[galaxy-commits] commit/galaxy-central: 2 new changesets

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c9c62f54cf16/ Changeset: c9c62f54cf16 User: carlfeberhard Date: 2014-08-14 20:16:07 Summary: Paired collection creator: add option to remove file extensions from pair names (note: will not change any manually changed names) Affected #: 3 files diff -r 3be5658bc5da1831860b367ad57deec0140cc10e -r c9c62f54cf168fe493f48549647b2e74cfd6a9ac static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -50,6 +50,10 @@ this.strategy = attributes.strategy; } + /** remove file extensions (\.*) from created pair names? */ + this.removeExtensions = true; + //this.removeExtensions = false; + /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */ this.oncancel = attributes.oncancel; /** fn to call when the collection is created (scoped to this) */ @@ -423,11 +427,19 @@ }, /** try to find a good pair name for the given fwd and rev datasets */ - _guessNameForPair : function( fwd, rev ){ + _guessNameForPair : function( fwd, rev, removeExtensions ){ + removeExtensions = ( removeExtensions !== undefined )?( removeExtensions ):( this.removeExtensions ); var lcs = this._naiveStartingAndEndingLCS( +//TODO: won't work with regex fwd.name.replace( this.filters[0], '' ), rev.name.replace( this.filters[1], '' ) ); + if( removeExtensions ){ + var lastDotIndex = lcs.lastIndexOf( '.' ); + if( lastDotIndex > 0 ){ + lcs = lcs.slice( 0, lastDotIndex ); + } + } //TODO: optionally remove extension return lcs || ( fwd.name + ' & ' + rev.name ); }, @@ -579,12 +591,15 @@ /** render the middle including unpaired and paired sections (which may be hidden) */ _renderMiddle : function( speed, callback ){ var $middle = this.$( '.middle' ).empty().html( PairedCollectionCreator.templates.middle() ); + + // (re-) hide the un/paired panels based on instance vars //TODO: use replaceWith if( this.unpairedPanelHidden ){ this.$( '.unpaired-columns' ).hide(); } else if( this.pairedPanelHidden ){ this.$( '.paired-columns' ).hide(); } + this._renderUnpaired(); this._renderPaired(); return $middle; @@ -666,7 +681,7 @@ //console.debug( '-- renderUnpairedEmpty' ); var $msg = $( '<div class="empty-message"></div>' ) .text( '(' + _l( 'no remaining unpaired datasets' ) + ')' ); - this.$( '.unpaired-columns .paired-column .column-datasets' ).prepend( $msg ); + this.$( '.unpaired-columns .paired-column .column-datasets' ).empty().prepend( $msg ); return $msg; }, /** a message to display when no unpaired can be shown with the current filters */ @@ -674,7 +689,7 @@ //console.debug( '-- renderUnpairedEmpty' ); var $msg = $( '<div class="empty-message"></div>' ) .text( '(' + _l( 'no datasets were found matching the current filters' ) + ')' ); - this.$( '.unpaired-columns .paired-column .column-datasets' ).prepend( $msg ); + this.$( '.unpaired-columns .paired-column .column-datasets' ).empty().prepend( $msg ); return $msg; }, @@ -691,6 +706,9 @@ if( this.paired.length === 0 ){ this._renderPairedEmpty(); //TODO: would be best to return here (the $columns) + } else { + // show/hide 'remove extensions link' when any paired and they seem to have extensions + this.$( '.remove-extensions-link' ).show(); } this.paired.forEach( function( pair, i ){ @@ -721,6 +739,7 @@ /** render the footer, completion controls, and cancel controls */ _renderFooter : function( speed, callback ){ var $footer = this.$( '.footer' ).empty().html( PairedCollectionCreator.templates.footer() ); + this.$( '.remove-extensions' ).prop( 'checked', this.removeExtensions ); if( typeof this.oncancel === 'function' ){ this.$( '.cancel-create.btn' ).show(); } @@ -861,12 +880,12 @@ 'mousedown .flexible-partition-drag' : '_startPartitionDrag', // paired 'click .paired-columns .paired-column .dataset-name' : '_clickPairName', + 'mouseover .dataset.paired' : '_hoverPaired', + 'mouseout .dataset.paired' : '_hoverOutPaired', 'click .unpair-btn' : '_clickUnpair', - 'mouseover .dataset.paired' : '_hoverPaired', - 'mouseout .dataset.paired' : '_hoverOutPaired', - // footer + 'change .remove-extensions' : function( ev ){ this.toggleExtensions(); }, 'change .collection-name' : '_changeName', 'click .cancel-create' : function( ev ){ if( typeof this.oncancel === 'function' ){ @@ -1130,6 +1149,10 @@ response = prompt( 'Enter a new name for the pair:', pair.name ); if( response ){ pair.name = response; + // set a flag (which won't be passed in json creation) for manual naming so we don't overwrite these + // when adding/removing extensions + //TODO: kinda hacky + pair.customizedName = true; $control.text( pair.name ); } }, @@ -1181,6 +1204,22 @@ }, // ........................................................................ footer + toggleExtensions : function( force ){ + var creator = this; + creator.removeExtensions = ( force !== undefined )?( force ):( !creator.removeExtensions ); + console.debug( 'toggleExtensions:', creator.removeExtensions ); + + _.each( creator.paired, function( pair ){ + console.debug( pair ); + // don't overwrite custom names + if( pair.customizedName ){ return; } + pair.name = creator._guessNameForPair( pair.forward, pair.reverse ); + }); + + creator._renderPaired(); + creator._renderFooter(); + }, + /** handle a collection name change */ _changeName : function( ev ){ this._validationWarning( 'name', !!this._getName() ); @@ -1330,9 +1369,17 @@ /** creation and cancel controls */ footer : _.template([ '<div class="attributes clear">', - '<input class="collection-name form-control pull-right" ', - 'placeholder="', _l( 'Enter a name for your new list' ), '" />', - '<div class="collection-name-prompt pull-right">', _l( 'Name' ), ':</div>', + '<div class="clear">', + '<label class="remove-extensions-prompt pull-right">', + _l( 'Remove file extensions from pair names' ), '?', + '<input class="remove-extensions pull-right" type="checkbox" />', + '</label>', + '</div>', + '<div class="clear">', + '<input class="collection-name form-control pull-right" ', + 'placeholder="', _l( 'Enter a name for your new list' ), '" />', + '<div class="collection-name-prompt pull-right">', _l( 'Name' ), ':</div>', + '</div>', '</div>', '<div class="actions clear vertically-spaced">', @@ -1411,6 +1458,10 @@ 'Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.' ].join( '' )), '</p>', '<p>', _l([ + 'You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ', + '<i data-target=".remove-extensions-prompt">"Remove file extensions from pair names?"</i> control.' + ].join( '' )), '</p>', + '<p>', _l([ 'Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ', 'click <i data-target=".create-collection">"Create list"</i>. ', '(Note: you do not have to pair all unpaired datasets to finish.)' diff -r 3be5658bc5da1831860b367ad57deec0140cc10e -r c9c62f54cf168fe493f48549647b2e74cfd6a9ac static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1840,16 +1840,19 @@ .collection-creator .unpaired-columns .paired-column .dataset.unpaired{border-color:lightgrey;color:lightgrey}.collection-creator .unpaired-columns .paired-column .dataset.unpaired:hover{border-color:black;color:black} .collection-creator .unpaired-columns .reverse-column .dataset.unpaired{text-align:right;margin-left:32px} .collection-creator .flexible-partition .flexible-partition-drag{width:100%;height:8px;cursor:ns-resize}.collection-creator .flexible-partition .flexible-partition-drag:hover{background:lightgrey} -.collection-creator .flexible-partition .column-header{width:100%;text-align:center}.collection-creator .flexible-partition .column-header .column-title{display:inline;margin-right:8px} +.collection-creator .flexible-partition .column-header{width:100%;text-align:center}.collection-creator .flexible-partition .column-header .column-title{display:inline} +.collection-creator .flexible-partition .column-header>*:not(:last-child){margin-right:8px} +.collection-creator .flexible-partition .column-header .remove-extensions-link{display:none} .collection-creator .paired-columns .dataset.paired{background:#AFF1AF;border-color:grey;border-width:2px}.collection-creator .paired-columns .dataset.paired:hover,.collection-creator .paired-columns .dataset.paired.emphasized{border-color:black} .collection-creator .paired-columns .forward-column .dataset.paired{margin-left:32px;border-radius:3px 0 0 3px;border-right-color:grey;border-right-width:1px;text-align:right}.collection-creator .paired-columns .forward-column .dataset.paired:after{margin-left:8px;font-family:FontAwesome;content:'\f061'} .collection-creator .paired-columns .paired-column .dataset.paired{border-radius:0;border-width:2px 0 2px 0}.collection-creator .paired-columns .paired-column .dataset.paired .dataset-name:hover{text-decoration:underline} .collection-creator .paired-columns .reverse-column .dataset.paired{margin-right:32px;border-radius:0 3px 3px 0;border-left-color:grey;border-left-width:1px}.collection-creator .paired-columns .reverse-column .dataset.paired:before{margin-right:8px;font-family:FontAwesome;content:'\f060'} .collection-creator .paired-columns .reverse-column .unpair-btn{float:right;margin-top:-34px;width:31px;height:32px;border-color:transparent;background:transparent;font-size:120%}.collection-creator .paired-columns .reverse-column .unpair-btn:hover{border-color:#BFBFBF;background:#DEDEDE} -.collection-creator .footer{padding-bottom:8px}.collection-creator .footer .collection-name-prompt.validation-warning:before{content:'(required)';margin-right:4px;color:red} -.collection-creator .footer .collection-name{width:50%}.collection-creator .footer .collection-name.validation-warning{border-color:red} -.collection-creator .footer .other-options>*{display:none;margin-left:4px} -.collection-creator .footer .collection-name-prompt{margin:5px 4px 0 0} +.collection-creator .footer{padding-bottom:8px}.collection-creator .footer .attributes .remove-extensions-prompt{line-height:32px}.collection-creator .footer .attributes .remove-extensions-prompt .remove-extensions{display:inline-block;width:24px;height:24px} +.collection-creator .footer .attributes .collection-name-prompt{margin:5px 4px 0 0} +.collection-creator .footer .attributes .collection-name-prompt.validation-warning:before{content:'(required)';margin-right:4px;color:red} +.collection-creator .footer .attributes .collection-name{width:50%}.collection-creator .footer .attributes .collection-name.validation-warning{border-color:red} +.collection-creator .footer .actions .other-options>*{display:none;margin-left:4px} .toolMenuContainer{color:#000;background:#dfe5f9;min-height:100%;padding:5px 10px} div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px} div.toolSectionWrapper{margin-bottom:5px} diff -r 3be5658bc5da1831860b367ad57deec0140cc10e -r c9c62f54cf168fe493f48549647b2e74cfd6a9ac static/style/src/less/ui/paired-collection-creator.less --- a/static/style/src/less/ui/paired-collection-creator.less +++ b/static/style/src/less/ui/paired-collection-creator.less @@ -301,8 +301,13 @@ text-align: center; .column-title { display: inline; + } + & > *:not(:last-child) { margin-right: 8px; } + .remove-extensions-link { + display: none; + } } } @@ -372,26 +377,39 @@ // ------------------------------------------------------------------------ footer .footer { - .collection-name-prompt.validation-warning:before { - //TODO: localize (somehow) - content: '(required)'; - margin-right: 4px; - color: red; - } - .collection-name { - width: 50%; - &.validation-warning { - border-color: red; + .attributes { + .remove-extensions-prompt { + //margin-right: 32px; + line-height: 32px; + .remove-extensions { + display: inline-block; + width: 24px; + height: 24px; + } + } + // actually appears/floats to the left of the input + .collection-name-prompt { + margin: 5px 4px 0 0; + } + .collection-name-prompt.validation-warning:before { + //TODO: localize (somehow) + content: '(required)'; + margin-right: 4px; + color: red; + } + .collection-name { + width: 50%; + &.validation-warning { + border-color: red; + } } } - .other-options > * { - // do not display the links to create other collections yet - display: none; - margin-left: 4px; - } - // actually appears/floats to the left of the input - .collection-name-prompt { - margin: 5px 4px 0 0; + .actions { + .other-options > * { + // do not display the links to create other collections yet + display: none; + margin-left: 4px; + } } padding-bottom: 8px; } https://bitbucket.org/galaxy/galaxy-central/commits/3179b324e9d5/ Changeset: 3179b324e9d5 User: carlfeberhard Date: 2014-08-14 20:16:34 Summary: (pack scripts) Affected #: 1 file diff -r c9c62f54cf168fe493f48549647b2e74cfd6a9ac -r 3179b324e9d5886962fe2acda12c1b481bbd1e6a static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(f,a,d){var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(g){g=_.defaults(g,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=g.datasets;this.historyId=g.historyId;this.filters=this.commonFilters[g.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(g.filters)){this.filters=g.filters}this.automaticallyPair=g.automaticallyPair;this.matchPercentage=g.matchPercentage;this.strategy=this.strategies[g.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(g.strategy)){this.strategy=g.strategy}this.oncancel=g.oncancel;this.oncreate=g.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(g){g.sort(function(i,h){return naturalSort(i.name,h.name)});return g},_ensureIds:function(){this.initialList.forEach(function(g){if(!g.hasOwnProperty("id")){g.