Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index d0ce86e..d52045c 100644 (file)
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -364,12 +364,7 @@ public enum FileFormat implements FileFormatI
               .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
       if (isParseWithJMOL)
       {
-        return new JmolParser(
-                StructureImportSettings.isVisibleChainAnnotation(),
-                StructureImportSettings.isProcessSecondaryStructure(),
-                StructureImportSettings.isExternalSecondaryStructure(),
-                inFile,
-                sourceType);
+        return new JmolParser(inFile, sourceType);
       }
       else
       {
@@ -391,11 +386,7 @@ public enum FileFormat implements FileFormatI
               .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
       if (isParseWithJMOL)
       {
-        return new JmolParser(
-                StructureImportSettings.isVisibleChainAnnotation(),
-                StructureImportSettings.isProcessSecondaryStructure(),
-                StructureImportSettings.isExternalSecondaryStructure(),
-                source);
+        return new JmolParser(source);
       }
       else
       {
@@ -421,22 +412,14 @@ public enum FileFormat implements FileFormatI
     public AlignmentFileI getAlignmentFile(String inFile,
             DataSourceType sourceType) throws IOException
     {
-      return new JmolParser(
-              StructureImportSettings.isVisibleChainAnnotation(),
-              StructureImportSettings.isProcessSecondaryStructure(),
-              StructureImportSettings.isExternalSecondaryStructure(),
-              inFile, sourceType);
+      return new JmolParser(inFile, sourceType);
     }
 
     @Override
     public AlignmentFileI getAlignmentFile(FileParse source)
             throws IOException
     {
-      return new JmolParser(
-              StructureImportSettings.isVisibleChainAnnotation(),
-              StructureImportSettings.isProcessSecondaryStructure(),
-              StructureImportSettings.isExternalSecondaryStructure(),
-              source);
+      return new JmolParser(source);
     }
 
     @Override