X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FFeatureProperties.java;h=f495624bf60b04394052a6b9b4be4d6614c94eec;hb=afffa24481a7d3cb65ae41e0948c16a5f490f302;hp=e5ad74aec69645e784ce4612e472b61f32342b68;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/datamodel/FeatureProperties.java b/src/jalview/datamodel/FeatureProperties.java
index e5ad74a..f495624 100644
--- 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 ($$Version-Rel$$)
+ * 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
@@ -26,6 +28,7 @@ package jalview.datamodel;
*/
public class FeatureProperties
{
+ public static final String EMBL_CODING_FEATURE = "CDS";
public static final String EXONPOS = "exon number";
@@ -41,9 +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;
}
}