import jalview.util.ColorUtils
import jalview.datamodel.SequenceFeature
import jalview.schemes.FeatureColour
import jalview.analysis.Finder

def af = jalview.bin.Jalview.currentAlignFrame
def av = af.viewport
def fr = af.featureRenderer
def finder = new Finder(av)

new File("/Users/gmcarstairs/Documents/temp/motifs.txt").eachLine 
{
  line -> 
   if (!line.startsWith('#'))
   {
    tokens = line.split("\\t")
    motif = tokens[0]
    featureName = tokens[1]
    featureColour = ColorUtils.parseColourString(tokens[2])
    featureScore = (tokens.length < 4 ? 0 : Float.parseFloat(tokens[3]))
    fr.setColour(featureName, new FeatureColour(featureColour))
    finder.findAll(motif, false, false)
    matches = finder.searchResults.results
    matches.each 
    {
        sf = new SequenceFeature(featureName, motif, it.start, it.end, featureScore, null)
        it.sequence.addSequenceFeature(sf)
    }
  }
}
av.setShowSequenceFeatures(true)
af.alignPanel.paintAlignment(false, false)