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

[jalview.git] / src / jalview / io / AnnotationFile.java

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 2491464..d40ee1b 100755 (executable)
--- 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)
       {