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Merge branch 'dev' into add_new_spectron_test
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@rbuels
rbuels committed May 2, 2018
2 parents a3101b0 + 987e5d4 commit 36eb4a9
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Showing 6 changed files with 159 additions and 131 deletions.
144 changes: 46 additions & 98 deletions src/JBrowse/Browser.js
View file
Expand Up @@ -1257,7 +1257,7 @@ openFastaElectron: function() {
window.location = window.location.href.split('?')[0] + "?data=" + Util.replacePath( dir );
} catch(e) { alert(e); }
}
else if( confs[0].store.blob ) {
else if( confs[0].store.type == 'JBrowse/Store/SeqFeature/TwoBit' ) {
var f2bit = Util.replacePath( confs[0].store.blob.url );

var refseqs = new TwoBit({'browser': this, 'urlTemplate': f2bit });
Expand Down Expand Up @@ -1333,76 +1333,49 @@ openFastaElectron: function() {
},

openFasta: function() {
var thisB=this;
this.fastaFileDialog = this.fastaFileDialog || new FastaFileDialog({browser: this});

var replaceBrowser = function (newBrowserGenerator) {
thisB.teardown()
newBrowserGenerator()
}

this.fastaFileDialog.show ({
openCallback: dojo.hitch(this, function(results) {
var confs = results.trackConfs || [];
function loadNewRefSeq(refSeqs, tracks) {
replaceBrowser(function() {
var newBrowser = new thisB.constructor({
refSeqs: { data: refSeqs },
refSeqOrder: results.refSeqOrder
});
newBrowser.afterMilestone('completely initialized', function() {
array.forEach( tracks, function( conf ) {
var storeConf = conf.store;
if( storeConf && typeof storeConf == 'object' ) {
delete conf.store;
storeConf.name = 'refseqs'; // important to make it the refseq store
conf.store = this.addStoreConfig( storeConf.name, storeConf );
}
}, newBrowser);
newBrowser.publish( '/jbrowse/v1/v/tracks/new', tracks );
});
});
}
if( confs.length ) {
if( confs[0].store.fasta && confs[0].store.fai ) {
new IndexedFasta({
browser: this,
fai: confs[0].store.fai,
fasta: confs[0].store.fasta
})
.getRefSeqs(
function(refSeqs) { loadNewRefSeq( refSeqs, confs ); },
function(error) { alert('Error getting refSeq: '+error); }
);
}
else if( confs[0].store.blob ) {
new TwoBit({
browser: this,
blob: confs[0].store.blob
})
.getRefSeqs(
function(refSeqs) { loadNewRefSeq( refSeqs, confs ); },
function(error) { alert('Error getting refSeq: '+error); }
);
}
else if( confs[0].store.fasta ) {
if( confs[0].store.fasta.size > 100000000 ) {
if(!confirm('Warning: you are opening a non-indexed fasta larger than 100MB. It is recommended to load a fasta (.fa) and the fasta index (.fai) to provide speedier loading. Do you wish to continue anyways?')) {
return;
}
}
new UnindexedFasta({
browser: this,
fasta: confs[0].store.fasta
})
.getRefSeqs(
function(refSeqs) { loadNewRefSeq( refSeqs, confs ); },
function(error) { alert('Error getting refSeq: '+error); }
);
}
openCallback: results => {
return new Promise((resolve,reject) => {
const trackConfigs = results.trackConfs || []
const [conf] = trackConfigs
if (!conf) return reject('no track configs')
const storeConf = conf.store
if (!storeConf) return reject('no store config')

dojo.global.require( [storeConf.type], (storeClass) => {
if( /\/Unindexed/i.test(storeConf.type) && storeConf.fasta && storeConf.fasta.size > 100000000 ) {
alert('Unindexed file too large. You must have an index file (.fai) for sequence files larger than 100 MB.')
return reject('sequence file too large')
}

