genoverse 3.2.0 → 4.0.0-beta1

package/js/lib/dalliance/js/das.js

@@ -1,749 +0,0 @@
-/* -*- mode: javascript; c-basic-offset: 4; indent-tabs-mode: nil -*- */
-
-//
-// Dalliance Genome Explorer
-// (c) Thomas Down 2006-2010
-//
-// das.js: queries and low-level data model.
-//
-
-var dasLibErrorHandler = function(errMsg) {
-    alert(errMsg);
-}
-var dasLibRequestQueue = new Array();
-
-
-
-function DASSegment(name, start, end, description) {
-    this.name = name;
-    this.start = start;
-    this.end = end;
-    this.description = description;
-}
-DASSegment.prototype.toString = function() {
-    return this.name + ':' + this.start + '..' + this.end;
-};
-DASSegment.prototype.isBounded = function() {
-    return this.start && this.end;
-}
-DASSegment.prototype.toDASQuery = function() {
-    var q = 'segment=' + this.name;
-    if (this.start && this.end) {
-        q += (':' + this.start + ',' + this.end);
-    }
-    return q;
-}
-
-
-function DASSource(a1, a2) {
-    var options;
-    if (typeof a1 == 'string') {
-        this.uri = a1;
-        options = a2 || {};
-    } else {
-        options = a1 || {};
-    }
-    for (var k in options) {
-        if (typeof(options[k]) != 'function') {
-            this[k] = options[k];
-        }
-    }
-
-
-    if (!this.coords) {
-        this.coords = [];
-    }
-    if (!this.props) {
-        this.props = {};
-    }
-
-    this.dasBaseURI = this.uri;
-    if (this.dasBaseURI && this.dasBaseURI.substr(this.uri.length - 1) != '/') {
-        this.dasBaseURI = this.dasBaseURI + '/';
-    }
-}
-
-function DASCoords() {
-}
-
-function coordsMatch(c1, c2) {
-    return c1.taxon == c2.taxon && c1.auth == c2.auth && c1.version == c2.version;
-}
-
-//
-// DAS 1.6 entry_points command
-//
-
-DASSource.prototype.entryPoints = function(callback) {
-    var dasURI = this.dasBaseURI + 'entry_points';
-    this.doCrossDomainRequest(dasURI, function(responseXML) {
-            if (!responseXML) {
-                return callback([]);
-            }
-
-                var entryPoints = new Array();
-
-                var segs = responseXML.getElementsByTagName('SEGMENT');
-                for (var i = 0; i < segs.length; ++i) {
-                    var seg = segs[i];
-                    var segId = seg.getAttribute('id');
-
-                    var segSize = seg.getAttribute('size');
-                    var segMin, segMax;
-                    if (segSize) {
-                        segMin = 1; segMax = segSize|0;
-                    } else {
-                        segMin = seg.getAttribute('start');
-                        if (segMin) {
-                            segMin |= 0;
-                        }
-                        segMax = seg.getAttribute('stop');
-                        if (segMax) {
-                            segMax |= 0;
-                        }
-                    }
-                    var segDesc = null;
-                    if (seg.firstChild) {
-                        segDesc = seg.firstChild.nodeValue;
-                    }
-                    entryPoints.push(new DASSegment(segId, segMin, segMax, segDesc));
-                }
-               callback(entryPoints);
-    });
-}
-
-//
-// DAS 1.6 sequence command
-// Do we need an option to fall back to the dna command?
