JAL-2228 removed FeatureCounterI in favour of FeatureSetCounterI with

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

diff --git a/examples/groovy/FeatureSetCounter.groovy b/examples/groovy/FeatureSetCounter.groovy
deleted file mode 100644 (file)
index 43f44a4..0000000
--- a/examples/groovy/FeatureSetCounter.groovy
+++ /dev/null
@@ -1,84 +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.workers.FeatureSetCounterI;
-import jalview.workers.AlignmentAnnotationFactory;
-
-/*
- * Demonstration of FeatureSetWorker 
- * compute annotation tracks counting number of displayed 
- * features of each type in each column
- */
-
-/*
- * discover features on the current view
- */
- 
-def featuresVis=jalview.bin.Jalview.currentAlignFrame.getCurrentView().getFeaturesDisplayed().getVisibleFeatures().toList();
-assert 'java.util.ArrayList' == featuresVis.class.name
-
-/*
- * A closure that returns a vector for featuresVis of 1 or 0 for any features of type observed
- * Argument should be a list of SequenceFeature 
- */
-def hasType = { features -> 
-                int[] obs=new int[featuresVis.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 featuresVis) {
-                      if (type.equals(sf.type)) {
-                      obs[pos]=1;
-                      } else {
-                      obs[pos]=0;
-                      }
-                      pos++;
-                    }
-                }
-                obs;
-              }
-  
-/*
- * Closure to generate a counter for feature types in featuresVis 
- * calls hasType to count types in the int[] count(String res, List<SequenceFeature> feats) method  
- */
-def getColumnSetCounter = { 
-    [
-     getNames: { featuresVis as String[] }, 
-     getDescriptions:  { featuresVis as String[] },
-     getMinColour: { [0, 255, 255] }, // cyan
-     getMaxColour: { [0, 0, 255] }, // blue
-     count: 
-         { res, feats -> 
-             hasType.call(feats) 
-         }
-     ] as FeatureSetCounterI }
-
-/*
- * and register a FeatuerSetCounter instance
- */
-AlignmentAnnotationFactory.newCalculator(getColumnSetCounter.call())