Merge branch 'develop' into trialMerge

[jalview.git] / test / jalview / analysis / DnaTest.java

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index 4c12905..cd5d3ca 100644 (file)
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -33,6 +33,8 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 
 import java.io.IOException;
@@ -129,8 +131,8 @@ public class DnaTest
           throws IOException
   {
     AlignmentI alf = new FormatAdapter().readFile(
-            JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
-            "FASTA");
+            JAL_1312_example_align_fasta, DataSourceType.PASTE,
+            FileFormat.Fasta);
     ColumnSelection cs = new ColumnSelection();
     AlignViewportI av = new AlignViewport(alf, cs);
     Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
@@ -150,8 +152,8 @@ public class DnaTest
           throws IOException
   {
     AlignmentI alf = new FormatAdapter().readFile(
-            JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
-            "FASTA");
+            JAL_1312_example_align_fasta, DataSourceType.PASTE,
+            FileFormat.Fasta);
     int vwidth = 15;
     for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
     {
@@ -185,7 +187,7 @@ public class DnaTest
   public void testTranslateCdna_simple() throws IOException
   {
     AlignmentI alf = new FormatAdapter().readFile(fasta,
-            FormatAdapter.PASTE, "FASTA");
+            DataSourceType.PASTE, FileFormat.Fasta);
     ColumnSelection cs = new ColumnSelection();
     AlignViewportI av = new AlignViewport(alf, cs);
     Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
@@ -205,8 +207,8 @@ public class DnaTest
   public void testTranslateCdna_hiddenColumns() throws IOException
   {
     AlignmentI alf = new FormatAdapter().readFile(fasta,
-            FormatAdapter.PASTE, "FASTA");
-    ColumnSelection cs = new jalview.datamodel.ColumnSelection();
+            DataSourceType.PASTE, FileFormat.Fasta);
+    ColumnSelection cs = new ColumnSelection();
     cs.hideColumns(6, 14); // hide codons 3/4/5
     cs.hideColumns(24, 35); // hide codons 9-12
     cs.hideColumns(177, 191); // hide codons 60-64