JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 302f3cd..674f1e7 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,24 +1,27 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
-import java.util.*;
+import java.util.Hashtable;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -40,7 +43,7 @@ public class SequenceFeature
 
   public Hashtable otherDetails;
 
-  public java.util.Vector links;
+  public Vector<String> links;
 
   // Feature group can be set from a features file
   // as a group of features between STARTGROUP and ENDGROUP markers
@@ -88,7 +91,7 @@ public class SequenceFeature
       }
       if (cpy.links != null && cpy.links.size() > 0)
       {
-        links = new Vector();
+        links = new Vector<String>();
         for (int i = 0, iSize = cpy.links.size(); i < iSize; i++)
         {
           links.addElement(cpy.links.elementAt(i));
@@ -209,7 +212,7 @@ public class SequenceFeature
   {
     if (links == null)
     {
-      links = new java.util.Vector();
+      links = new Vector<String>();
     }
 
     links.insertElementAt(labelLink, 0);
@@ -230,7 +233,7 @@ public class SequenceFeature
    * for GFF file
    * 
    * @param key
-   *                String
+   *          String
    */
   public Object getValue(String key)
   {
@@ -249,9 +252,9 @@ public class SequenceFeature
    * for GFF file
    * 
    * @param key
-   *                eg STRAND
+   *          eg STRAND
    * @param value
-   *                eg +
+   *          eg +
    */
   public void setValue(String key, Object value)
   {
@@ -281,7 +284,9 @@ public class SequenceFeature
     {
       String stat = (String) otherDetails.get("status");
       if (stat != null)
+      {
         return new String(stat);
+      }
     }
     return null;
   }
@@ -297,4 +302,23 @@ public class SequenceFeature
     return begin;
   }
 
+  public int getStrand()
+  {
+    String str;
+    if (otherDetails == null
+            || (str = otherDetails.get("STRAND").toString()) == null)
+    {
+      return 0;
+    }
+    if (str.equals("-"))
+    {
+      return -1;
+    }
+    if (str.equals("+"))
+    {
+      return 1;
+    }
+    return 0;
+  }
+
 }