Merge branch 'develop' into features/filetypeEnum

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

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index bca365f..a7113f6 100644 (file)
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -1,5 +1,6 @@
 package jalview.io;
 
+import jalview.datamodel.PDBEntry;
 import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
 
@@ -334,13 +335,13 @@ public enum FileFormat implements FileFormatI
     {
       // TODO obtain config value from preference settings.
       // Set value to 'true' to test PDB processing with Jmol: JAL-1213
-      boolean isParseWithJMOL = !StructureImportSettings
-              .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
+      boolean isParseWithJMOL = StructureImportSettings
+              .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
       if (isParseWithJMOL)
       {
         return new JmolParser(
                 StructureImportSettings.isVisibleChainAnnotation(),
-                StructureImportSettings.isPredictSecondaryStructure(),
+                StructureImportSettings.isProcessSecondaryStructure(),
                 StructureImportSettings.isExternalSecondaryStructure(),
                 inFile,
                 sourceType);
@@ -350,7 +351,7 @@ public enum FileFormat implements FileFormatI
         StructureImportSettings.setShowSeqFeatures(true);
         return new MCview.PDBfile(
                 StructureImportSettings.isVisibleChainAnnotation(),
-                StructureImportSettings.isPredictSecondaryStructure(),
+                StructureImportSettings.isProcessSecondaryStructure(),
                 StructureImportSettings.isExternalSecondaryStructure(),
                 inFile,
                 sourceType);
@@ -361,13 +362,13 @@ public enum FileFormat implements FileFormatI
     public AlignmentFileI getAlignmentFile(FileParse source)
             throws IOException
     {
-      boolean isParseWithJMOL = !StructureImportSettings
-              .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
+      boolean isParseWithJMOL = StructureImportSettings
+              .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
       if (isParseWithJMOL)
       {
         return new JmolParser(
                 StructureImportSettings.isVisibleChainAnnotation(),
-                StructureImportSettings.isPredictSecondaryStructure(),
+                StructureImportSettings.isProcessSecondaryStructure(),
                 StructureImportSettings.isExternalSecondaryStructure(),
                 source);
       }
@@ -376,7 +377,7 @@ public enum FileFormat implements FileFormatI
         StructureImportSettings.setShowSeqFeatures(true);
         return new MCview.PDBfile(
                 StructureImportSettings.isVisibleChainAnnotation(),
-                StructureImportSettings.isPredictSecondaryStructure(),
+                StructureImportSettings.isProcessSecondaryStructure(),
                 StructureImportSettings.isExternalSecondaryStructure(),
                 source);
       }
@@ -397,7 +398,7 @@ public enum FileFormat implements FileFormatI
     {
       return new JmolParser(
               StructureImportSettings.isVisibleChainAnnotation(),
-              StructureImportSettings.isPredictSecondaryStructure(),
+              StructureImportSettings.isProcessSecondaryStructure(),
               StructureImportSettings.isExternalSecondaryStructure(),
               inFile, sourceType);
     }
@@ -408,7 +409,7 @@ public enum FileFormat implements FileFormatI
     {
       return new JmolParser(
               StructureImportSettings.isVisibleChainAnnotation(),
-              StructureImportSettings.isPredictSecondaryStructure(),
+              StructureImportSettings.isProcessSecondaryStructure(),
               StructureImportSettings.isExternalSecondaryStructure(),
               source);
     }