JAL-3547 groovy script to get the conservation sequence and output it as fasta

diff --git a/examples/groovy/exportconsensus.groovy b/examples/groovy/exportconsensus.groovy
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+/*
+ * 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 <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";
+}
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