Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/examples/groovy/annotationForSelectedSequence.groovy b/examples/groovy/annotationForSelectedSequence.groovy
index 851e035..7cb3082 100644 (file)
--- a/examples/groovy/annotationForSelectedSequence.groovy
+++ b/examples/groovy/annotationForSelectedSequence.groovy
@@ -1,3 +1,23 @@
+/*
+ * 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.
+ */
 // Requested by David M Garcia (v3)
 // very messy script to output the scores in annotation rows
 // for the first sequence in a selection on the topmost alignment
@@ -11,7 +31,7 @@ import java.awt.datatransfer.StringSelection
 import static java.awt.Toolkit.*
 
 
-def curviewport = Jalview.getAlignframes()[Jalview.getAlignframes().length-1].getViewport();
+def curviewport = Jalview.getCurrentAlignFrame().getViewport();
 
 // TSV output by default.
 // change "\t" to "," to output CSV file
@@ -30,9 +50,15 @@ if (curviewport.getSelectionGroup()) {
     String csv=""
     gaps.eachWithIndex{col,spos -> if (col>=selreg.getStartRes() && col<=selreg.getEndRes()) { 
       // add sequence for debugging
-      if (count>sseq.length()) { sseq+=sep+selreg.getSequenceAt(0).getCharAt(col); count=sseq.length()+1;};
+      if (count>sseq.length()) { 
+          sseq+=sep+selreg.getSequenceAt(0).getCharAt(col); count=sseq.length()+1;
+      };
       // output height of histogram
-      csv+=sep+aa.annotations[col].value; 
+      csv+=sep;
+      def annot = aa.annotations[col];
+      if (annot != null) {
+          csv+=aa.annotations[col].value; 
+      }
       // Uncomment to output string shown in tooltip
       // csv+=sep+aa.annotations[col].description; 
     }}