X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FFeatureProperties.java;h=f495624bf60b04394052a6b9b4be4d6614c94eec;hb=96d8ee2740a68f9fce6aa6de0f91097a73c8f608;hp=8c238ef0a5156f96f37980b72f4216e29a64d561;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/datamodel/FeatureProperties.java b/src/jalview/datamodel/FeatureProperties.java
index 8c238ef..f495624 100644
--- a/src/jalview/datamodel/FeatureProperties.java
+++ b/src/jalview/datamodel/FeatureProperties.java
@@ -1,48 +1,72 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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 .
- */
-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 .
+ * 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;
+ }
+}