X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fgroovy%2FfeaturesCounter.html;fp=help%2Fhtml%2Fgroovy%2FfeaturesCounter.html;h=3b6705b31b1a9a72628df6e8a556057abd820518;hb=9f70ff4b6d193b340031997634c9e3602486bc8e;hp=0000000000000000000000000000000000000000;hpb=76844c43faeeeba369deaf42f1998ca0fb33d956;p=jalview.git diff --git a/help/html/groovy/featuresCounter.html b/help/html/groovy/featuresCounter.html new file mode 100644 index 0000000..3b6705b --- /dev/null +++ b/help/html/groovy/featuresCounter.html @@ -0,0 +1,123 @@ + + + +Extending Jalview with Groovy - Feature Counter Example + + +

+ Extending Jalview with Groovy - A customisable + feature counter

The groovy script below shows how to + add a new calculation track to a Jalview alignment window. +

+

As currently written, it will add two tracks to a protein + alignment view which count Pfam features in each column, and ones + where a charge residue also occur.

+

To try it for yourself:

+
    +
  1. Copy and paste it into the groovy script console
    2. +
  2. Load the example Feredoxin project (the one that opens by + default when you first launched Jalview)
    3. +
  3. Select Calculations→Execute Groovy + Script from the alignment window's menu bar to run the script on + the current view. +
    4. +
+ Please note: The 2.10.2 feature counting interface is not compatible with earlier versions.

+ http://www.jalview.org/examples/groovy/featuresCounter.groovy + - rendered with hilite.me + 
/*
+ * 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.AlignmentAnnotationFactory;
+import jalview.workers.FeatureSetCounterI;
+
+/*
+ * 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.
+ * 
+ * Note: The feature api provided by 2.10.2 is not compatible with scripts
+ * that worked with earlier Jalview versions. Apologies for the inconvenience.
+ */
+ 
+def annotator = 
+    [
+     getNames: { ['Phosphorylation', 'Turn'] as String[] }, 
+     getDescriptions:  { ['Count of Phosphorylation features', 'Count of Turn features'] as String[] },
+     getMinColour: { [0, 255, 255] as int[] }, // cyan
+     getMaxColour: { [0, 0, 255] as int[] }, // blue
+     count: 
+         { res, feats -> 
+                int phos
+                int turn
+                for (sf in feats)
+                {
+ 		          /*
+		           * 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
+		           */
+		           if (sf.type.contains('TURN'))
+                   {
+                      turn++
+                   }
+                   if (sf.type.contains('PHOSPHORYLATION'))
+                   {
+                      phos++
+                   }
+                }
+                [phos, turn] as int[]
+         }
+     ] as FeatureSetCounterI
+    
+/*
+ * Register the annotation calculator with Jalview
+ */
+AlignmentAnnotationFactory.newCalculator(annotator) 
+
+ +