/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import java.util.Arrays;
import java.util.List;
import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
public interface AlignmentFileReaderI
{
SequenceI[] getSeqsAsArray();
void addAnnotations(AlignmentI al);
void addGroups(AlignmentI al);
void setSeqs(SequenceI[] sequencesArray);
boolean hasWarningMessage();
String getWarningMessage();
String getInFile();
DataSourceType getDataSourceType();
FeatureSettingsModelI getFeatureColourScheme();
default int getTreeCount() {
return 0;
}
default boolean hasTrees() {
return false;
}
default List getNewickTrees() {
return Arrays.asList(new String[][] {});
}
}