-//
-
-function DASSequence(name, start, end, alpha, seq) {
-    this.name = name;
-    this.start = start;
-    this.end = end;
-    this.alphabet = alpha;
-    this.seq = seq;
-}
-
-DASSource.prototype.sequence = function(segment, callback) {
-    var dasURI = this.dasBaseURI + 'sequence?' + segment.toDASQuery();
-    this.doCrossDomainRequest(dasURI, function(responseXML) {
-        if (!responseXML) {
-            callback([]);
-            return;
-        } else {
-                var seqs = new Array();
-
-                var segs = responseXML.getElementsByTagName('SEQUENCE');
-                for (var i = 0; i < segs.length; ++i) {
-                    var seg = segs[i];
-                    var segId = seg.getAttribute('id');
-                    var segMin = seg.getAttribute('start');
-                    var segMax = seg.getAttribute('stop');
-                    var segAlpha = 'DNA';
-                    var segSeq = null;
-                    if (seg.firstChild) {
-                        var rawSeq = seg.firstChild.nodeValue;
-                        segSeq = '';
-                        var idx = 0;
-                        while (true) {
-                            var space = rawSeq.indexOf('\n', idx);
-                            if (space >= 0) {
-                                segSeq += rawSeq.substring(idx, space);
-                                idx = space + 1;
-                            } else {
-                                segSeq += rawSeq.substring(idx);
-                                break;
-                            }
-                        }
-                    }
-                    seqs.push(new DASSequence(segId, segMin, segMax, segAlpha, segSeq));
-                }
-
-                callback(seqs);
-        }
-    });
-}
-
-//
-// DAS 1.6 features command
-//
-
-function DASFeature() {
-    // We initialize these in the parser...
-}
-
-function DASGroup() {
-    // We initialize these in the parser, too...
-}
-
-function DASLink(desc, uri) {
-    this.desc = desc;
-    this.uri = uri;
-}
-
-DASSource.prototype.features = function(segment, options, callback) {
-    options = options || {};
-    var thisB = this;
-
-    var dasURI;
-    if (this.features_uri) {
-        dasURI = this.features_uri;
-    } else {
-        var filters = [];
-
-        if (segment) {
-            filters.push(segment.toDASQuery());
-        } else if (options.group) {
-            var g = options.group;
-            if (typeof g == 'string') {
-                filters.push('group_id=' + g);
-            } else {
-                for (var gi = 0; gi < g.length; ++gi) {
-                    filters.push('group_id=' + g[gi]);
-                }
-            }
-        }
-
-        if (options.adjacent) {
-            var adj = options.adjacent;
-            if (typeof adj == 'string') {
-                adj = [adj];
-            }
-            for (var ai = 0; ai < adj.length; ++ai) {
-                filters.push('adjacent=' + adj[ai]);
-            }
-        }
-
-        if (options.type) {
-            if (typeof options.type == 'string') {
-                filters.push('type=' + options.type);
-            } else {
-                for (var ti = 0; ti < options.type.length; ++ti) {
-                    filters.push('type=' + options.type[ti]);
-                }
-            }
-        }
-
-        if (options.maxbins) {
-            filters.push('maxbins=' + options.maxbins);
-        }
-
-        if (filters.length > 0) {
-            dasURI = this.dasBaseURI + 'features?' + filters.join(';');
-        } else {
-            callback([], 'No filters specified');
-        }
-    }
-
-
-    this.doCrossDomainRequest(dasURI, function(responseXML, req) {
-        if (!responseXML) {
-            var msg;
-            if (req.status == 0) {
-                msg = 'server may not support CORS';
-            } else {
-                msg = 'status=' + req.status;
-            }
-            callback([], 'Failed request: ' + msg);