}
})
const store = new storeClass(
Object.assign({ browser: this }, storeConf)
)
.getRefSeqs(
refSeqs => {
this.teardown()
var newBrowser = new this.constructor({
refSeqs: { data: refSeqs },
refSeqOrder: results.refSeqOrder
})
newBrowser.afterMilestone('completely initialized', () => {
storeConf.name = 'refseqs' // important to make it the refseq store
newBrowser.addStoreConfig( storeConf.name, storeConf )
conf.store = 'refseqs'
newBrowser.publish( '/jbrowse/v1/v/tracks/new', [conf] )
})
resolve()
},
error => {
this.fatalError('Error getting refSeq: '+error)
reject(error)
}
);
})
})
}
});
},

Expand Down Expand Up @@ -2092,9 +2065,12 @@ loadConfig: function () {
this._addTrackConfigs( tracks );

// coerce some config keys to boolean
dojo.forEach( ['show_tracklist','show_nav','show_overview','show_menu', 'show_fullviewlink', 'show_tracklabels', 'update_browser_title'], function(v) {
this.config[v] = this._coerceBoolean( this.config[v] );
},this);
[
'show_tracklist','show_nav','show_overview','show_menu',
'show_fullviewlink', 'show_tracklabels', 'update_browser_title'
].forEach( v => {
this.config[v] = Util.coerceBoolean( this.config[v] );
})

// set empty tracks array if we have none
if( ! this.config.tracks )
Expand Down Expand Up @@ -2204,34 +2180,6 @@ _configDefaults: function() {
};
},

/**
* Coerce a value of unknown type to a boolean, treating string 'true'
* and 'false' as the values they indicate, and string numbers as
* numbers.
* @private
*/
_coerceBoolean: function(val) {
if( typeof val == 'string' ) {
val = val.toLowerCase();
if( val == 'true' ) {
return true;
}
else if( val == 'false' )
return false;
else
return parseInt(val);
}
else if( typeof val == 'boolean' ) {
return val;
}
else if( typeof val == 'number' ) {
return !!val;
}
else {
return true;
}
},

/**
* @param refSeqs {Array} array of refseq records to add to the browser
*/
Expand Down
29 changes: 29 additions & 0 deletions src/JBrowse/Util.js
View file
Expand Up @@ -515,6 +515,35 @@ Util = {
}
return r;
},

/**
* Coerce a value of unknown type to a boolean, treating string 'true'
* and 'false' as the values they indicate, and string numbers as
* numbers.
* @private
*/
coerceBoolean: function(val) {
if( typeof val == 'string' ) {
val = val.toLowerCase();
if( val == 'true' ) {
return true;
}
else if( val == 'false' )
return false;
else
return parseInt(val);
}
else if( typeof val == 'boolean' ) {
return val;
}
else if( typeof val == 'number' ) {
return !!val;
}
else {
return true;
}
},

};

return Util;
Expand Down
29 changes: 16 additions & 13 deletions src/JBrowse/View/FastaFileDialog.js
View file
Expand Up @@ -70,19 +70,22 @@ return declare( FileDialog, {
})
.placeAt( actionBar );

new Button({ iconClass: 'dijitIconFolderOpen',
label: 'Open',
onClick: dojo.hitch( this, function() {
openCallback && openCallback({
trackConfs: this.trackList.getTrackConfigurations(),
refSeqOrder: this.refSeqOrderChoice[0].checked ? "alphabetic descending" :
this.refSeqOrderChoice[1].checked ? "length descending" :
undefined
});
this.dialog.hide();
})
})
.placeAt( actionBar );
new Button({
iconClass: 'dijitIconFolderOpen',
label: 'Open',
onClick: () => {
if (openCallback) {
openCallback({
trackConfs: this.trackList.getTrackConfigurations(),
refSeqOrder: this.refSeqOrderChoice[0].checked ? "alphabetic descending" :
this.refSeqOrderChoice[1].checked ? "length descending" :
undefined
})
.then( () => this.dialog.hide(), err => { console.error(err) } )
}
}
})
.placeAt( actionBar );

