From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 8 Feb 2017 15:01:21 +0000 (+0000)
Subject: JAL-2136 update merged code for JAL-2040 for new FileFormat/Protocol interface (JAL... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Freviews%2Ffeatures%2FJAL-2136_phyre2_integration_withJims;p=jalview.git

JAL-2136 update merged code for JAL-2040 for new FileFormat/Protocol interface (JAL-2344)

---

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 2491464..d40ee1b 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1262,7 +1262,8 @@ public class AnnotationFile
   private boolean add_structmodel(AlignmentI al, SequenceI refSeq2, String tempId,
           String urlToModel, String urlToPairwise)
   {
-    String warningMessage = null, modelPath = null, modelProt = null, aliPath = null, aliProt = null;
+    String warningMessage = null, modelPath = null, aliPath = null;
+    DataSourceType modelProt = null, aliProt = null;
     boolean added = false;
     try {
       // locate tempId. if it exists, will need to merge, otherwise:
@@ -1278,7 +1279,7 @@ public class AnnotationFile
       aliProt = AppletFormatAdapter.checkProtocol(aliPath);
       // 2. load urlToPairwise
       AlignmentI pwa = new AppletFormatAdapter().readFile(aliPath, aliProt,
-              "FASTA");
+              FileFormat.Fasta);
       SequenceI qPw = null, tPw = null;
       if (pwa != null)
       {
diff --git a/test/jalview/io/ImportHomologyModelTest.java b/test/jalview/io/ImportHomologyModelTest.java
index 292a34d..8827c9c 100644
--- a/test/jalview/io/ImportHomologyModelTest.java
+++ b/test/jalview/io/ImportHomologyModelTest.java
@@ -62,10 +62,11 @@ public class ImportHomologyModelTest
             Boolean.TRUE.toString());
     FileLoader loader = new FileLoader(false);
     af = loader.LoadFileWaitTillLoaded(profile_msa,
-            FormatAdapter.FILE);
+            jalview.io.DataSourceType.FILE);
     Desktop.addInternalFrame(af, "homology models", 800, 500);
     al = af.getViewport().getAlignment();
-    af.loadJalviewDataFile(profile_annot, FormatAdapter.FILE, null, null);
+    af.loadJalviewDataFile(profile_annot, jalview.io.DataSourceType.FILE,
+            null, null);
     // if file was loaded, the view should have a reference sequence set
     Assert.assertTrue(al.hasSeqrep());
   }