-            return;
-        }
-/*      if (req) {
-            var caps = req.getResponseHeader('X-DAS-Capabilties');
-            if (caps) {
-                alert(caps);
-            }
-        } */
-
-        var features = new Array();
-        var segmentMap = {};
-
-        var segs = responseXML.getElementsByTagName('SEGMENT');
-        for (var si = 0; si < segs.length; ++si) {
-            var segmentXML = segs[si];
-            var segmentID = segmentXML.getAttribute('id');
-            segmentMap[segmentID] = {
-                min: segmentXML.getAttribute('start'),
-                max: segmentXML.getAttribute('stop')
-            };
-
-            var featureXMLs = segmentXML.getElementsByTagName('FEATURE');
-            for (var i = 0; i < featureXMLs.length; ++i) {
-                var feature = featureXMLs[i];
-                var dasFeature = new DASFeature();
-
-                dasFeature.segment = segmentID;
-                dasFeature.id = feature.getAttribute('id');
-                dasFeature.label = feature.getAttribute('label');
-
-
-/*
-                var childNodes = feature.childNodes;
-                for (var c = 0; c < childNodes.length; ++c) {
-                    var cn = childNodes[c];
-                    if (cn.nodeType == Node.ELEMENT_NODE) {
-                        var key = cn.tagName;
-                        //var val = null;
-                        //if (cn.firstChild) {
-                        //   val = cn.firstChild.nodeValue;
-                        //}
-                        dasFeature[key] = 'x';
-                    }
-                } */
-
-
-                var spos = elementValue(feature, "START");
-                var epos = elementValue(feature, "END");
-                if ((spos|0) > (epos|0)) {
-                    dasFeature.min = epos|0;
-                    dasFeature.max = spos|0;
-                } else {
-                    dasFeature.min = spos|0;
-                    dasFeature.max = epos|0;
-                }
-                {
-                    var tec = feature.getElementsByTagName('TYPE');
-                    if (tec.length > 0) {
-                        var te = tec[0];
-                        if (te.firstChild) {
-                            dasFeature.type = te.firstChild.nodeValue;
-                        }
-                        dasFeature.typeId = te.getAttribute('id');
-                        dasFeature.typeCv = te.getAttribute('cvId');
-                    }
-                }
-                dasFeature.type = elementValue(feature, "TYPE");
-                if (!dasFeature.type && dasFeature.typeId) {
-                    dasFeature.type = dasFeature.typeId; // FIXME?
-                }
-
-                dasFeature.method = elementValue(feature, "METHOD");
-                {
-                    var ori = elementValue(feature, "ORIENTATION");
-                    if (!ori) {
-                        ori = '0';
-                    }
-                    dasFeature.orientation = ori;
-                }
-                dasFeature.score = elementValue(feature, "SCORE");
-                dasFeature.links = dasLinksOf(feature);
-                dasFeature.notes = dasNotesOf(feature);
-
-                var groups = feature.getElementsByTagName("GROUP");
-                for (var gi  = 0; gi < groups.length; ++gi) {
-                    var groupXML = groups[gi];
-                    var dasGroup = new DASGroup();
-                    dasGroup.type = groupXML.getAttribute('type');
-                    dasGroup.id = groupXML.getAttribute('id');
-                    dasGroup.links = dasLinksOf(groupXML);
-                    dasGroup.notes = dasNotesOf(groupXML);
-                    if (!dasFeature.groups) {
-                        dasFeature.groups = new Array(dasGroup);
-                    } else {
-                        dasFeature.groups.push(dasGroup);
-                    }
-                }
-
-                // Magic notes.  Check with TAD before changing this.
