From 0e5112a3b21f6bdcad4f5550463a7c8d672ab582 Mon Sep 17 00:00:00 2001
From: Zhemin Zhou <zhemin.zhou@warwick.ac.uk>
Date: Mon, 3 Jul 2017 17:24:03 +0100
Subject: [PATCH] bug fixing

---
 MSTree_holder.html                     |  1 +
 grapetree/templates/MSTree_launch.html |  2 +-
 static/js/tree/base_tree.js            |  4 ++--
 static/js/tree/context.js              |  5 +++--
 static/js/tree/d3_m_tree.js            | 23 +++++++++++++++++------
 static/js/tree/grid.js                 |  3 +++
 6 files changed, 27 insertions(+), 11 deletions(-)

diff --git a/MSTree_holder.html b/MSTree_holder.html
index 5827633..5f519e6 100644
--- a/MSTree_holder.html
+++ b/MSTree_holder.html
@@ -832,6 +832,7 @@ <h3 id="headertag" style="font-family: times, serif; font-size:12pt; font-style:
 				if (the_tree) {
 					the_tree.svg.remove();
 					the_tree.legend_div[0].remove();
+					resetGridColumns();
 				}
                 $("#waiting-information").text("Loading Data");
                 the_tree = null;
diff --git a/grapetree/templates/MSTree_launch.html b/grapetree/templates/MSTree_launch.html
index b368d3a..5f519e6 100644
--- a/grapetree/templates/MSTree_launch.html
+++ b/grapetree/templates/MSTree_launch.html
@@ -597,7 +597,6 @@ <h3 id="headertag" style="font-family: times, serif; font-size:12pt; font-style:
                         var item = the_tree.metadata[id];
                         var barcode = Enterobase.encodeBarcode(id,db_code);
                         lines.push(barcode+"\t"+item["Name"]);
-
                 }
                 var text= lines.join("\n");
                 Enterobase.showSaveDialog(text,"tree.json");
@@ -833,6 +832,7 @@ <h3 id="headertag" style="font-family: times, serif; font-size:12pt; font-style:
 				if (the_tree) {
 					the_tree.svg.remove();
 					the_tree.legend_div[0].remove();
+					resetGridColumns();
 				}
                 $("#waiting-information").text("Loading Data");
                 the_tree = null;
diff --git a/static/js/tree/base_tree.js b/static/js/tree/base_tree.js
index fe5089c..ec617c5 100644
--- a/static/js/tree/base_tree.js
+++ b/static/js/tree/base_tree.js
@@ -1234,8 +1234,8 @@ D3BaseTree.prototype.updateLegend = function(title, ordered_groups){
 	legend.selectAll('.legend-title').remove();
 	legend.append('text').attr('class', 'legend-title').attr('x', 22).attr('y', 20).attr('font-weight', 'bold').text(title);
 	var legend_dim = legend_svg[0][0].getBBox();
-	legend_svg.attr('width', 180).attr('height', legend_dim.height + 10);
-	this.legend_div.width(180);
+	legend_svg.attr('width', 220).attr('height', legend_dim.height + 10);
+	this.legend_div.width(220);
 	var l_height = $("#legend-svg").height();
 	var height = l_height+10;
 	this.legend_div.css({"top":"0px","right":"0px","max-height":height+"px"});
diff --git a/static/js/tree/context.js b/static/js/tree/context.js
index 243eb8e..0a32231 100644
--- a/static/js/tree/context.js
+++ b/static/js/tree/context.js
@@ -243,13 +243,14 @@ $("#collapse_node").click(function(e) {
 	for (var id in selected_nodes) {
 		var node_id = selected_nodes[id].id;
 		for (var jd in the_tree.hypo_record[node_id]) {
-			the_tree.manual_collapsing[jd] = 1;
+			the_tree.manual_collapsing[jd] = 2;
 		}
 	}
 	$( "#spinner-collapse-nodes" ).trigger("change");
 });
 $("#uncollapse_all").click(function(e) {
 	the_tree.manual_collapsing = {};
+	$( "#spinner-collapse-nodes" ).val(0);
 	$( "#spinner-collapse-nodes" ).trigger("change");
 });
 
