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.
22 // export a consensus sequence
23 // execute this script via command line for an alignment - e.g.
24 // jalview -groovy exportconsensus.groovy -headless -open examples/uniref50.fa
26 def alf = Jalview.getAlignFrames();
29 // ala is an jalview.gui.AlignFrame object
30 jalview.datamodel.SequenceI seq = ala.viewport.getConsensusSeq();
31 print new jalview.io.FastaFile().print(((jalview.datamodel.SequenceI[]) [seq]),false)+"\n";