null) {
+if (!leaf.isPlaceholder ()) {
+}leaf.setPlaceholder (false);
+leaf.setElement (nam);
+} else {
+if (!leaf.isPlaceholder ()) {
+leaf.setElement ( new jalview.datamodel.Sequence (leaf.getName (), "THISISAPLACEHLDER"));
+}leaf.setPlaceholder (true);
+}}}
+}, "java.util.List");
+Clazz.defineMethod (c$, "renameAssociatedNodes", 
+function () {
+this.applyToNodes (((Clazz.isClassDefined ("jalview.analysis.NJTree$1") ? 0 : jalview.analysis.NJTree.$NJTree$1$ ()), Clazz.innerTypeInstance (jalview.analysis.NJTree$1, this, null)));
+});
+Clazz.defineMethod (c$, "cluster", 
+function () {
+while (this.noClus > 2) {
+if (this.type.equals ("NJ")) {
+this.findMinNJDistance ();
+} else {
+this.findMinDistance ();
+}var c = this.joinClusters (this.mini, this.minj);
+this.done[this.minj] = 1;
+this.$cluster.setElementAt (null, this.minj);
+this.$cluster.setElementAt (c, this.mini);
+this.noClus--;
+}
+var onefound = false;
+var one = -1;
+var two = -1;
+for (var i = 0; i < this.noseqs; i++) {
+if (this.done[i] != 1) {
+if (onefound == false) {
+two = i;
+onefound = true;
+} else {
+one = i;
+}}}
+this.joinClusters (one, two);
+this.top = (this.node.elementAt (one));
+this.reCount (this.top);
+this.findHeight (this.top);
+this.findMaxDist (this.top);
+});
+Clazz.defineMethod (c$, "joinClusters", 
+function (i, j) {
+var dist = this.distance[i][j];
+var noi = (this.$cluster.elementAt (i)).value.length;
+var noj = (this.$cluster.elementAt (j)).value.length;
+var value =  Clazz.newIntArray (noi + noj, 0);
+for (var ii = 0; ii < noi; ii++) {
+value[ii] = (this.$cluster.elementAt (i)).value[ii];
+}
+for (var ii = noi; ii < (noi + noj); ii++) {
+value[ii] = (this.$cluster.elementAt (j)).value[ii - noi];
+}
+var c =  new jalview.analysis.Cluster (value);
+this.ri = this.findr (i, j);
+this.rj = this.findr (j, i);
+if (this.type.equals ("NJ")) {
+this.findClusterNJDistance (i, j);
+} else {
+this.findClusterDistance (i, j);
+}var sn =  new jalview.datamodel.SequenceNode ();
+sn.setLeft ((this.node.elementAt (i)));
+sn.setRight ((this.node.elementAt (j)));
+var tmpi = (this.node.elementAt (i));
+var tmpj = (this.node.elementAt (j));
+if (this.type.equals ("NJ")) {
+this.findNewNJDistances (tmpi, tmpj, dist);
+} else {
+this.findNewDistances (tmpi, tmpj, dist);
+}tmpi.setParent (sn);
+tmpj.setParent (sn);
+this.node.setElementAt (sn, i);
+return c;
+}, "~N,~N");
+Clazz.defineMethod (c$, "findNewNJDistances", 
+function (tmpi, tmpj, dist) {
+tmpi.dist = ((dist + this.ri) - this.rj) / 2;
+tmpj.dist = (dist - tmpi.dist);
+if (tmpi.dist < 0) {
+tmpi.dist = 0;
+}if (tmpj.dist < 0) {
+tmpj.dist = 0;
+}}, "jalview.datamodel.SequenceNode,jalview.datamodel.SequenceNode,~N");
+Clazz.defineMethod (c$, "findNewDistances", 
+function (tmpi, tmpj, dist) {
+var ih = 0;
+var jh = 0;
+var sni = tmpi;
+var snj = tmpj;
+while (sni != null) {
+ih = ih + sni.dist;
+sni = sni.left ();
+}
+while (snj != null) {
+jh = jh + snj.dist;
+snj = snj.left ();
+}
+tmpi.dist = ((dist / 2) - ih);
+tmpj.dist = ((dist / 2) - jh);
+}, "jalview.datamodel.SequenceNode,jalview.datamodel.SequenceNode,~N");
+Clazz.defineMethod (c$, "findClusterDistance", 
+function (i, j) {
+var noi = (this.$cluster.elementAt (i)).value.length;
+var noj = (this.$cluster.elementAt (j)).value.length;
+var newdist =  Clazz.newFloatArray (this.noseqs, 0);
