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trackster: Fix BAM reads without cigar string (assume all match); datasets added into a new track browser will now index immediately instead of after changing a chrom

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This commit is contained in:
Kanwei Li
2011-03-11 17:54:06 -05:00
parent 6d8eb1015e
commit dcfa7af7cc
4 changed files with 49 additions and 41 deletions
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static/june_2007_style/blue/trackster.css
+1
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@@ -28,6 +28,7 @@
.track-tile canvas{position:relative;z-index:100;border:solid white;border-width:2px 0px 0px 0px;}
.track.error .track-content{background-color:#ECB4AF;background-image:none;padding:2px 0;}
.track.nodata .track-content{background-color:#eee;background-image:none;padding:2px 0;}
.track.pending .track-content{background-color:white;background-image:none;padding:2px 0;}
.loading{min-height:100px;}
.label-track{font-size:10px;border:none;padding:0;margin:0;height:1.5em;overflow:hidden;}
.label-track .label{border-left:solid #999 1px;padding:1px;padding-bottom:2px;display:inline-block;}
static/june_2007_style/trackster.css.tmpl
+5
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@@ -177,6 +177,11 @@
background-image: none;
padding: 2px 0;
}
.track.pending .track-content {
background-color: white;
background-image: none;
padding: 2px 0;
}
.loading {
min-height: 100px;
static/scripts/packed/trackster.js
+1 -1
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File diff suppressed because one or more lines are too long
static/scripts/trackster.js
+42 -40
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@@ -1067,47 +1067,45 @@ $.extend( Track.prototype, {
return;
}
if ( track.view.chrom !== null ) {
// Get dataset state; if state is fine, enable and draw track. Otherwise, show message
// about track status.
$.getJSON(converted_datasets_state_url, { hda_ldda: track.hda_ldda, dataset_id: track.dataset_id, chrom: track.view.chrom},
function (result) {
if (!result || result === "error" || result.kind === "error") {
track.container_div.addClass("error");
track.content_div.text(DATA_ERROR);
if (result.message) {
var track_id = track.view.tracks.indexOf(track);
var error_link = $(" <a href='javascript:void(0);'></a>").text("View error").bind("click", function() {
show_modal( "Trackster Error", "<pre>" + result.message + "</pre>", { "Close" : hide_modal } );
});
track.content_div.append(error_link);
}
} else if (result === "no converter") {
track.container_div.addClass("error");
track.content_div.text(DATA_NOCONVERTER);
} else if (result === "no data" || (result.data !== undefined && (result.data === null || result.data.length === 0))) {
track.container_div.addClass("nodata");
track.content_div.text(DATA_NONE);
} else if (result === "pending") {
track.container_div.addClass("pending");
track.content_div.text(DATA_PENDING);
setTimeout(function() { track.init(); }, track.data_query_wait);
} else if (result['status'] === "data") {
if (result['valid_chroms']) {
track.valid_chroms = result['valid_chroms'];
track.make_name_popup_menu();
}
track.content_div.text(DATA_OK);
if (track.view.chrom) {
track.content_div.text("");
track.content_div.css( "height", track.height_px + "px" );
track.enabled = true;
// predraw_init may be asynchronous, wait for it and then draw
$.when( track.predraw_init() ).done( function() { track.draw() } );
}
// Get dataset state; if state is fine, enable and draw track. Otherwise, show message
// about track status.
$.getJSON(converted_datasets_state_url, { hda_ldda: track.hda_ldda, dataset_id: track.dataset_id, chrom: track.view.chrom},
function (result) {
if (!result || result === "error" || result.kind === "error") {
track.container_div.addClass("error");
track.content_div.text(DATA_ERROR);
if (result.message) {
var track_id = track.view.tracks.indexOf(track);
var error_link = $(" <a href='javascript:void(0);'></a>").text("View error").bind("click", function() {
show_modal( "Trackster Error", "<pre>" + result.message + "</pre>", { "Close" : hide_modal } );
});
track.content_div.append(error_link);
}
});
}
} else if (result === "no converter") {
track.container_div.addClass("error");
track.content_div.text(DATA_NOCONVERTER);
} else if (result === "no data" || (result.data !== undefined && (result.data === null || result.data.length === 0))) {
track.container_div.addClass("nodata");
track.content_div.text(DATA_NONE);
} else if (result === "pending") {
track.container_div.addClass("pending");
track.content_div.text(DATA_PENDING);
setTimeout(function() { track.init(); }, track.data_query_wait);
} else if (result['status'] === "data") {
if (result['valid_chroms']) {
track.valid_chroms = result['valid_chroms'];
track.make_name_popup_menu();
}
track.content_div.text(DATA_OK);
if (track.view.chrom) {
track.content_div.text("");
track.content_div.css( "height", track.height_px + "px" );
track.enabled = true;
// predraw_init may be asynchronous, wait for it and then draw
$.when( track.predraw_init() ).done( function() { track.draw() } );
}
}
});
},
/**
* Additional initialization required before drawing track for the first time.
@@ -2779,6 +2777,10 @@ $.extend(ReadTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, {
if ((mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) {
gap = Math.round(w_scale/2);
}
if (!cigar) {
// If no cigar string, then assume all matches
cigar = [ [0, orig_seq.length] ]
}
for (var cig_id = 0, len = cigar.length; cig_id < len; cig_id++) {
var cig = cigar[cig_id],
cig_op = "MIDNSHP=X"[cig[0]],