-                if (dasFeature.notes) {
-                    for (var ni = 0; ni < dasFeature.notes.length; ++ni) {
-                        var n = dasFeature.notes[ni];
-                        if (n.indexOf('Genename=') == 0) {
-                            var gg = new DASGroup();
-                            gg.type='gene';
-                            gg.id = n.substring(9);
-                            if (!dasFeature.groups) {
-                                dasFeature.groups = new Array(gg);
-                            } else {
-                                dasFeature.groups.push(gg);
-                            }
-                        }
-                    }
-                }
-
-                {
-                    var pec = feature.getElementsByTagName('PART');
-                    if (pec.length > 0) {
-                        var parts = [];
-                        for (var pi = 0; pi < pec.length; ++pi) {
-                            parts.push(pec[pi].getAttribute('id'));
-                        }
-                        dasFeature.parts = parts;
-                    }
-                }
-                {
-                    var pec = feature.getElementsByTagName('PARENT');
-                    if (pec.length > 0) {
-                        var parents = [];
-                        for (var pi = 0; pi < pec.length; ++pi) {
-                            parents.push(pec[pi].getAttribute('id'));
-                        }
-                        dasFeature.parents = parents;
-                    }
-                }
-
-                features.push(dasFeature);
-            }
-        }
-
-        callback(features, undefined, segmentMap);
-    },
-    function (err) {
-        callback([], err);
-    });
-}
-
-function DASAlignment(type) {
-    this.type = type;
-    this.objects = {};
-    this.blocks = [];
-}
-
-DASSource.prototype.alignments = function(segment, options, callback) {
-    var dasURI = this.dasBaseURI + 'alignment?query=' + segment;
-    this.doCrossDomainRequest(dasURI, function(responseXML) {
-        if (!responseXML) {
-            callback([], 'Failed request ' + dasURI);
-            return;
-        }
-
-        var alignments = [];
-        var aliXMLs = responseXML.getElementsByTagName('alignment');
-        for (var ai = 0; ai < aliXMLs.length; ++ai) {
-            var aliXML = aliXMLs[ai];
-            var ali = new DASAlignment(aliXML.getAttribute('alignType'));
-            var objXMLs = aliXML.getElementsByTagName('alignObject');
-            for (var oi = 0; oi < objXMLs.length; ++oi) {
-                var objXML = objXMLs[oi];
-                var obj = {
-                    id:          objXML.getAttribute('intObjectId'),
-                    accession:   objXML.getAttribute('dbAccessionId'),
-                    version:     objXML.getAttribute('objectVersion'),
-                    dbSource:    objXML.getAttribute('dbSource'),
-                    dbVersion:   objXML.getAttribute('dbVersion')
-                };
-                ali.objects[obj.id] = obj;
-            }
-
-            var blockXMLs = aliXML.getElementsByTagName('block');
-            for (var bi = 0; bi < blockXMLs.length; ++bi) {
-                var blockXML = blockXMLs[bi];
-                var block = {
-                    order:      blockXML.getAttribute('blockOrder'),
-                    segments:   []
-                };
-                var segXMLs = blockXML.getElementsByTagName('segment');
-                for (var si = 0; si < segXMLs.length; ++si) {
-                    var segXML = segXMLs[si];
-                    var seg = {
-                        object:      segXML.getAttribute('intObjectId'),
-                        min:         segXML.getAttribute('start'),
-                        max:         segXML.getAttribute('end'),
-                        strand:      segXML.getAttribute('strand'),
-                        cigar:       elementValue(segXML, 'cigar')
-                    };
-                    block.segments.push(seg);
-                }
-                ali.blocks.push(block);
-            }
-
-            alignments.push(ali);
-        }
-        callback(alignments);
-    });
-}
-
-
-function DASStylesheet() {
-/*
-    this.highZoomStyles = new Object();
-    this.mediumZoomStyles = new Object();
-    this.lowZoomStyles = new Object();
-*/
-
-    this.styles = [];
-}
-
-DASStylesheet.prototype.pushStyle = function(filters, zoom, style) {
-    /*
-
-    if (!zoom) {
-        this.highZoomStyles[type] = style;
-        this.mediumZoomStyles[type] = style;
-        this.lowZoomStyles[type] = style;
-    } else if (zoom == 'high') {
-        this.highZoomStyles[type] = style;
-    } else if (zoom == 'medium') {
-        this.mediumZoomStyles[type] = style;
-    } else if (zoom == 'low') {
-        this.lowZoomStyles[type] = style;
-    }
-
-    */
-
-    if (!filters) {
-        filters = {type: 'default'};
-    }
-    var styleHolder = shallowCopy(filters);
-    if (zoom) {
-        styleHolder.zoom = zoom;
-    }
-    styleHolder.style = style;
-    this.styles.push(styleHolder);
-}
-
-function DASStyle() {
-}
-
-DASSource.prototype.stylesheet = function(successCB, failureCB) {
-    var dasURI, creds = this.credentials;
-    if (this.stylesheet_uri) {
-        dasURI = this.stylesheet_uri;
-        creds = false;
-    } else {
-        dasURI = this.dasBaseURI + 'stylesheet';
-    }
-
-    doCrossDomainRequest(dasURI, function(responseXML) {
-        if (!responseXML) {
-            if (failureCB) {
-                failureCB();
-            }
-            return;
-        }
-        var stylesheet = new DASStylesheet();
-        var typeXMLs = responseXML.getElementsByTagName('TYPE');
-        for (var i = 0; i < typeXMLs.length; ++i) {
-            var typeStyle = typeXMLs[i];
-
-            var filter = {};
-            filter.type = typeStyle.getAttribute('id'); // Am I right in thinking that this makes DASSTYLE XML invalid?  Ugh.
