Merge branch 'develop' into features/JAL-250_hideredundantseqs

[jalview.git] / examples / groovy / multipleFeatureAnnotations.groovy

diff --git a/examples/groovy/multipleFeatureAnnotations.groovy b/examples/groovy/multipleFeatureAnnotations.groovy
deleted file mode 100644 (file)
index 592c7f5..0000000
--- a/examples/groovy/multipleFeatureAnnotations.groovy
+++ /dev/null
@@ -1,110 +0,0 @@
-import jalview.workers.AlignmentAnnotationFactory;
-import jalview.workers.AnnotationProviderI;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.util.ColorUtils;
-import jalview.util.Comparison;
-import java.awt.Color;
-
-/*
- * Example script to compute two alignment annotations
- * - count of Phosphorylation features
- * - count of Turn features
- * To try this, first load example file uniref50.fa and load on features file
- * exampleFeatures.txt, before running this script
- *
- * The script only needs to be run once - it will be registered by Jalview
- * and recalculated automatically when the alignment changes.
- */
-
-/*
- * A closure that returns true if value includes "PHOSPHORYLATION"
- */
-def phosCounter = { type ->    type.contains("PHOSPHORYLATION") }
-
-/*
- * A closure that returns true if value includes "TURN"
- */
-def turnCounter = { type ->    type.contains("TURN") }
-
-/*
- * A closure that computes and returns an array of Annotation values,
- * one for each column of the alignment
- */
-def getAnnotations(al, fr, counter) 
-{
-    def width = al.width
-    def counts = new int[width] 
-    def max = 0
-    
-    /*
-     * count features in each column, record the maximum value
-     */
-    for (col = 0 ; col < width ; col++)
-    {
-        def count = 0
-        for (row = 0 ; row < al.height ; row++)
-        {
-            seq = al.getSequenceAt(row)
-            if (seq != null && col < seq.getLength())
-            {
-                def res = seq.getCharAt(col)
-                if (!Comparison.isGap(res))
-                {
-                    pos = seq.findPosition(col)
-                    features = fr.findFeaturesAtRes(seq, pos)
-                    for (feature in features)
-                    {
-                        if (counter.call(feature.type))
-                        {
-                            count++
-                        }
-                    }
-                }
-            }
-        }
-        counts[col] = count
-        if (count > max)
-        {
-            max = count
-        }
-    }
-    
-    /*
-     * make the Annotation objects, with a graduated colour scale 
-     * (from min value to max value) for the histogram bars 
-     */
-    def zero = '0' as char
-    def anns = new Annotation[width] 
-    for (col = 0 ; col < width ; col++)
-    {
-        def c = counts[col]
-        if (c > 0)
-        {
-            Color color = ColorUtils.getGraduatedColour(c, 0, Color.cyan,
-                max, Color.blue)
-            anns[col] = AlignmentAnnotationFactory.newAnnotation(String.valueOf(c),
-                String.valueOf(c), zero, c, color)
-        }
-    }
-    anns
-}
-
-/*
- * Define the method that performs the calculations, and builds two
- * AlignmentAnnotation objects
- */
-def annotator = 
-    [ calculateAnnotation: { al, fr ->
-        def phosAnns = getAnnotations(al, fr, phosCounter)
-        def ann1 = AlignmentAnnotationFactory.newAlignmentAnnotation("Phosphorylation", "Count of Phosphorylation features", phosAnns)
-        def turnAnns = getAnnotations(al, fr, turnCounter)
-        def ann2 = AlignmentAnnotationFactory.newAlignmentAnnotation("Turn", "Count of Turn features", turnAnns)
-        return [ann1, ann2]
-      } 
-    ] as AnnotationProviderI
-    
-/*
- * Register the annotation calculator with Jalview
- */
-AlignmentAnnotationFactory.newCalculator(annotator)