JAL-2344 added FileFormatI.isStructureFile()

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

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index d0ce86e..5f441d2 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
       {
@@ -413,6 +404,12 @@ public enum FileFormat implements FileFormatI
     {
       return new JmolParser(); // todo or null?
     }
+
+    @Override
+    public boolean isStructureFile()
+    {
+      return true;
+    }
   },
   MMCif("mmCIF", "cif", true, false)
   {
@@ -421,22 +418,14 @@ 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
@@ -444,6 +433,12 @@ public enum FileFormat implements FileFormatI
     {
       return new JmolParser(); // todo or null?
     }
+
+    @Override
+    public boolean isStructureFile()
+    {
+      return true;
+    }
   },
   Jalview("Jalview", "jar,jvp", true, true)
   {
@@ -608,4 +603,10 @@ public enum FileFormat implements FileFormatI
   {
     return true;
   }
+
+  @Override
+  public boolean isStructureFile()
+  {
+    return false;
+  }
 }