+for (var l = 0; l < this.noseqs; l++) {
+if ((l != i) && (l != j)) {
+newdist[l] = ((this.distance[i][l] * noi) + (this.distance[j][l] * noj)) / (noi + noj);
+} else {
+newdist[l] = 0;
+}}
+for (var ii = 0; ii < this.noseqs; ii++) {
+this.distance[i][ii] = newdist[ii];
+this.distance[ii][i] = newdist[ii];
+}
+}, "~N,~N");
+Clazz.defineMethod (c$, "findClusterNJDistance", 
+function (i, j) {
+var newdist =  Clazz.newFloatArray (this.noseqs, 0);
+for (var l = 0; l < this.noseqs; l++) {
+if ((l != i) && (l != j)) {
+newdist[l] = ((this.distance[i][l] + this.distance[j][l]) - this.distance[i][j]) / 2;
+} else {
+newdist[l] = 0;
+}}
+for (var ii = 0; ii < this.noseqs; ii++) {
+this.distance[i][ii] = newdist[ii];
+this.distance[ii][i] = newdist[ii];
+}
+}, "~N,~N");
+Clazz.defineMethod (c$, "findr", 
+function (i, j) {
+var tmp = 1;
+for (var k = 0; k < this.noseqs; k++) {
+if ((k != i) && (k != j) && (this.done[k] != 1)) {
+tmp = tmp + this.distance[i][k];
+}}
+if (this.noClus > 2) {
+tmp = tmp / (this.noClus - 2);
+}return tmp;
+}, "~N,~N");
+Clazz.defineMethod (c$, "findMinNJDistance", 
+function () {
+var min = 100000;
+for (var i = 0; i < (this.noseqs - 1); i++) {
+for (var j = i + 1; j < this.noseqs; j++) {
+if ((this.done[i] != 1) && (this.done[j] != 1)) {
+var tmp = this.distance[i][j] - (this.findr (i, j) + this.findr (j, i));
+if (tmp < min) {
+this.mini = i;
+this.minj = j;
+min = tmp;
+}}}
+}
+return min;
+});
+Clazz.defineMethod (c$, "findMinDistance", 
+function () {
+var min = 100000;
+for (var i = 0; i < (this.noseqs - 1); i++) {
+for (var j = i + 1; j < this.noseqs; j++) {
+if ((this.done[i] != 1) && (this.done[j] != 1)) {
+if (this.distance[i][j] < min) {
+this.mini = i;
+this.minj = j;
+min = this.distance[i][j];
+}}}
+}
+return min;
+});
+Clazz.defineMethod (c$, "findDistances", 
+function (_pwmatrix) {
+var distance =  Clazz.newFloatArray (this.noseqs, this.noseqs, 0);
+if (_pwmatrix == null) {
+_pwmatrix = jalview.schemes.ResidueProperties.getScoreModel (this.pwtype);
+if (_pwmatrix == null) {
+_pwmatrix = jalview.schemes.ResidueProperties.getScoreMatrix ("BLOSUM62");
+}}distance = _pwmatrix.findDistances (this.seqData);
+return distance;
+}, "jalview.api.analysis.ScoreModelI");
+Clazz.defineMethod (c$, "makeLeaves", 
+function () {
+this.$cluster =  new java.util.Vector ();
+for (var i = 0; i < this.noseqs; i++) {
+var sn =  new jalview.datamodel.SequenceNode ();
+sn.setElement (this.sequence[i]);
+sn.setName (this.sequence[i].getName ());
+this.node.addElement (sn);
+var value =  Clazz.newIntArray (1, 0);
+value[0] = i;
+var c =  new jalview.analysis.Cluster (value);
+this.$cluster.addElement (c);
+}
+});
+Clazz.defineMethod (c$, "findLeaves", 
+function (node, leaves) {
+if (node == null) {
+return leaves;
+}if ((node.left () == null) && (node.right () == null)) {
+leaves.addElement (node);
+return leaves;
+} else {
+this.findLeaves (node.left (), leaves);
+this.findLeaves (node.right (), leaves);
+}return leaves;
+}, "jalview.datamodel.SequenceNode,java.util.Vector");
+Clazz.defineMethod (c$, "findLeaf", 
+function (node, count) {
+this.found = this._findLeaf (node, count);
+return this.found;
+}, "jalview.datamodel.SequenceNode,~N");
+Clazz.defineMethod (c$, "_findLeaf", 
+function (node, count) {
+if (node == null) {
