JAL-1919 set default structure file format to mmCIF, refactored some StructureImportS...

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 1a639f1..fca7263 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;
@@ -280,10 +280,12 @@ public class AppletFormatAdapter
       {
         // TODO obtain config value from preference settings.
         // Set value to 'true' to test PDB processing with Jmol: JAL-1213
-        boolean isParseWithJMOL = false;
+        boolean isParseWithJMOL = StructureImportSettings
+                .getDefaultPDBFileParser().equalsIgnoreCase(
+                        StructureImportSettings.JMOL_PARSER);
         if (isParseWithJMOL)
         {
-          StructureViewSettings.addSettings(annotFromStructure,
+          StructureImportSettings.addSettings(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct);
           alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
@@ -291,18 +293,22 @@ public class AppletFormatAdapter
         }
         else
         {
-          StructureViewSettings.setShowSeqFeatures(true);
+          StructureImportSettings.addSettings(annotFromStructure,
+                  localSecondaryStruct, serviceSecondaryStruct);
+          StructureImportSettings.setShowSeqFeatures(true);
           alignFile = new MCview.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
                   type);
         }
+        ((StructureFile) alignFile).setDbRefType(format);
       }
       else if (format.equals("mmCIF"))
       {
-        StructureViewSettings.addSettings(annotFromStructure,
+        StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
         alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct, inFile, type);
+        ((StructureFile) alignFile).setDbRefType(format);
       }
       else if (format.equals("STH"))
       {
@@ -433,24 +439,28 @@ 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);
         }
+        ((StructureFile) alignFile)
+                .setDbRefType(StructureImportSettings.PDB);
       }
       else if (format.equals("mmCIF"))
       {
-        StructureViewSettings.addSettings(annotFromStructure,
+        StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
         alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct, source);
+        ((StructureFile) alignFile)
+                .setDbRefType(StructureImportSettings.MMCIF);
       }
       else if (format.equals("STH"))
       {