X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FFeatureProperties.java;h=f495624bf60b04394052a6b9b4be4d6614c94eec;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=e6f2cb8a3ac625d392bc48b9df47695b0d2c0d9f;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/datamodel/FeatureProperties.java b/src/jalview/datamodel/FeatureProperties.java
index e6f2cb8..f495624 100644
--- a/src/jalview/datamodel/FeatureProperties.java
+++ b/src/jalview/datamodel/FeatureProperties.java
@@ -1,49 +1,72 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- * 
- * This program 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 2
- * of the License, or (at your option) any later version.
- * 
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-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) || dbrefsource
-            .equalsIgnoreCase(DBRefSource.EMBLCDS)) && 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;
+  }
+}