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(i){var h=[],g=[];this.unpaired.forEach(function(j){if(this._filterFwdFn(j)){h.push(j)}if(this._filterRevFn(j)){g.push(j)}}.bind(this));return[h,g]},_filterFwdFn:function(h){var g=new RegExp(this.filters[0]);return g.test(h.name)},_filterRevFn:function(h){var g=new RegExp(this.filters[1]);return g.test(h.name)},_addToUnpaired:function(h){var g=function(i,k){if(i===k){return i}var j=Math.floor((k-i)/2)+i,l=naturalSort(h.name,this.unpaired[j].name);if(l<0){return g(i,j)}else{if(l>0){return g(j+1,k)}}while(this.unpaired[j]&&this.unpaired[j].name===h.name){j++}return j}.bind(this);this.unpaired.splice(g(0,this.unpaired.length),0,h)},autoPair:function(g){g=g||this.strategy;this.simpleAutoPair();return this[g].call(this)},simpleAutoPair:function(){var m=0,k,q=this._splitByFilters(),g=q[0],p=q[1],o,r,h=false;while(m<g.length){var l=g[m];o=l.name.replace(this.filters[0],"");h=false;for(k=0;k<p.length;k++){var n=p[k];r=n.name.replace(this.filters[1],"");if(l!==n&&o===r){h=true;this._pair(g.splice(m,1)[0],p.splice(k,1)[0],{silent:true});break}}if(!h){m+=1}}},autoPairLevenshtein:function(){var n=0,l,s=this._splitByFilters(),g=s[0],q=s[1],p,u,h,r,k;while(n<g.length){var m=g[n];p=m.name.replace(this.filters[0],"");k=Number.MAX_VALUE;for(l=0;l<q.length;l++){var o=q[l];u=o.name.replace(this.filters[1],"");if(m!==o){if(p===u){r=l;k=0;break}h=levenshteinDistance(p,u);if(h<k){r=l;k=h}}}var t=1-(k/(Math.max(p.length,u.length)));if(t>=this.matchPercentage){this._pair(g.splice(n,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{n+=1}}},autoPairLCSs:function(){var l=0,h,s=this._splitByFilters(),g=s[0],q=s[1],p,v,u,r,n;if(!g.length||!q.length){return}while(l<g.length){var k=g[l];p=k.name.replace(this.filters[0],"");n=0;for(h=0;h<q.length;h++){var o=q[h];v=o.name.replace(this.filters[1],"");if(k!==o){if(p===v){r=h;n=p.length;break}var m=this._naiveStartingAndEndingLCS(p,v);u=m.length;if(u>n){r=h;n=u}}}var t=n/(Math.min(p.length,v.length));if(t>=this.matchPercentage){this._pair(g.splice(l,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{l+=1}}},_naiveStartingAndEndingLCS:function(l,h){var m="",n="",k=0,g=0;while(k<l.length&&k<h.length){if(l[k]!==h[k]){break}m+=l[k];k+=1}if(k===l.length){return l}if(k===h.length){return h}k=(l.length-1);g=(h.length-1);while(k>=0&&g>=0){if(l[k]!==h[g]){break}n=[l[k],n].join("");k-=1;g-=1}return m+n},_pair:function(i,g,h){h=h||{};var j=this._createPair(i,g,h.name);this.paired.push(j);this.unpaired=_.without(this.unpaired,i,g);if(!h.silent){this.trigger("pair:new",j)}return j},_createPair:function(i,g,h){if(!(i&&g)||(i===g)){throw new Error("Bad pairing: "+[JSON.stringify(i),JSON.stringify(g)])}h=h||this._guessNameForPair(i,g);return{forward:i,name:h,reverse:g}},_guessNameForPair:function(i,g){var h=this._naiveStartingAndEndingLCS(i.name.replace(this.filters[0],""),g.name.replace(this.filters[1],""));return h||(i.name+" & "+g.name)},_unpair:function(h,g){g=g||{};if(!h){throw new Error("Bad pair: "+JSON.stringify(h))}this.paired=_.without(this.paired,h);this._addToUnpaired(h.forward);this._addToUnpaired(h.reverse);if(!g.silent){this.trigger("pair:unpair",[h])}return h},unpairAll:function(){var g=[];while(this.paired.length){g.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",g)},_pairToJSON:function(g){return{collection_type:"paired",src:"new_collection",name:g.name,element_identifiers:[{name:"forward",id:g.forward.id,src:"hda"},{name:"reverse",id:g.reverse.id,src:"hda"}]}},createList:function(){var i=this,h;if(i.historyId){h="/api/histories/"+this.historyId+"/contents/dataset_collections"}var g={type:"dataset_collection",collection_type:"list:paired",name:_.escape(i.$(".collection-name").val()),element_identifiers:i.paired.map(function(j){return i._pairToJSON(j)})};return jQuery.ajax(h,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(g)}).fail(function(l,j,k){i._ajaxErrHandler(l,j,k)}).done(function(j,k,l){i.trigger("collection:created",j,k,l);if(typeof i.oncreate==="function"){i.oncreate.call(this,j,k,l)}})},_ajaxErrHandler:function(j,g,i){console.error(j,g,i);var h=d("An error occurred while creating this collection");if(j){if(j.readyState===0&&j.status===0){h+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(j.responseJSON){h+="<br /><pre>"+JSON.stringify(j.responseJSON)+"</pre>"}else{h+=": "+i}}}creator._showAlert(h,"alert-danger")},render:function(g,h){this.