Merge branch 'develop' into features/filetypeEnum

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 68245b6..35d4685 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -36,6 +36,8 @@ import jalview.datamodel.StructureViewerModel;
 import jalview.datamodel.StructureViewerModel.StructureData;
 import jalview.ext.varna.RnaModel;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
 import jalview.schemabinding.version2.AlcodMap;
 import jalview.schemabinding.version2.AlcodonFrame;
 import jalview.schemabinding.version2.Annotation;
@@ -974,14 +976,14 @@ public class Jalview2XML
           if (entry.getProperty() != null && !entry.getProperty().isEmpty())
           {
             PdbentryItem item = new PdbentryItem();
-            Hashtable properties = entry.getProperty();
-            Enumeration en2 = properties.keys();
+            Hashtable<String, String> properties = entry.getProperty();
+            Enumeration<String> en2 = properties.keys();
             while (en2.hasMoreElements())
             {
               Property prop = new Property();
-              String key = en2.nextElement().toString();
+              String key = en2.nextElement();
               prop.setName(key);
-              prop.setValue(properties.get(key).toString());
+              prop.setValue(properties.get(key));
               item.addProperty(prop);
             }
             pdb.addPdbentryItem(item);
@@ -4144,8 +4146,7 @@ public class Jalview2XML
       StructureData filedat = oldFiles.get(id);
       String pdbFile = filedat.getFilePath();
       SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
-      binding.getSsm().setMapping(seq, null, pdbFile,
-              jalview.io.AppletFormatAdapter.FILE);
+      binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE);
       binding.addSequenceForStructFile(pdbFile, seq);
     }
     // and add the AlignmentPanel's reference to the view panel
@@ -4260,7 +4261,7 @@ public class Jalview2XML
     af = new AlignFrame(al, view.getWidth(), view.getHeight(),
             uniqueSeqSetId, viewId);
 
-    af.setFileName(file, "Jalview");
+    af.setFileName(file, FileFormat.Jalview);
 
     for (int i = 0; i < JSEQ.length; i++)
     {