-            filter.label = typeStyle.getAttribute('label');
-            filter.method = typeStyle.getAttribute('method');
-            var glyphXMLs = typeStyle.getElementsByTagName('GLYPH');
-            for (var gi = 0; gi < glyphXMLs.length; ++gi) {
-                var glyphXML = glyphXMLs[gi];
-                var zoom = glyphXML.getAttribute('zoom');
-                var glyph = childElementOf(glyphXML);
-                var style = new DASStyle();
-                style.glyph = glyph.localName;
-                var child = glyph.firstChild;
-
-                while (child) {
-                    if (child.nodeType == Node.ELEMENT_NODE) {
-                        // alert(child.localName);
-                        style[child.localName] = child.firstChild.nodeValue;
-                    }
-                    child = child.nextSibling;
-                }
-                stylesheet.pushStyle(filter, zoom, style);
-            }
-        }
-        successCB(stylesheet);
-    }, creds);
-}
-
-//
-// sources command
-//
-
-function DASRegistry(uri, opts)
-{
-    opts = opts || {};
-    this.uri = uri;
-    this.opts = opts;
-}
-
-DASRegistry.prototype.sources = function(callback, failure, opts)
-{
-    if (!opts) {
-        opts = {};
-    }
-
-    var filters = [];
-    if (opts.taxon) {
-        filters.push('organism=' + opts.taxon);
-    }
-    if (opts.auth) {
-        filters.push('authority=' + opts.auth);
-    }
-    if (opts.version) {
-        filters.push('version=' + opts.version);
-    }
-    var quri = this.uri;
-    if (filters.length > 0) {
-        quri = quri + '?' + filters.join('&');   // '&' as a separator to hack around dasregistry.org bug.
-    }
-
-    doCrossDomainRequest(quri, function(responseXML) {
-        if (!responseXML && failure) {
-            failure();
-            return;
-        }
-
-        var sources = [];
-        var sourceXMLs = responseXML.getElementsByTagName('SOURCE');
-        for (var si = 0; si < sourceXMLs.length; ++si) {
-            var sourceXML = sourceXMLs[si];
-            var versionXMLs = sourceXML.getElementsByTagName('VERSION');
-            if (versionXMLs.length < 1) {
-                continue;
-            }
-            var versionXML = versionXMLs[0];
-
-            var coordXMLs = versionXML.getElementsByTagName('COORDINATES');
-            var coords = [];
-            for (var ci = 0; ci < coordXMLs.length; ++ci) {
-                var coordXML = coordXMLs[ci];
-                var coord = new DASCoords();
-                coord.auth = coordXML.getAttribute('authority');
-                coord.taxon = coordXML.getAttribute('taxid');
-                coord.version = coordXML.getAttribute('version');
-                coords.push(coord);
-            }
-
-            var caps = [];
-            var capXMLs = versionXML.getElementsByTagName('CAPABILITY');
-            var uri;
-            for (var ci = 0; ci < capXMLs.length; ++ci) {
-                var capXML = capXMLs[ci];
-
-                caps.push(capXML.getAttribute('type'));
-
-                if (capXML.getAttribute('type') == 'das1:features') {
-                    var fep = capXML.getAttribute('query_uri');
-                    uri = fep.substring(0, fep.length - ('features'.length));
-                }
-            }
-
-            var props = {};
-            var propXMLs = versionXML.getElementsByTagName('PROP');
-            for (var pi = 0; pi < propXMLs.length; ++pi) {