$el.empty().html(e.templates.main());this._renderHeader(g);this._renderMiddle(g);this._renderFooter(g);this._addPluginComponents();return this},_renderHeader:function(h,i){var g=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return g},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(h,i){var g=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return g},_renderUnpaired:function(l,m){var j=this,k,h,g=[],i=this._splitByFilters();this.$(".forward-column .title").text([i[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[0].length));this.$(".reverse-column .title").text([i[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[1].length));this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}h=i[1].map(function(o,n){if((i[0][n]!==undefined)&&(i[0][n]!==o)){g.push(j._renderPairButton())}return j._renderUnpairedDataset(o)});k=i[0].map(function(n){return j._renderUnpairedDataset(n)});if(!k.length&&!h.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .column-datasets").empty();this.$(".unpaired-columns .forward-column .column-datasets").append(k).add(this.$(".unpaired-columns .paired-column .column-datasets").append(g)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(h))},_renderUnpairedDisplayStr:function(g){return["(",g," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(g){return $("<li/>").attr("id","dataset-"+g.id).addClass("dataset unpaired").attr("draggable",true).addClass(g.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(g.name)).data("dataset",g)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var g=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").prepend(g);return g},_renderUnpairedNotShown:function(){var g=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").prepend(g);return g},_renderPaired:function(j,k){var i=[],g=[],h=[];this.$(".paired-column-title .title").text([this.paired.length,d("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty()}this.paired.forEach(function(m,l){i.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.forward.name)));g.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.name)));h.push($("<li/>").addClass("dataset paired").append($("<span/>").addClass("dataset-name").text(m.reverse.name)));h.push($("<button/>").addClass("unpair-btn").append($("<span/>").addClass("fa fa-unlink").attr("title",d("Unpair"))))});this.$(".paired-columns .column-datasets").empty();return this.$(".paired-columns .forward-column .column-datasets").prepend(i).add(this.$(".paired-columns .paired-column .column-datasets").prepend(g)).add(this.$(".paired-columns .reverse-column .column-datasets").prepend(h))},_renderPairedEmpty:function(){var g=$('<div class="empty-message"></div>').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .paired-column .column-datasets").prepend(g);return g},_renderFooter:function(h,i){var g=this.$(".footer").empty().html(e.templates.footer());if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return g},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 192, 255, 255, 1.0 )")},_chooseFiltersPopover:function(g){function h(k,j){return['<button class="filter-choice btn" ','data-forward="',k,'" data-reverse="',j,'">',d("Forward"),": ",k,", ",d("Reverse"),": ",j,"</button>"].join("")}var i=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the 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g,h=null;if(this.paired.length){h="alert-success";g=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){g+=": "+d("all datasets have been successfully paired");this.hideUnpaired()}}else{g=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(g,h)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(g){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(g){$(g.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter 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+define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(f,a,d){var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(g){g=_.defaults(g,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=g.datasets;this.historyId=g.historyId;this.filters=this.commonFilters[g.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(g.filters)){this.filters=g.filters}this.automaticallyPair=g.automaticallyPair;this.matchPercentage=g.matchPercentage;this.strategy=this.strategies[g.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(g.strategy)){this.strategy=g.strategy}this.removeExtensions=true;this.oncancel=g.oncancel;this.oncreate=g.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(g){g.sort(function(i,h){return 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