+/*
+ * 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.
+ */
package jalview.io.gff;
import java.util.List;
/*
* selected commonly used values for quick reference
*/
+ // SO:0000104
public static final String POLYPEPTIDE = "polypeptide";
+ // SO:0000349
public static final String PROTEIN_MATCH = "protein_match";
+ // SO:0000347
public static final String NUCLEOTIDE_MATCH = "nucleotide_match";
// SO:0000316
// SO:0001060
public static final String SEQUENCE_VARIANT = "sequence_variant";
+ // SO:0001819
+ public static final String SYNONYMOUS_VARIANT = "synonymous_variant";
+
+ // SO:0001992
+ public static final String NONSYNONYMOUS_VARIANT = "nonsynonymous_variant";
+
+ // SO:0001587
+ public static final String STOP_GAINED = "stop_gained";
+
// SO:0000147
public static final String EXON = "exon";
// SO:0000673
public static final String TRANSCRIPT = "transcript";
+ // SO:0001621 isA sequence_variant but used in Ensembl as a transcript
+ public static final String NMD_TRANSCRIPT_VARIANT = "NMD_transcript_variant";
+
// SO:0000704
public static final String GENE = "gene";