return { domNode: actionBar };
}
Expand Down
23 changes: 4 additions & 19 deletions src/JBrowse/View/FileDialog/TrackList/IndexedFASTADriver.js
View file
@@ -1,11 +1,12 @@
define([
'dojo/_base/declare',
'./_IndexedFileDriver'
'./_OptionallyIndexedFileDriver'
],
function( declare, IndexedFileDriver ) {
return declare( IndexedFileDriver, {
function( declare, OptionallyIndexedFileDriver ) {
return declare( OptionallyIndexedFileDriver, {
name: 'FASTA',
storeType: 'JBrowse/Store/SeqFeature/IndexedFasta',
unindexedStoreType: 'JBrowse/Store/SeqFeature/UnindexedFasta',

fileExtension: 'fasta',
fileConfKey: 'fasta',
Expand All @@ -14,21 +15,5 @@ return declare( IndexedFileDriver, {
indexExtension: 'fai',
indexConfKey: 'fai',
indexUrlConfKey: 'faiUrlTemplate',


tryResource: function(configs, resource) {
this.inherited(arguments);
},
finalizeConfiguration: function(configs) {
this.inherited(arguments);
for(var i in configs) {
var config = configs[i];
if( !config.fai && !config.blob ) {
// if no fai, change to UnindexedFasta
config.type = "JBrowse/Store/SeqFeature/UnindexedFasta";
}
}
}
});

});
62 changes: 62 additions & 0 deletions src/JBrowse/View/FileDialog/TrackList/_OptionallyIndexedFileDriver.js
View file
@@ -0,0 +1,62 @@
define([
'dojo/_base/declare',
'JBrowse/Util',
'./_IndexedFileDriver',
],
function( declare, Util, _IndexedFileDriver ) {
return declare( _IndexedFileDriver, {

// try to merge any singleton file and index stores. currently can only do this if there is one of each
finalizeConfiguration: function( configs ) {
var singletonIndexes = {};
var singletonIndexCount = 0;
var singletonFiles = {};
var singletonFileCount = 0;
for( var n in configs ) {
var conf = configs[n];
if( conf.type === this.storeType ) {
if( (conf[this.indexConfKey] || conf[this.indexUrlConfKey]) && ! ( conf[this.fileConfKey] || conf[this.fileUrlConfKey] ) ) {
// singleton Index
singletonIndexCount++;
singletonIndexes[n] = conf;
}
else if(( conf[this.fileConfKey] || conf[this.fileUrlConfKey] ) && ! ( conf[this.indexConfKey] || conf[this.indexUrlConfKey]) ) {
// singleton File
singletonFileCount++;
singletonFiles[n] = conf;
}
}
}

// if we have a single File and single Index left at the end,
// stick them together and we'll see what happens
if( singletonFileCount == 1 && singletonIndexCount == 1 ) {
for( var indexName in singletonIndexes ) {
for( var fileName in singletonFiles ) {
if( singletonIndexes[indexName][this.indexUrlConfKey] )
singletonFiles[fileName][this.indexUrlConfKey] = singletonIndexes[indexName][this.indexUrlConfKey];
if( singletonIndexes[indexName][this.indexConfKey] )
singletonFiles[fileName][this.indexConfKey] = singletonIndexes[indexName][this.indexConfKey];

delete configs[indexName];
}
}
}

// delete any remaining singleton Indexes, since they don't have
// a hope of working
for( var indexName in singletonIndexes ) {
delete configs[indexName];
}

// make any remaining singleton data files be unindexed stores
for( var fileName in singletonFiles ) {
configs[fileName].type = this.unindexedStoreType;
}
},

confIsValid: function( conf ) {
return (conf[this.fileConfKey] || conf[this.fileUrlConfKey]);
}
});
});
3 changes: 2 additions & 1 deletion src/JBrowse/View/TrackConfigEditor.js
View file
Expand Up @@ -108,6 +108,7 @@ return declare( null, {
realChange();
previousText = textArea.value;
}
// TODO: do not renew this timeout if the dialog is destroyed
window.setTimeout( checkForChange, checkFrequency );
}
};
Expand Down Expand Up @@ -160,4 +161,4 @@ return declare( null, {
}

});
});
});

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