zForDevelopers – API

Please note that this page is for developers and system administrators, and likely does not contain any information relevant to users of MicrobeTrace.

This is the MicrobeTrace API (as of 2019-05). All functions are accessed through the app global (e.g. app.DFS).

In general, these are stateless functions, but there are a few exceptions. These are exceptions indicated by a *.

• ab2str(buf):
• addLink(newLink, check):
• addNode(newNode):
• align(params, callback):
• applyGHOST(ghost):
• applyHIVTrace(hivtrace):
• applySession(data, startTime):
• applyStyle(style):
• blobifySVG(svgString, width, height, callback):
• cacheLayout(contentItem) -
• capitalize(c) -
• componentCache*: {}
• computeConsensus(callback):
• computeConsensusDistances(callback)
• computeDM(callback)
• computeDegree()
• computeDirectionality(callback)
• computeLinks(subset, callback)
• computeNN(metric, callback)
• computePatristicMatrix(type, callback)
• computeTree(type, callback)
• computeTriangulation(metric, callback)
• contrastColor(hexcolor)
• createLinkColorMap()
• createNodeColorMap()
• dataSkeleton()
• decoder*: TextDecoder
• defaultLink()
• defaultNode()
• defaultWidgets*: {...}
• DFS(id)
• exportHIVTRACE()
• finishUp(oldSession)
• generateSeqs(idPrefix, count, snps, seed)
• geoDM()
• getHelp(target, callback)
• getMapData(type, callback)
• getVisibleClusters(copy)
• getVisibleLinks(copy)
• getVisibleNodes(copy)
• haversine(a, b)
• launchView(view, callback)
• loadLayout(component, parent)
• manifest*: {} - literally just a parsed copy of package.json
• mapData*: {} - caches the GeoJSON required by the Map and Globe views. Data is lazy-loaded, so this should be empty until such a view is launched.
• parseFASTA(text, callback)
• processJSON(json, extension)
• processSVG(svg)
• r01() - a mask on Math.random to help my automated security scanner chill out.
• reset()
• sessionSkeleton()
• setLinkVisibility()
• setNodeVisibility()
• str2ab(str)
• tagClusters()
• tempSkeleton()
• titleize(title)
• unparseDM(dm)
• unparseFASTA(nodes)
• unparseMEGA(nodes)
• unparseSVG(svgNode)
• updateNetwork(hideSingletons)
• updateStatistics()
• updateThresholdHistogram()
• watermark*: data-encoded string of the MicrobeTrace logo