X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblFeatureLocations.java;h=94105ae6f5efec4f292e2c13ea7e8e8b0513d35e;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=92fa4e3e5a92acbf226cf35c174955c7e020ca7f;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
index 92fa4e3..94105ae 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
@@ -1,30 +1,36 @@
 /*
- * 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.xdb.embl;
 
-import java.util.Enumeration;
-import java.util.Iterator;
 import java.util.Vector;
 
+/**
+ * Data model for a &lt;loctaion&gt; child element of a &lt;feature&gt; read
+ * from an EMBL query reply
+ * 
+ * @see embl_mapping.xml
+ */
 public class EmblFeatureLocations
 {
-  Vector locElements;
+  Vector<EmblFeatureLocElement> locElements;
 
   String locationType;
 
@@ -40,7 +46,7 @@ public class EmblFeatureLocations
 
   /**
    * @param locationComplement
-   *                the locationComplement to set
+   *          the locationComplement to set
    */
   public void setLocationComplement(boolean locationComplement)
   {
@@ -57,7 +63,7 @@ public class EmblFeatureLocations
 
   /**
    * @param locationType
-   *                the locationType to set
+   *          the locationType to set
    */
   public void setLocationType(String locationType)
   {
@@ -67,16 +73,16 @@ public class EmblFeatureLocations
   /**
    * @return the locElements
    */
-  public Vector getLocElements()
+  public Vector<EmblFeatureLocElement> getLocElements()
   {
     return locElements;
   }
 
   /**
    * @param locElements
-   *                the locElements to set
+   *          the locElements to set
    */
-  public void setLocElements(Vector locElements)
+  public void setLocElements(Vector<EmblFeatureLocElement> locElements)
   {
     this.locElements = locElements;
   }
@@ -100,8 +106,8 @@ public class EmblFeatureLocations
    * TODO: deal with multiple accessions
    * 
    * @param accession
-   *                the accession string for which locations are requested, or
-   *                null for all locations
+   *          the accession string for which locations are requested, or null
+   *          for all locations
    * @return null or int[] { start1, end1, ... }
    */
 
@@ -109,12 +115,10 @@ public class EmblFeatureLocations
   {
     int sepos = 0;
     int[] se = new int[locElements.size() * 2];
-    if (locationType.equalsIgnoreCase("single"))
+    if (locationType.equalsIgnoreCase("single")) // TODO: or "simple" ?
     {
-      for (Enumeration le = locElements.elements(); le.hasMoreElements();)
+      for (EmblFeatureLocElement loce : locElements)
       {
-        EmblFeatureLocElement loce = (EmblFeatureLocElement) le
-                .nextElement();
         if (accession == null || loce.accession != null
                 && accession.equals(loce.accession))
         {
@@ -129,10 +133,8 @@ public class EmblFeatureLocations
     }
     else if (locationType.equalsIgnoreCase("join"))
     {
-      for (Enumeration le = locElements.elements(); le.hasMoreElements();)
+      for (EmblFeatureLocElement loce : locElements)
       {
-        EmblFeatureLocElement loce = (EmblFeatureLocElement) le
-                .nextElement();
         if (accession == null || loce.accession != null
                 && accession.equals(loce.accession))
         {
@@ -149,13 +151,17 @@ public class EmblFeatureLocations
     else if (locationType != null)
     {
       if (jalview.bin.Cache.log != null)
+      {
         jalview.bin.Cache.log
                 .error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"
                         + locationType + "'");
+      }
       else
+      {
         System.err
                 .println("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"
                         + locationType + "'");
+      }
     }
     // trim range if necessary.
     if (se != null && sepos != se.length)