-                pusho(props, propXMLs[pi].getAttribute('name'), propXMLs[pi].getAttribute('value'));
-            }
-
-            if (uri) {
-                var source = new DASSource(uri, {
-                    source_uri: sourceXML.getAttribute('uri'),
-                    name:  sourceXML.getAttribute('title'),
-                    desc:  sourceXML.getAttribute('description'),
-                    coords: coords,
-                    props: props,
-                    capabilities: caps
-                });
-                sources.push(source);
-            }
-        }
-
-        callback(sources);
-    });
-}
-
-
-//
-// Utility functions
-//
-
-function elementValue(element, tag)
-{
-    var children = element.getElementsByTagName(tag);
-    if (children.length > 0 && children[0].firstChild) {
-        return children[0].firstChild.nodeValue;
-    } else {
-        return null;
-    }
-}
-
-function childElementOf(element)
-{
-    if (element.hasChildNodes()) {
-        var child = element.firstChild;
-        do {
-            if (child.nodeType == Node.ELEMENT_NODE) {
-                return child;
-            }
-            child = child.nextSibling;
-        } while (child != null);
-    }
-    return null;
-}
-
-
-function dasLinksOf(element)
-{
-    var links = new Array();
-    var maybeLinkChilden = element.getElementsByTagName('LINK');
-    for (var ci = 0; ci < maybeLinkChilden.length; ++ci) {
-        var linkXML = maybeLinkChilden[ci];
-        if (linkXML.parentNode == element) {
-            links.push(new DASLink(linkXML.firstChild ? linkXML.firstChild.nodeValue : 'Unknown', linkXML.getAttribute('href')));
-        }
-    }
-
-    return links;
-}
-
-function dasNotesOf(element)
-{
-    var notes = [];
-    var maybeNotes = element.getElementsByTagName('NOTE');
-    for (var ni = 0; ni < maybeNotes.length; ++ni) {
-        if (maybeNotes[ni].firstChild) {
-            notes.push(maybeNotes[ni].firstChild.nodeValue);
-        }
-    }
-    return notes;
-}
-
-function doCrossDomainRequest(url, handler, credentials, custAuth) {
-    // TODO: explicit error handlers?
-
-    if (window.XDomainRequest) {
-        var req = new XDomainRequest();
-        req.onload = function() {
-            var dom = new ActiveXObject("Microsoft.XMLDOM");
-            dom.async = false;
-            dom.loadXML(req.responseText);
-            handler(dom);
-        }
-        req.open("get", url);
-        req.send('');
-    } else {
-        var reqStart = Date.now();
-        var req = new XMLHttpRequest();
-
-        req.onreadystatechange = function() {
-            if (req.readyState == 4) {
-              if (req.status >= 200 || req.status == 0) {
-                  handler(req.responseXML, req);
-              }
-            }
-        };
-        req.open("get", url, true);
-        if (credentials) {
-            req.withCredentials = true;
-        }
-        if (custAuth) {
-            req.setRequestHeader('X-DAS-Authorisation', custAuth);
-        }
-        req.setRequestHeader('Accept', 'application/xml,*/*');
-        req.send('');
-    }
-}
-
-DASSource.prototype.doCrossDomainRequest = function(url, handler, errHandler) {
-    var custAuth;
-    if (this.xUser) {
-        custAuth = 'Basic ' + btoa(this.xUser + ':' + this.xPass);
-    }
-
-    try {
-        return doCrossDomainRequest(url, handler, this.credentials, custAuth);
-    } catch (err) {
-        if (errHandler) {
-            errHandler(err);
-        } else {
-            throw err;
-        }
-    }
-}