1 /* 2 * Jalview - A Sequence Alignment Editor and Viewer (2.11.1.4) 3 * Copyright (C) 2021 The Jalview Authors 4 * 5 * This file is part of Jalview. 6 * 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. 11 * 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. 16 * 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. 20 */ 21 package jalview.io; 22 23 import jalview.api.AlignExportSettingI; 24 import jalview.api.AlignmentViewPanel; 25 import jalview.api.FeatureSettingsModelI; 26 import jalview.datamodel.AlignmentI; 27 import jalview.datamodel.SequenceI; 28 29 public interface AlignmentFileReaderI 30 { 31 getSeqsAsArray()32 SequenceI[] getSeqsAsArray(); 33 addAnnotations(AlignmentI al)34 void addAnnotations(AlignmentI al); 35 addGroups(AlignmentI al)36 void addGroups(AlignmentI al); 37 setSeqs(SequenceI[] sequencesArray)38 void setSeqs(SequenceI[] sequencesArray); 39 hasWarningMessage()40 boolean hasWarningMessage(); 41 getWarningMessage()42 String getWarningMessage(); 43 getInFile()44 String getInFile(); 45 getDataSourceType()46 DataSourceType getDataSourceType(); 47 getFeatureColourScheme()48 FeatureSettingsModelI getFeatureColourScheme(); 49 50 } 51