*/
package jalview.io;
-import jalview.api.AlignExportSettingI;
+import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.Preferences;
import jalview.util.Comparison;
import java.io.File;
}
public FormatAdapter(AlignmentViewPanel alignPanel,
- AlignExportSettingI settings)
+ AlignExportSettingsI settings)
{
super(alignPanel, settings);
}
private void init()
{
- if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+ if (jalview.bin.Cache.getDefault(Preferences.STRUCT_FROM_PDB, true))
{
- annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+ annotFromStructure = jalview.bin.Cache.getDefault(
+ Preferences.ADD_TEMPFACT_ANN,
true);
- localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+ localSecondaryStruct = jalview.bin.Cache.getDefault(
+ Preferences.ADD_SS_ANN,
true);
- serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+ serviceSecondaryStruct = jalview.bin.Cache
+ .getDefault(Preferences.USE_RNAVIEW,
true);
}
else