JAL-2113 embl_mapping.xml and code updated for EMBL XML v1.2

[jalview.git] / src / jalview / datamodel / xdb / embl / EmblFeatureLocations.java

diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
deleted file mode 100644 (file)
index 9774004..0000000
--- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
+++ /dev/null
@@ -1,191 +0,0 @@
-/*
- * 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.xdb.embl;
-
-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<EmblFeatureLocElement> locElements;
-
-  String locationType;
-
-  boolean locationComplement;
-
-  /**
-   * @return the locationComplement
-   */
-  public boolean isLocationComplement()
-  {
-    return locationComplement;
-  }
-
-  /**
-   * @param locationComplement
-   *          the locationComplement to set
-   */
-  public void setLocationComplement(boolean locationComplement)
-  {
-    this.locationComplement = locationComplement;
-  }
-
-  /**
-   * @return the locationType
-   */
-  public String getLocationType()
-  {
-    return locationType;
-  }
-
-  /**
-   * @param locationType
-   *          the locationType to set
-   */
-  public void setLocationType(String locationType)
-  {
-    this.locationType = locationType;
-  }
-
-  /**
-   * @return the locElements
-   */
-  public Vector<EmblFeatureLocElement> getLocElements()
-  {
-    return locElements;
-  }
-
-  /**
-   * @param locElements
-   *          the locElements to set
-   */
-  public void setLocElements(Vector<EmblFeatureLocElement> locElements)
-  {
-    this.locElements = locElements;
-  }
-
-  /**
-   * Return all location elements as start-end pairs (without accessions) TODO:
-   * pass back complement and 'less than or more than' range information Note:
-   * do not use this since it throws away any accessionIds associated with each
-   * location!
-   * 
-   * @return int[] { start1, end1, ... }
-   */
-  public int[] getElementRanges()
-  {
-    return getElementRanges(null);
-  }
-
-  /**
-   * 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 int[] { start1, end1, ... }
-   */
-  int[] getElementRanges(String accession)
-  {
-    int sepos = 0;
-    int[] se = new int[locElements.size() * 2];
-    if ("single".equalsIgnoreCase(locationType)
-            || "join".equalsIgnoreCase(locationType))
-    {
-      for (EmblFeatureLocElement loce : locElements)
-      {
-        if (accession == null || loce.accession != null
-                && accession.equals(loce.accession))
-        {
-          BasePosition bp[] = loce.getBasePositions();
-          if (bp.length == 2)
-          {
-            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
-          {
-            System.err
-                    .println("format error in EMBL CDS location, basePosition count = "
-                            + bp.length);
-          }
-        }
-      }
-    }
-    else if (locationType != null)
-    {
-      if (Cache.log != null)
-      {
-        Cache.log
-                .error("EmblFeatureLocations.getElementRanges cannot deal with locationType=='"
-                        + locationType + "'");
-      }
-      else
-      {
-        System.err
-                .println("EmblFeatureLocations.getElementRanges cannot deal with locationType=='"
-                        + locationType + "'");
-      }
-    }
-
-    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)
-    {
-      ArrayUtils.reverseIntArray(se);
-    }
-    return se;
-  }
-}