+return null;
+}if (node.ycount == count) {
+this.found = node.element ();
+return this.found;
+} else {
+this._findLeaf (node.left (), count);
+this._findLeaf (node.right (), count);
+}return this.found;
+}, "jalview.datamodel.SequenceNode,~N");
+Clazz.defineMethod (c$, "printNode", 
+function (node) {
+if (node == null) {
+return;
+}if ((node.left () == null) && (node.right () == null)) {
+System.out.println ("Leaf = " + (node.element ()).getName ());
+System.out.println ("Dist " + node.dist);
+System.out.println ("Boot " + node.getBootstrap ());
+} else {
+System.out.println ("Dist " + node.dist);
+this.printNode (node.left ());
+this.printNode (node.right ());
+}}, "jalview.datamodel.SequenceNode");
+Clazz.defineMethod (c$, "findMaxDist", 
+function (node) {
+if (node == null) {
+return;
+}if ((node.left () == null) && (node.right () == null)) {
+var dist = node.dist;
+if (dist > this.maxDistValue) {
+this.maxdist = node;
+this.maxDistValue = dist;
+}} else {
+this.findMaxDist (node.left ());
+this.findMaxDist (node.right ());
+}}, "jalview.datamodel.SequenceNode");
+Clazz.defineMethod (c$, "getGroups", 
+function () {
+return this.groups;
+});
+Clazz.defineMethod (c$, "getMaxHeight", 
+function () {
+return this.maxheight;
+});
+Clazz.defineMethod (c$, "groupNodes", 
+function (node, threshold) {
+if (node == null) {
+return;
+}if ((node.height / this.maxheight) > threshold) {
+this.groups.addElement (node);
+} else {
+this.groupNodes (node.left (), threshold);
+this.groupNodes (node.right (), threshold);
+}}, "jalview.datamodel.SequenceNode,~N");
+Clazz.defineMethod (c$, "findHeight", 
+function (node) {
+if (node == null) {
+return this.maxheight;
+}if ((node.left () == null) && (node.right () == null)) {
+node.height = (node.parent ()).height + node.dist;
+if (node.height > this.maxheight) {
+return node.height;
+} else {
+return this.maxheight;
+}} else {
+if (node.parent () != null) {
+node.height = (node.parent ()).height + node.dist;
+} else {
+this.maxheight = 0;
+node.height = 0.0;
+}this.maxheight = this.findHeight ((node.left ()));
+this.maxheight = this.findHeight ((node.right ()));
+}return this.maxheight;
+}, "jalview.datamodel.SequenceNode");
+Clazz.defineMethod (c$, "reRoot", 
+function () {
+if (this.maxdist != null) {
+this.ycount = 0;
+var tmpdist = this.maxdist.dist;
+var sn =  new jalview.datamodel.SequenceNode ();
+sn.setParent (null);
+var snr = this.maxdist.parent ();
+this.changeDirection (snr, this.maxdist);
+System.out.println ("Printing reversed tree");
+this.printN (snr);
+snr.dist = tmpdist / 2;
+this.maxdist.dist = tmpdist / 2;
+snr.setParent (sn);
+this.maxdist.setParent (sn);
+sn.setRight (snr);
+sn.setLeft (this.maxdist);
+this.top = sn;
+this.ycount = 0;
+this.reCount (this.top);
+this.findHeight (this.top);
+}return this.top;
+});
+Clazz.defineMethod (c$, "hasOriginalSequenceData", 
+function () {
+return this.seqData != null;
+});
+Clazz.defineMethod (c$, "printOriginalSequenceData", 
+function (gapChar) {
+if (this.seqData == null) {
+return null;
+}var sb =  new StringBuffer ();
+var seqdatas = this.seqData.getSequenceStrings (gapChar);
+for (var i = 0; i < seqdatas.length; i++) {
+sb.append ( new jalview.util.Format ("%-15s").form (this.sequence[i].getName ()));
+sb.append (" " + seqdatas[i] + "\n");
+}
+return sb.toString ();
