-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- * \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.datamodel;\r
-\r
-/**\r
- * A set of feature property constants used by jalview\r
- * \r
- * @author JimP\r
- * \r
- */\r
-public class FeatureProperties\r
-{\r
-\r
- public static final String EXONPOS = "exon number";\r
-\r
- public static final String EXONPRODUCT = "product";\r
-\r
- /**\r
- * lookup feature type for a particular database to see if its a coding region\r
- * feature\r
- * \r
- * @param dbrefsource\r
- * @param string\r
- * @return\r
- */\r
- public static boolean isCodingFeature(String dbrefsource, String type)\r
- {\r
- return ((dbrefsource == null\r
- || dbrefsource.equalsIgnoreCase(DBRefSource.EMBL) || dbrefsource\r
- .equalsIgnoreCase(DBRefSource.EMBLCDS)) && type\r
- .equalsIgnoreCase("CDS"));\r
- }\r
-}\r
+/*
+ * 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.datamodel;
+
+/**
+ * A set of feature property constants used by jalview
+ *
+ * @author JimP
+ *
+ */
+public class FeatureProperties
+{
+ public static final String EMBL_CODING_FEATURE = "CDS";
+
+ public static final String EXONPOS = "exon number";
+
+ public static final String EXONPRODUCT = "product";
+
+ /**
+ * lookup feature type for a particular database to see if its a coding region
+ * feature
+ *
+ * @param dbrefsource
+ * @param string
+ * @return
+ */
+ public static boolean isCodingFeature(String dbrefsource, String type)
+ {
+ if (type.equalsIgnoreCase(EMBL_CODING_FEATURE))
+ {
+ return (dbrefsource == null
+ || dbrefsource.equalsIgnoreCase(DBRefSource.EMBL)
+ || dbrefsource.equalsIgnoreCase(DBRefSource.EMBLCDS));
+ }
+ return false;
+ }
+
+ /**
+ * Returns the coding feature name for a database source. Currently just
+ * hard-coded to return CDS for EMBL/EMBLCDS, else null.
+ *
+ * @param dbrefsource
+ * @return
+ */
+ public static String getCodingFeature(String dbrefsource)
+ {
+ if (DBRefSource.EMBL.equalsIgnoreCase(dbrefsource)
+ || DBRefSource.EMBLCDS.equalsIgnoreCase(dbrefsource))
+ {
+ return EMBL_CODING_FEATURE;
+ }
+ return null;
+ }
+}