/*
 * Jalview - A Sequence Alignment Editor and Viewer (2.11.2.2)
 * Copyright (C) 2022 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.
 */
 
// export a consensus sequence
// execute this script via command line for an alignment - e.g.
// jalview -groovy exportconsensus.groovy -headless -open examples/uniref50.fa

def alf = Jalview.getAlignFrames();
for (ala in alf)
{
  // ala is an jalview.gui.AlignFrame object
  jalview.datamodel.SequenceI seq = ala.viewport.getConsensusSeq();
  print new jalview.io.FastaFile().print(((jalview.datamodel.SequenceI[]) [seq]),false)+"\n";
}