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 java.util.Arrays;
24 import java.util.List;
26 import jalview.api.AlignExportSettingsI;
27 import jalview.api.AlignmentViewPanel;
28 import jalview.api.FeatureSettingsModelI;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.SequenceI;
32 public interface AlignmentFileReaderI
35 SequenceI[] getSeqsAsArray();
37 void addAnnotations(AlignmentI al);
39 void addGroups(AlignmentI al);
41 void setSeqs(SequenceI[] sequencesArray);
43 boolean hasWarningMessage();
45 String getWarningMessage();
49 DataSourceType getDataSourceType();
51 FeatureSettingsModelI getFeatureColourScheme();
53 default int getTreeCount() {
57 default boolean hasTrees() {
61 default List<String[]> getNewickTrees() {
62 return Arrays.asList(new String[][] {});