JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/datamodel/FeatureProperties.java b/src/jalview/datamodel/FeatureProperties.java
index eaf5874..2306bec 100644 (file)
--- a/src/jalview/datamodel/FeatureProperties.java
+++ b/src/jalview/datamodel/FeatureProperties.java
@@ -1,48 +1,72 @@
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE.  See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.datamodel;\r
-\r
-/**\r
- * A set of feature property constants used by jalview\r
- * \r
- * @author JimP\r
- * \r
- */\r
-public class FeatureProperties\r
-{\r
-\r
-  public static final String EXONPOS = "exon number";\r
-\r
-  public static final String EXONPRODUCT = "product";\r
-\r
-  /**\r
-   * lookup feature type for a particular database to see if its a coding region\r
-   * feature\r
-   * \r
-   * @param dbrefsource\r
-   * @param string\r
-   * @return\r
-   */\r
-  public static boolean isCodingFeature(String dbrefsource, String type)\r
-  {\r
-    return ((dbrefsource == null\r
-            || dbrefsource.equalsIgnoreCase(DBRefSource.EMBL) || dbrefsource\r
-            .equalsIgnoreCase(DBRefSource.EMBLCDS)) && type\r
-            .equalsIgnoreCase("CDS"));\r
-  }\r
-}\r
+/*
+ * 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;
+  }
+}