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improved 3D panel initialization #58

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merged 3 commits into from
Oct 21, 2016
Merged

improved 3D panel initialization #58

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a8bcccc
improved 3D panel initialization
onursumer Oct 7, 2016
d8b15cc
minor fix for lollipop highlighting
onursumer Oct 14, 2016
ac28e91
updated binaries
onursumer Oct 21, 2016
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3 changes: 2 additions & 1 deletion build/mutationMapper.css
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Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,8 @@
z-index: 2;
overflow: hidden;
}
.mutation-3d-vis-loader {
.mutation-3d-vis-loader,
.mutation-3d-vis-main-loader {
text-align: center;
}
.mutation-3d-vis-help-init {
Expand Down
140 changes: 104 additions & 36 deletions build/mutationMapper.js
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Expand Up @@ -7819,7 +7819,7 @@ var Mutation3dVisView = Backbone.View.extend({

// initially hide the 3d visualizer container
var container3d = self.$el;
container3d.hide();
//container3d.hide();

// initially hide the residue warning message
self.hideResidueWarning();
Expand All @@ -7837,6 +7837,7 @@ var Mutation3dVisView = Backbone.View.extend({
if (mut3dVis != null)
{
mut3dVis.updateContainer(container3d);
mut3dVis.show();
}

// add listeners to panel (header) buttons
Expand Down Expand Up @@ -7874,6 +7875,8 @@ var Mutation3dVisView = Backbone.View.extend({
// init buttons
self._initButtons();

self.showMainLoader();

// make the main container draggable
container3d.draggable({
handle: ".mutation-3d-info-title",
Expand Down Expand Up @@ -8267,7 +8270,6 @@ var Mutation3dVisView = Backbone.View.extend({
chain.positionMap = positionMap;

// reload the selected pdb and chain data
mut3dVis.show();
self.refreshView(pdbId, chain);

// store pdb id and chain for future reference
Expand All @@ -8290,6 +8292,8 @@ var Mutation3dVisView = Backbone.View.extend({
model.molInfo = summary.molecule;
}

self.hideMainLoader();

// init info view
var infoView = new Mutation3dVisInfoView(
{el: self.$el.find(".mutation-3d-info"), model: model});
Expand All @@ -8300,6 +8304,8 @@ var Mutation3dVisView = Backbone.View.extend({
pdbProxy.getPositionMap(geneSymbol, chain, mapCallback);
};

self.showMainLoader();
mut3dVis.show();
pdbProxy.getPdbInfo(pdbId, infoCallback);
},
/**
Expand Down Expand Up @@ -8526,6 +8532,20 @@ var Mutation3dVisView = Backbone.View.extend({
self.dispatcher.trigger(
MutationDetailsEvents.VIEW_3D_PANEL_CLOSED);
},
/**
* Shows the 3D visualizer panel.
*/
showView: function()
{
var self = this;
var mut3dVis = self.options.mut3dVis;

// hide the vis pane
if (mut3dVis != null)
{
mut3dVis.show();
}
},
isVisible: function()
{
var self = this;
Expand Down Expand Up @@ -8621,6 +8641,36 @@ var Mutation3dVisView = Backbone.View.extend({
// show actual vis container
container.css("height", self._actualHeight);
},
/**
* Shows the loader for the entire panel body.
*/
showMainLoader: function()
{
var self = this;
var loaderImage = self.$el.find(".mutation-3d-vis-main-loader");
var mainContent = self.$el.find(".mutation-3d-vis-body");

// show the image
loaderImage.show();

// hide the main body
mainContent.hide();
},
/**
* Hides the loader image and shows the main content (panel body).
*/
hideMainLoader: function()
{
var self = this;
var loaderImage = self.$el.find(".mutation-3d-vis-main-loader");
var mainContent = self.$el.find(".mutation-3d-vis-body");

// show the image
loaderImage.hide();

// hide the main body
mainContent.show();
},
/**
* Shows a warning message for unmapped residues.
*
Expand Down Expand Up @@ -13687,48 +13737,53 @@ function Mutation3dVis(name, options)
if (_container != null)
{
_container.show();

// this is a workaround. see the hide() function below for details

var currentTop = parseInt(_container.css('top'));

// update the top position only if it is negative
if (currentTop < 0)
{
if (_prevTop != null && _prevTop > 0)
{
_container.css('top', _prevTop);
}
else
{
_container.css('top', 0);
}
}
}

// // this is a workaround. see the hide() function below for details
//
// var currentTop = parseInt(_container.css('top'));
//
// // update the top position only if it is negative
// if (currentTop < 0)
// {
// if (_prevTop != null && _prevTop > 0)
// {
// _container.css('top', _prevTop);
// }
// else
// {
// _container.css('top', 0);
// }
// }
//}
}

/**
* Hides the visualizer panel.
*/
function hide()
{
// TODO jQuery.hide function is problematic after Jmol init
// Reloading the PDB data throws an error message (Error: Bad NPObject as private data!)
// see https://code.google.com/p/gdata-issues/issues/detail?id=4820

// So, the current workaround is to reposition instead of hiding
if (_container != null)
{
//_container.hide();
var currentTop = parseInt(_container.css('top'));

if (currentTop > 0)
{
_prevTop = currentTop;
}

_container.css('top', -9999);
_container.hide();
}

// jQuery.hide function is problematic after Jmol init
// Reloading the PDB data throws an error message (Error: Bad NPObject as private data!)
// see https://code.google.com/p/gdata-issues/issues/detail?id=4820
// So, the current workaround is to reposition instead of hiding
//if (_container != null)
//{
// //_container.hide();
// var currentTop = parseInt(_container.css('top'));
//
// if (currentTop > 0)
// {
// _prevTop = currentTop;
// }
//
// _container.css('top', -9999);
//}
}

/**
Expand Down Expand Up @@ -17931,11 +17986,17 @@ MutationDiagram.prototype.highlightMutation = function(mutationSid)
var self = this;

var pileupId = self.mutationPileupMap[mutationSid];
var pileup = self.svg.select("#" + pileupId);

if (pileup.length > 0)
// there may not be a pileup corresponding to the given sid,
// because not every mutation is mapped onto the diagram
if (pileupId != null)
{
self.highlight(pileup[0][0]);
var pileup = self.svg.select("#" + pileupId);

if (pileup.length > 0)
{
self.highlight(pileup[0][0]);
}
}
};

Expand Down Expand Up @@ -21074,6 +21135,13 @@ function Mutation3dController(mutationDetailsView, mainMutationView, viewOptions
}
};

if (mut3dView != null &&
_mut3dVisView != null)
{
_mut3dVisView.showMainLoader();
_mut3dVisView.showView();
}

// init view with the pdb data
pdbProxy.getPdbData(uniprotId, initView);
}
Expand Down
2 changes: 1 addition & 1 deletion build/mutationMapper.min.css
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12 changes: 6 additions & 6 deletions build/mutationMapper.min.js
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