/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
public class FeatureProperties
{
+ public static final String EMBL_CODING_FEATURE = "CDS";
public static final String EXONPOS = "exon number";
*/
public static boolean isCodingFeature(String dbrefsource, String type)
{
- return ((dbrefsource == null
- || dbrefsource.equalsIgnoreCase(DBRefSource.EMBL) || dbrefsource
- .equalsIgnoreCase(DBRefSource.EMBLCDS)) && type
- .equalsIgnoreCase("CDS"));
+ 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;
}
}