File Parsing returns Alignments, not Sequence[]

[jalview.git] / src / jalview / jbgui / GFinder.java

diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index 3cbef12..016e9d1 100755 (executable)
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -23,7 +23,7 @@ import java.awt.event.*;
 import javax.swing.*;\r
 import javax.swing.event.*;\r
 import jalview.io.FormatAdapter;\r
-import jalview.datamodel.SequenceI;\r
+import jalview.datamodel.Alignment;;\r
 import java.awt.BorderLayout;\r
 \r
 public class GFinder\r
@@ -163,14 +163,14 @@ public class GFinder
         public void run()\r
         {\r
           String str = textfield.getText();\r
-          SequenceI[] sequences = null;\r
-          try{sequences = new FormatAdapter().readFile(str, "Paste", "FASTA");}\r
+          Alignment al = null;\r
+          try{al = new FormatAdapter().readFile(str, "Paste", "FASTA");}\r
           catch(Exception ex){}\r
-          if(sequences!=null && sequences.length>0)\r
+          if(al!=null && al.getHeight()>0)\r
           {\r
             str = jalview.analysis.AlignSeq.extractGaps(\r
                 jalview.util.Comparison.GapChars,\r
-                sequences[0].getSequenceAsString());\r
+                al.getSequenceAt(0).getSequenceAsString());\r
 \r
             textfield.setText(str);\r
           }\r