+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.api;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
+/**
+ * This interface should be implemented by complex file parser with the ability
+ * to store linked data and complex view states in addition to Alignment data
+ *
+ *
+ */
public interface ComplexAlignFile
{
+ /**
+ * Determines if Sequence features should be shown
+ *
+ * @return
+ */
public boolean isShowSeqFeatures();
- public ColourSchemeI getColourScheme();
+ /**
+ * Obtains the colour scheme from a complex file parser
+ *
+ * @return
+ */
+ public String getGlobalColourScheme();
- public ColumnSelection getColumnSelection();
+ /**
+ * Retrieves the Column selection/hidden column from a complex file parser
+ *
+ * @return
+ */
+ public HiddenColumns getHiddenColumns();
+ /**
+ * Retrieves hidden sequences from a complex file parser
+ *
+ * @return
+ */
public SequenceI[] getHiddenSequences();
+ /**
+ * Retrieves displayed features from a complex file parser
+ *
+ * @return
+ */
+ public FeaturesDisplayedI getDisplayedFeatures();
}