Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/examples/groovy/visibleFeaturesCounter.groovy b/examples/groovy/visibleFeaturesCounter.groovy
index b3180f8..510f600 100644 (file)
--- a/examples/groovy/visibleFeaturesCounter.groovy
+++ b/examples/groovy/visibleFeaturesCounter.groovy
@@ -1,38 +1,37 @@
 /*
  * 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 
+ * 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 
+ *
+ * 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 
+ * 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
+
+def featuresDisp=Jalview.getCurrentAlignFrame().currentView.featuresDisplayed
 if (featuresDisp == null) {
     print 'Need at least one feature visible on alignment'
 }
@@ -40,12 +39,12 @@ def visibleFeatures=featuresDisp.visibleFeatures.toList()
 assert 'java.util.ArrayList' == visibleFeatures.class.name
 
 /*
- * A closure that returns an array of features present 
+ * A closure that returns an array of features present
  * for each feature type in visibleFeatures
- * Argument 'features' will be a list of SequenceFeature 
+ * Argument 'features' will be a list of SequenceFeature
  */
-def getCounts = 
-    { features -> 
+def getCounts =
+    { features ->
         int[] obs = new int[visibleFeatures.size]
         for (sf in features)
         {
@@ -56,9 +55,9 @@ def getCounts =
              * or sf.getValue(attributeName) for GFF 'column 9' properties
              */
             int pos = 0
-            for (type in visibleFeatures) 
+            for (type in visibleFeatures)
             {
-              if (type.equals(sf.type)) 
+              if (type.equals(sf.type))
               {
                   obs[pos]++
               }
@@ -67,19 +66,19 @@ def getCounts =
         }
         obs
 }
-  
+
 /*
  * Define something that counts each visible feature type
  */
 def columnSetCounter =
     [
-     getNames: { visibleFeatures as String[] }, 
+     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) 
+     count:
+         { res, feats ->
+             getCounts.call(feats)
          }
      ] as FeatureSetCounterI