X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fws%2Febi%2FHmmerJSONProcessTest.java;h=bf68906540ab320493be5d4c020d192007c89356;hb=8dcca4766ed3d696a6160565ef43e21662557008;hp=291a5a32395256030c5110653a79b30d587c5b04;hpb=a012c2cde7ad7dbc155b17415227e163c5f20882;p=jalview.git

diff --git a/test/jalview/ws/ebi/HmmerJSONProcessTest.java b/test/jalview/ws/ebi/HmmerJSONProcessTest.java
index 291a5a3..bf68906 100644
--- a/test/jalview/ws/ebi/HmmerJSONProcessTest.java
+++ b/test/jalview/ws/ebi/HmmerJSONProcessTest.java
@@ -3,6 +3,8 @@ package jalview.ws.ebi;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
 import jalview.io.FileParse;
 import jalview.io.FormatAdapter;
 
@@ -20,8 +22,8 @@ public class HmmerJSONProcessTest {
   private AlignmentI getSearchResultFragmentAlignment() throws Exception
   {
     AlignmentI alf = new FormatAdapter().readFile(
-            alignmentFragFile.getAbsolutePath(), FormatAdapter.FILE,
-            "FASTA");
+            alignmentFragFile.getAbsolutePath(), DataSourceType.FILE,
+            FileFormat.Fasta);
 
     return alf;
   }
@@ -32,8 +34,8 @@ public class HmmerJSONProcessTest {
   private AlignmentI getSearchResultAlignment() throws Exception
   {
     AlignmentI alf = new FormatAdapter().readFile(
-            alignmentResultFile.getAbsolutePath(), FormatAdapter.FILE,
-            "FASTA");
+            alignmentResultFile.getAbsolutePath(), DataSourceType.FILE,
+            FileFormat.Fasta);
 
     return alf;
   }
@@ -52,7 +54,7 @@ public class HmmerJSONProcessTest {
     JSONParser jp = new JSONParser();
     // read JSON in same way - via fileparse
     Object hitfragment = jp.parse(new FileParse(hitTestFile,
-            FormatAdapter.FILE).getReader());
+            DataSourceType.FILE).getReader());
     Assert.assertTrue((hitfragment instanceof JSONObject),
             "Didn't find a JSON object map in " + hitTestFile);
     AlignmentI searchResult = getSearchResultFragmentAlignment();
@@ -79,7 +81,7 @@ public class HmmerJSONProcessTest {
             "Didn't read search result alignment from " + alignmentFragFile);
 
     HmmerJSONProcessor hjsp = new HmmerJSONProcessor(searchResult);
-    hjsp.parseFrom(new FileParse(hmmerResultFile, FormatAdapter.FILE));
+    hjsp.parseFrom(new FileParse(hmmerResultFile, DataSourceType.FILE));
     AlignmentAnnotation[] aa = searchResult.getSequenceAt(5)
             .getAnnotation();
     Assert.assertNotNull(aa);
@@ -112,7 +114,9 @@ public class HmmerJSONProcessTest {
   }
   // Groovy test
   // def al = Jalview.getAlignFrames()[0].getViewport().getAlignment()
-  // new jalview.ws.ebi.HmmerJSONProcessor(al).parseFrom(new
+  // def jproc = new jalview.ws.ebi.HmmerJSONProcessor(al)
+  // jproc.parseFrom(new
   // jalview.io.FileParse("examples/testdata/hmmer3/hmmeresult.json.gz","File"))
+  // jproc.updateView(Jalview.getAlignFrames()[0].getViewport())
 
 }