+}, "~S");
+Clazz.defineMethod (c$, "printN", 
+function (node) {
+if (node == null) {
+return;
+}if ((node.left () != null) && (node.right () != null)) {
+this.printN (node.left ());
+this.printN (node.right ());
+} else {
+System.out.println (" name = " + (node.element ()).getName ());
+}System.out.println (" dist = " + node.dist + " " + node.count + " " + node.height);
+}, "jalview.datamodel.SequenceNode");
+Clazz.defineMethod (c$, "reCount", 
+function (node) {
+this.ycount = 0;
+this._lycount = 0;
+this._reCount (node);
+}, "jalview.datamodel.SequenceNode");
+Clazz.defineMethod (c$, "_reCount", 
+function (node) {
+if (node == null) {
+return;
+}this._lycount++;
+if ((node.left () != null) && (node.right () != null)) {
+this._reCount (node.left ());
+this._reCount (node.right ());
+var l = node.left ();
+var r = node.right ();
+node.count = l.count + r.count;
+node.ycount = (l.ycount + r.ycount) / 2;
+} else {
+node.count = 1;
+node.ycount = this.ycount++;
+}this._lycount--;
+}, "jalview.datamodel.SequenceNode");
+Clazz.defineMethod (c$, "swapNodes", 
+function (node) {
+if (node == null) {
+return;
+}var tmp = node.left ();
+node.setLeft (node.right ());
+node.setRight (tmp);
+}, "jalview.datamodel.SequenceNode");
+Clazz.defineMethod (c$, "changeDirection", 
+function (node, dir) {
+if (node == null) {
+return;
+}if (node.parent () !== this.top) {
+this.changeDirection (node.parent (), node);
+var tmp = node.parent ();
+if (dir === node.left ()) {
+node.setParent (dir);
+node.setLeft (tmp);
+} else if (dir === node.right ()) {
+node.setParent (dir);
+node.setRight (tmp);
+}} else {
+if (dir === node.left ()) {
+node.setParent (node.left ());
+if (this.top.left () === node) {
+node.setRight (this.top.right ());
+} else {
+node.setRight (this.top.left ());
+}} else {
+node.setParent (node.right ());
+if (this.top.left () === node) {
+node.setLeft (this.top.right ());
+} else {
+node.setLeft (this.top.left ());
+}}}}, "jalview.datamodel.SequenceNode,jalview.datamodel.SequenceNode");
+Clazz.defineMethod (c$, "getMaxDist", 
+function () {
+return this.maxdist;
+});
+Clazz.defineMethod (c$, "getTopNode", 
+function () {
+return this.top;
+});
+Clazz.defineMethod (c$, "isHasDistances", 
+function () {
+return this.hasDistances;
+});
+Clazz.defineMethod (c$, "isHasBootstrap", 
+function () {
+return this.hasBootstrap;
+});
+Clazz.defineMethod (c$, "isHasRootDistance", 
+function () {
+return this.hasRootDistance;
+});
+Clazz.defineMethod (c$, "applyToNodes", 
+function (nodeTransformI) {
+for (var nodes = this.node.elements (); nodes.hasMoreElements (); nodeTransformI.transform (nodes.nextElement ())) {
+;}
+}, "jalview.datamodel.NodeTransformI");
+c$.$NJTree$1$ = function () {
+Clazz.pu$h ();
+c$ = Clazz.declareAnonymous (jalview.analysis, "NJTree$1", null, jalview.datamodel.NodeTransformI);
+Clazz.defineMethod (c$, "transform", 
+function (node) {
+var el = node.element ();
+if (el != null && Clazz.instanceOf (el, jalview.datamodel.SequenceI)) {
+node.setName ((el).getName ());
+}}, "jalview.datamodel.BinaryNode");
+c$ = Clazz.p0p ();
+};
+c$ = Clazz.decorateAsClass (function () {
+this.value = null;
+Clazz.instantialize (this, arguments);
+}, jalview.analysis, "Cluster");
+Clazz.makeConstructor (c$, 
+function (value) {
+this.value = value;
+}, "~A");
+});