X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fgroovy%2FfeaturesCounter.html;fp=help%2Fhtml%2Fgroovy%2FfeaturesCounter.html;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=3b6705b31b1a9a72628df6e8a556057abd820518;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/help/html/groovy/featuresCounter.html b/help/html/groovy/featuresCounter.html deleted file mode 100644 index 3b6705b..0000000 --- a/help/html/groovy/featuresCounter.html +++ /dev/null @@ -1,123 +0,0 @@ - - - -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) 
-
- -