JAL-3187 initial refactoring towards peptide variant in tooltip

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

diff --git a/src/jalview/datamodel/FeatureProperties.java b/src/jalview/datamodel/FeatureProperties.java
index b940eb1..f495624 100644 (file)
--- a/src/jalview/datamodel/FeatureProperties.java
+++ b/src/jalview/datamodel/FeatureProperties.java
@@ -28,6 +28,7 @@ package jalview.datamodel;
  */
 public class FeatureProperties
 {
+  public static final String EMBL_CODING_FEATURE = "CDS";
 
   public static final String EXONPOS = "exon number";
 
@@ -43,9 +44,29 @@ 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;
   }
 }