JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/examples/groovy/visibleFeaturesCounter.groovy b/examples/groovy/visibleFeaturesCounter.groovy
deleted file mode 100644 (file)
index b3180f8..0000000
--- a/examples/groovy/visibleFeaturesCounter.groovy
+++ /dev/null
@@ -1,89 +0,0 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- * 
- * This file is part of Jalview.
- * 
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *  
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License
- * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-import jalview.bin.Jalview
-import jalview.workers.FeatureSetCounterI
-import jalview.workers.AlignmentAnnotationFactory
-
-/*
- * Demonstration of FeatureSetCounterI
- * compute annotation tracks counting number of displayed 
- * features of each type in each column
- */
-
-/*
- * discover features on the current view
- */
- 
-def featuresDisp=Jalview.currentAlignFrame.currentView.featuresDisplayed
-if (featuresDisp == null) {
-    print 'Need at least one feature visible on alignment'
-}
-def visibleFeatures=featuresDisp.visibleFeatures.toList()
-assert 'java.util.ArrayList' == visibleFeatures.class.name
-
-/*
- * A closure that returns an array of features present 
- * for each feature type in visibleFeatures
- * Argument 'features' will be a list of SequenceFeature 
- */
-def getCounts = 
-    { features -> 
-        int[] obs = new int[visibleFeatures.size]
-        for (sf in features)
-        {
-            /*
-             * Here we inspect the type of the sequence feature.
-             * You can also test sf.description, sf.score, sf.featureGroup,
-             * sf.strand, sf.phase, sf.begin, sf.end
-             * or sf.getValue(attributeName) for GFF 'column 9' properties
-             */
-            int pos = 0
-            for (type in visibleFeatures) 
-            {
-              if (type.equals(sf.type)) 
-              {
-                  obs[pos]++
-              }
-              pos++
-            }
-        }
-        obs
-}
-  
-/*
- * Define something that counts each visible feature type
- */
-def columnSetCounter =
-    [
-     getNames: { visibleFeatures as String[] }, 
-     getDescriptions:  { visibleFeatures as String[] },
-     getMinColour: { [0, 255, 255] as int[] }, // cyan
-     getMaxColour: { [0, 0, 255] as int[] }, // blue
-     count: 
-         { res, feats -> 
-             getCounts.call(feats) 
-         }
-     ] as FeatureSetCounterI
-
-/*
- * and register the counter
- */
-AlignmentAnnotationFactory.newCalculator(columnSetCounter)