@@ -258,7 +259,7 @@ $("#uncollapse_node").click(function(e) {
 	for (var id in selected_nodes) {
 		var node_id = selected_nodes[id].id;
 		for (var jd in the_tree.hypo_record[node_id]) {
-			delete the_tree.manual_collapsing[jd];
+			the_tree.manual_collapsing[jd] = 1;
 		}
 	}
 	$( "#spinner-collapse-nodes" ).trigger("change");
diff --git a/static/js/tree/d3_m_tree.js b/static/js/tree/d3_m_tree.js
index 5681b3a..54e7617 100644
--- a/static/js/tree/d3_m_tree.js
+++ b/static/js/tree/d3_m_tree.js
@@ -486,7 +486,13 @@ D3MSTree.prototype._collapseNodes=function(max_distance,layout){
                         }
                 }
         }
-
+		if (max_distance > this.node_collapsed_value) {
+			for(var id in this.manual_collapsing) {
+				if (this.manual_collapsing[id] == 1) {
+					delete this.manual_collapsing[id];
+				}
+			}
+		}
         if (max_distance<=this.node_collapsed_value || (! this.force_nodes) || this.force_nodes.length == 0){
 
                 this.clearSelection();
@@ -513,7 +519,7 @@ D3MSTree.prototype._collapseNodes=function(max_distance,layout){
   		this.manual_collapsing_value = Object.keys(this.manual_collapsing).length;
         if (this.manual_collapsing_value > 0) {
                 for (var id in this.manual_collapsing) {
-                        to_collapse[id] = 1;
+                        to_collapse[id] = this.manual_collapsing[id];
                 }
 
                 var collapsed = 1;
@@ -521,8 +527,10 @@ D3MSTree.prototype._collapseNodes=function(max_distance,layout){
                         collapsed = 0;
                         for(var jd in this.force_links) {
                                 var link = this.force_links[jd];
-                                if (to_collapse[link.source.id] && ! to_collapse[link.target.id]) {
-                                        to_collapse[link.target.id] = 1;
+                                var s_c = to_collapse[link.source.id] ? to_collapse[link.source.id] : 0;
+                                var t_c = to_collapse[link.target.id] ? to_collapse[link.target.id] : 0;
+                                if (s_c > t_c) {
+                                        to_collapse[link.target.id] = s_c;
                                         collapsed = 1;
                                 }
                         }
@@ -533,6 +541,7 @@ D3MSTree.prototype._collapseNodes=function(max_distance,layout){
                 var link = this.force_links[index];
                 link.target.link = link;
         }
+        /*
         this.force_links.sort(function(l1, l2) {return l1.value - l2.value;});
         var link_len = [];
         for (var index in this.force_links) {
@@ -558,8 +567,10 @@ D3MSTree.prototype._collapseNodes=function(max_distance,layout){
                                         }
                                 }
                         }
-                }
-                if (!l || (l.value > max_distance && ! to_collapse[l.source.id])) continue;
+                }*/
+        for (var index=this.force_links.length-1; index >=0; index --) {
+        		var l = this.force_links[index];
+                if ( !l || (l.value > max_distance && to_collapse[l.source.id] !== 2) || (l.value > 1e-8 && to_collapse[l.source.id] === 1) ) continue;
                 l.remove=l.target.remove=true;
                 this.grouped_nodes[l.source.id]=this.grouped_nodes[l.source.id].concat(this.grouped_nodes[l.target.id]);
 		
diff --git a/static/js/tree/grid.js b/static/js/tree/grid.js
index dbb5130..b1eea12 100644
--- a/static/js/tree/grid.js
+++ b/static/js/tree/grid.js
@@ -264,6 +264,9 @@
 			$("#replace-div").toggle(150).css("top",yy).css("left",xx).css("position","fixed").show();
 		});
 	
+	function resetGridColumns() {
+		grid.setColumns(default_columns);
+	};
 
 	function updateMetadataTable(select_moveUp) {
 		if (! the_tree) {