X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblFeatureLocations.java;h=977400497f9fbd8367ebd7caf4bcaf10c86cdf35;hb=f8e603128476ca6e093ea2fc65435d1294978c53;hp=6a6997091a68a959ac9a2c1be74f4309f9bd8d8b;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
index 6a69970..9774004 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
@@ -1,29 +1,41 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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/>.
+ * 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.xdb.embl;
 
-import java.util.Enumeration;
-import java.util.Iterator;
+import jalview.bin.Cache;
+import jalview.util.ArrayUtils;
+
+import java.util.Arrays;
 import java.util.Vector;
 
+/**
+ * Data model for a &lt;location&gt; child element of a &lt;feature&gt; read
+ * from an EMBL query reply
+ * 
+ * @see embl_mapping.xml
+ * @see http://www.insdc.org/files/feature_table.html#3.4.2
+ */
 public class EmblFeatureLocations
 {
-  Vector locElements;
+  Vector<EmblFeatureLocElement> locElements;
 
   String locationType;
 
@@ -66,7 +78,7 @@ public class EmblFeatureLocations
   /**
    * @return the locElements
    */
-  public Vector getLocElements()
+  public Vector<EmblFeatureLocElement> getLocElements()
   {
     return locElements;
   }
@@ -75,7 +87,7 @@ public class EmblFeatureLocations
    * @param locElements
    *          the locElements to set
    */
-  public void setLocElements(Vector locElements)
+  public void setLocElements(Vector<EmblFeatureLocElement> locElements)
   {
     this.locElements = locElements;
   }
@@ -94,74 +106,85 @@ public class EmblFeatureLocations
   }
 
   /**
-   * Return all location elements concerning given accession as start-end pairs
-   * TODO: pass back complement and 'less than or more than' range information
-   * TODO: deal with multiple accessions
+   * Return all location elements concerning given accession as start-end pairs.
+   * If the CDS feature is on the forward strand, then start <= end, if on the
+   * reverse strand then start > end.
    * 
    * @param accession
    *          the accession string for which locations are requested, or null
    *          for all locations
-   * @return null or int[] { start1, end1, ... }
+   * @return int[] { start1, end1, ... }
    */
-
-  public int[] getElementRanges(String accession)
+  int[] getElementRanges(String accession)
   {
     int sepos = 0;
     int[] se = new int[locElements.size() * 2];
-    if (locationType.equalsIgnoreCase("single"))
+    if ("single".equalsIgnoreCase(locationType)
+            || "join".equalsIgnoreCase(locationType))
     {
-      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))
         {
           BasePosition bp[] = loce.getBasePositions();
           if (bp.length == 2)
           {
-            se[sepos++] = Integer.parseInt(bp[0].getPos());
-            se[sepos++] = Integer.parseInt(bp[1].getPos());
+            try
+            {
+              int start = Integer.parseInt(bp[0].getPos());
+              int end = Integer.parseInt(bp[1].getPos());
+              se[sepos++] = start;
+              se[sepos++] = end;
+            } catch (NumberFormatException e)
+            {
+              System.err
+                      .println("format error in EMBL CDS location basePosition: "
+                              + e.getMessage());
+            }
           }
-        }
-      }
-    }
-    else if (locationType.equalsIgnoreCase("join"))
-    {
-      for (Enumeration le = locElements.elements(); le.hasMoreElements();)
-      {
-        EmblFeatureLocElement loce = (EmblFeatureLocElement) le
-                .nextElement();
-        if (accession == null || loce.accession != null
-                && accession.equals(loce.accession))
-        {
-          BasePosition bp[] = loce.getBasePositions();
-          if (bp.length == 2)
+          else
           {
-            se[sepos++] = Integer.parseInt(bp[0].getPos());
-            se[sepos++] = Integer.parseInt(bp[1].getPos());
+            System.err
+                    .println("format error in EMBL CDS location, basePosition count = "
+                            + bp.length);
           }
         }
       }
-      return se;
     }
     else if (locationType != null)
     {
-      if (jalview.bin.Cache.log != null)
-        jalview.bin.Cache.log
-                .error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"
+      if (Cache.log != null)
+      {
+        Cache.log
+                .error("EmblFeatureLocations.getElementRanges cannot deal with locationType=='"
                         + locationType + "'");
+      }
       else
+      {
         System.err
-                .println("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"
+                .println("EmblFeatureLocations.getElementRanges cannot deal with locationType=='"
                         + locationType + "'");
+      }
     }
-    // trim range if necessary.
-    if (se != null && sepos != se.length)
+
+    if (sepos != se.length)
+    {
+      /*
+       * we failed to parse something - trim off null values
+       */
+      se = Arrays.copyOf(se, sepos);
+    }
+
+    /*
+     * If on the complement, reverse the ranges to [end, start, ...end1, start1].
+     * For an example of a joined complement, see (tRNA feature) CAGL0B00165r on
+     * http://www.ebi.ac.uk/ena/data/view/CR380948&display=xml
+     * http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/CR380948/emblxml
+     */
+    if (locationComplement)
     {
-      int[] trimmed = new int[sepos];
-      System.arraycopy(se, 0, trimmed, 0, sepos);
-      se = trimmed;
+      ArrayUtils.reverseIntArray(se);
     }
     return se;
   }