JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / src / jalview / datamodel / FeatureProperties.java

diff --git a/src/jalview/datamodel/FeatureProperties.java b/src/jalview/datamodel/FeatureProperties.java
index e5ad74a..17a2e64 100644 (file)
--- a/src/jalview/datamodel/FeatureProperties.java
+++ b/src/jalview/datamodel/FeatureProperties.java
@@ -1,19 +1,21 @@
 /*
- * 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 2.9)
+ * Copyright (C) 2015 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.
+ * 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/>.
+ * 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;
@@ -27,6 +29,8 @@ package jalview.datamodel;
 public class FeatureProperties
 {
 
+  private static final String EMBL_CODING_FEATURE = "CDS";
+
   public static final String EXONPOS = "exon number";
 
   public static final String EXONPRODUCT = "product";
@@ -41,9 +45,29 @@ public class FeatureProperties
    */
   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;
   }
 }