File Parsing returns Alignments, not Sequence[]

[jalview.git] / src / jalview / io / FileLoader.java

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index c662ccf..34e5886 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -133,7 +133,7 @@ public class FileLoader implements Runnable
         if (Desktop.instance != null)\r
           Desktop.instance.startLoading(file);\r
 \r
-        SequenceI[] sequences = null;\r
+        Alignment al = null;\r
 \r
         if (format.equalsIgnoreCase("Jalview"))\r
         {\r
@@ -147,7 +147,7 @@ public class FileLoader implements Runnable
           {\r
             try\r
             {\r
-              sequences = new FormatAdapter().readFile(file, protocol, format);\r
+              al = new FormatAdapter().readFile(file, protocol, format);\r
             }\r
             catch (java.io.IOException ex)\r
             {\r
@@ -155,13 +155,13 @@ public class FileLoader implements Runnable
             }\r
           }\r
 \r
-          if ( (sequences != null) && (sequences.length > 0))\r
+          if ( (al != null) && (al.getHeight() > 0))\r
           {\r
             if (viewport != null)\r
             {\r
-              for (int i = 0; i < sequences.length; i++)\r
+              for (int i = 0; i < al.getHeight(); i++)\r
               {\r
-                viewport.getAlignment().addSequence(sequences[i]);\r
+                viewport.getAlignment().addSequence(al.getSequenceAt(i));\r
               }\r
               viewport.firePropertyChange("alignment", null,\r
                                           viewport.getAlignment().getSequences());\r
@@ -169,8 +169,6 @@ public class FileLoader implements Runnable
             }\r
             else\r
             {\r
-              Alignment al = new Alignment(sequences);\r
-\r
               alignFrame = new AlignFrame(al,\r
                                            AlignFrame.DEFAULT_WIDTH,\r
                                            AlignFrame.DEFAULT_HEIGHT);\r