JAL-1919 Fixed failing tests, enabled HETATM processing from structure file to be...

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 42a8ead..fb414f4 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -26,7 +26,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
 import jalview.util.MessageManager;
 
 import java.io.File;
@@ -280,11 +280,11 @@ public class AppletFormatAdapter
       {
         // TODO obtain config value from preference settings.
         // Set value to 'true' to test PDB processing with Jmol: JAL-1213
-        boolean isParseWithJMOL = !StructureViewSettings
+        boolean isParseWithJMOL = !StructureImportSettings
                 .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
         if (isParseWithJMOL)
         {
-          StructureViewSettings.addSettings(annotFromStructure,
+          StructureImportSettings.addSettings(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct);
           alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
@@ -292,9 +292,9 @@ public class AppletFormatAdapter
         }
         else
         {
-          StructureViewSettings.addSettings(annotFromStructure,
+          StructureImportSettings.addSettings(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct);
-          StructureViewSettings.setShowSeqFeatures(true);
+          StructureImportSettings.setShowSeqFeatures(true);
           alignFile = new MCview.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
                   type);
@@ -302,7 +302,7 @@ public class AppletFormatAdapter
       }
       else if (format.equals("mmCIF"))
       {
-        StructureViewSettings.addSettings(annotFromStructure,
+        StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
         alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct, inFile, type);
@@ -436,21 +436,21 @@ public class AppletFormatAdapter
         boolean isParseWithJMOL = false;
         if (isParseWithJMOL)
         {
-          StructureViewSettings.addSettings(annotFromStructure,
+          StructureImportSettings.addSettings(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct);
           alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, source);
         }
         else
         {
-          StructureViewSettings.setShowSeqFeatures(true);
+          StructureImportSettings.setShowSeqFeatures(true);
           alignFile = new MCview.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, source);
         }
       }
       else if (format.equals("mmCIF"))
       {
-        StructureViewSettings.addSettings(annotFromStructure,
+        StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
         alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct, source);