2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.datamodel.ColumnSelection;
24 import jalview.datamodel.SequenceI;
25 import jalview.schemes.ColourSchemeI;
28 * This interface should be implemented by complex file parser with the ability
29 * to store linked data and complex view states in addition to Alignment data
33 public interface ComplexAlignFile
36 * Determines if Sequence features should be shown
40 public boolean isShowSeqFeatures();
43 * Obtains the colour scheme from a complex file parser
47 public ColourSchemeI getColourScheme();
50 * Retrieves the Column selection/hidden column from a complex file parser
54 public ColumnSelection getColumnSelection();
57 * Retrieves hidden sequences from a complex file parser
61 public SequenceI[] getHiddenSequences();
64 * Retrieves displayed features from a complex file parser
68 public FeaturesDisplayedI getDisplayedFeatures();