X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FMappingUtilsTest.java;h=6780af7b8c3b42ae51c45fbfa967d2c636f36e30;hb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;hp=6d046617f97dc42de62ff67e7b4fa8ccee465fa9;hpb=3e29fb36af9c48e07837e32b7e99c081b2461b2f;p=jalview.git

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 6d04661..6780af7 100644
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -39,7 +39,9 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignViewport;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 
 import java.awt.Color;
@@ -197,10 +199,10 @@ public class MappingUtilsTest
      * viewport).
      */
     AlignmentI cdna = loadAlignment(">Seq1\nACG\n>Seq2\nTGA\n>Seq3\nTAC\n",
-            "FASTA");
+            FileFormat.Fasta);
     cdna.setDataset(null);
     AlignmentI protein = loadAlignment(">Seq1\nK\n>Seq2\nL\n>Seq3\nQ\n",
-            "FASTA");
+            FileFormat.Fasta);
     protein.setDataset(null);
     AlignedCodonFrame acf = new AlignedCodonFrame();
     MapList map = new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 3, 1);
@@ -268,11 +270,11 @@ public class MappingUtilsTest
    * @return
    * @throws IOException
    */
-  protected AlignmentI loadAlignment(final String data, String format)
+  protected AlignmentI loadAlignment(final String data, FileFormatI format)
           throws IOException
   {
     AlignmentI a = new FormatAdapter().readFile(data,
-            AppletFormatAdapter.PASTE, format);
+            DataSourceType.PASTE, format);
     a.setDataset(null);
     return a;
   }
@@ -351,11 +353,11 @@ public class MappingUtilsTest
      */
     AlignmentI cdna = loadAlignment(">Seq1/10-18\nAC-GctGtC-T\n"
             + ">Seq2/20-27\nTc-GA-G-T-Tc\n" + ">Seq3/30-38\nTtTT-AaCGg-\n",
-            "FASTA");
+            FileFormat.Fasta);
     cdna.setDataset(null);
     AlignmentI protein = loadAlignment(
             ">Seq1/40-41\n-K-P\n>Seq2/50-51\nL--Q\n>Seq3/60-61\nG--S\n",
-            "FASTA");
+            FileFormat.Fasta);
     protein.setDataset(null);
 
     // map first dna to first protein seq
@@ -466,10 +468,11 @@ public class MappingUtilsTest
      * viewport).
      */
     AlignmentI cdna = loadAlignment(
-            ">Seq1\nACGGCA\n>Seq2\nTGACAG\n>Seq3\nTACGTA\n", "FASTA");
+            ">Seq1\nACGGCA\n>Seq2\nTGACAG\n>Seq3\nTACGTA\n",
+            FileFormat.Fasta);
     cdna.setDataset(null);
     AlignmentI protein = loadAlignment(">Seq1\nKA\n>Seq2\nLQ\n>Seq3\nQV\n",
-            "FASTA");
+            FileFormat.Fasta);
     protein.setDataset(null);
     AlignedCodonFrame acf = new AlignedCodonFrame();
     MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
@@ -549,10 +552,10 @@ public class MappingUtilsTest
      */
     AlignmentI cdna = loadAlignment(
             ">Seq1\nA-CG-GC--AT-CA\n>Seq2\n-TG-AC-AG-T-AT\n>Seq3\n-T--ACG-TAAT-G\n",
-            "FASTA");
+            FileFormat.Fasta);
     cdna.setDataset(null);
     AlignmentI protein = loadAlignment(
-            ">Seq1\n-KA-S\n>Seq2\n--L-QY\n>Seq3\nQ-V-M\n", "FASTA");
+            ">Seq1\n-KA-S\n>Seq2\n--L-QY\n>Seq3\nQ-V-M\n", FileFormat.Fasta);
     protein.setDataset(null);
     AlignedCodonFrame acf = new AlignedCodonFrame();
     MapList map = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3, 1);