X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FFeatureProperties.java;h=f495624bf60b04394052a6b9b4be4d6614c94eec;hb=HEAD;hp=7eadf7b8f6d208a460f61c2521df6177101f6488;hpb=3bf07ba3afb39cea37a1e3eb32da7d498a1fd901;p=jalview.git

diff --git a/src/jalview/datamodel/FeatureProperties.java b/src/jalview/datamodel/FeatureProperties.java
index 7eadf7b..f495624 100644
--- a/src/jalview/datamodel/FeatureProperties.java
+++ b/src/jalview/datamodel/FeatureProperties.java
@@ -1,24 +1,72 @@
-package jalview.datamodel;
-
-/**
- * A set of feature property constants used by jalview
- * @author JimP
- *
- */
-public class FeatureProperties
-{
-
-  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)
-  {
-    return ((dbrefsource==null || dbrefsource.equalsIgnoreCase(DBRefSource.EMBL))
-            && type.equalsIgnoreCase("CDS"));
-  }
-}
+/*
+ * 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;
+  }
+}