JAL-1740 implemented auto-update of BioJsMSA, introduced FTP client for downloading...

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

diff --git a/examples/groovy/annotationForSelectedSequence.groovy b/examples/groovy/annotationForSelectedSequence.groovy
index 851e035..c9e8563 100644 (file)
--- a/examples/groovy/annotationForSelectedSequence.groovy
+++ b/examples/groovy/annotationForSelectedSequence.groovy
@@ -11,7 +11,7 @@ import java.awt.datatransfer.StringSelection
 import static java.awt.Toolkit.*
 
 
-def curviewport = Jalview.getAlignframes()[Jalview.getAlignframes().length-1].getViewport();
+def curviewport = Jalview.getAlignFrames()[Jalview.getAlignFrames().length-1].getViewport();
 
 // TSV output by default.
 // change "\t" to "," to output CSV file
@@ -30,9 +30,15 @@ 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; 
     }}