Merge branch 'develop' into trialMerge

[jalview.git] / test / jalview / ws / jabaws / DisorderAnnotExportImport.java

diff --git a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
index 94a5fe0..3573f50 100644 (file)
--- a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@ -28,6 +28,8 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.gui.JvOptionPane;
 import jalview.io.AnnotationFile;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
 import jalview.ws.jws2.AADisorderClient;
@@ -80,7 +82,7 @@ public class DisorderAnnotExportImport
     assertTrue("Couldn't discover any IUPred services to use to test.",
             iupreds.size() > 0);
     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
-    af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
+    af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
   }
 
@@ -136,8 +138,8 @@ public class DisorderAnnotExportImport
   {
     try
     {
-      String aligfileout = new FormatAdapter().formatSequences("PFAM",
-              al.getSequencesArray());
+      String aligfileout = FileFormat.Pfam.getAlignmentFile().print(
+              al.getSequencesArray(), true);
       String anfileout = new AnnotationFile()
               .printAnnotationsForAlignment(al);
       assertTrue(
@@ -155,13 +157,13 @@ public class DisorderAnnotExportImport
               + "\n<<EOF\n");
 
       AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
-              FormatAdapter.PASTE, "PFAM");
+              DataSourceType.PASTE, FileFormat.Pfam);
       assertTrue(
               "Test "
                       + testname
                       + "\nregenerated annotation file did not annotate alignment.",
               new AnnotationFile().readAnnotationFile(al_new, anfileout,
-                      FormatAdapter.PASTE));
+                      DataSourceType.PASTE));
 
       // test for consistency in io
       StockholmFileTest.testAlignmentEquivalence(al, al_new, true);