- final Object[] args = new Object[] { true, true, true,
- new FileParse(getDataName(),
- type) };
-
- StructureViewSettings.setShowSeqFeatures(false);
- StructureViewSettings.setPredictSecondaryStructure(true);
+ final Object[] args = new Object[] { visibleChainAnnotation,
+ predictSecondaryStructure, externalSecondaryStructure,
+ new FileParse(getDataName(), type) };
+
+ StructureImportSettings.setShowSeqFeatures(false);
+ StructureImportSettings.setVisibleChainAnnotation(false);
+ StructureImportSettings
+ .setProcessSecondaryStructure(predictSecondaryStructure);
+ StructureImportSettings
+ .setExternalSecondaryStructure(externalSecondaryStructure);