X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblFeatureLocations.java;h=94105ae6f5efec4f292e2c13ea7e8e8b0513d35e;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=bbd394874c0ab2da599d69bece68dae47384fbfd;hpb=2ea52575d29eccae73a4262f52f59ff3fcf713b1;p=jalview.git

diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
index bbd3948..94105ae 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
@@ -1,84 +1,175 @@
-package jalview.datamodel.xdb.embl;
-
-import java.util.Iterator;
-import java.util.Vector;
-
-public class EmblFeatureLocations {
-    Vector 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 getLocElements() {
-        return locElements;
-    }
-    /**
-     * @param locElements the locElements to set
-     */
-    public void setLocElements(Vector locElements) {
-        this.locElements = locElements;
-    }
-    /**
-     * Return all location elements as start-end pairs on referenced sequence 
-     * TODO: pass back complement and 'less than or more than' range information
-     * @return int[] { start1, end1, ... }
-     */
-    public int[] getElementRanges() {
-        if (locationType.equalsIgnoreCase("single")) {
-            int[] se = new int[locElements.size()*2];            
-            int sepos=0;
-            for (Iterator le=locElements.iterator();le.hasNext();) {
-                EmblFeatureLocElement loce = (EmblFeatureLocElement) le.next();
-                BasePosition bp[] = loce.getBasePositions();
-                if (bp.length==2) {
-                    se[sepos++] = Integer.parseInt(bp[0].getPos());
-                    se[sepos++] = Integer.parseInt(bp[1].getPos());
-                }
-            }
-            return se;
-        }
-        if (locationType.equalsIgnoreCase("join")) {
-            int[] se = new int[locElements.size()*2];            
-            int sepos=0;
-            for (Iterator le=locElements.iterator();le.hasNext();) {
-                EmblFeatureLocElement loce = (EmblFeatureLocElement) le.next();
-                BasePosition bp[] = loce.getBasePositions();
-                if (bp.length==2) {
-                    se[sepos++] = Integer.parseInt(bp[0].getPos());
-                    se[sepos++] = Integer.parseInt(bp[1].getPos());
-                }
-            }
-            return se;
-        }
-        if (locationType!=null)
-        {
-          jalview.bin.Cache.log.error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"+locationType+"'");
-        }
-        return null;
-    }
-}
\ No newline at end of file
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 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<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
+   * TODO: pass back complement and 'less than or more than' range information
+   * TODO: deal with multiple accessions
+   * 
+   * @param accession
+   *          the accession string for which locations are requested, or null
+   *          for all locations
+   * @return null or int[] { start1, end1, ... }
+   */
+
+  public int[] getElementRanges(String accession)
+  {
+    int sepos = 0;
+    int[] se = new int[locElements.size() * 2];
+    if (locationType.equalsIgnoreCase("single")) // TODO: or "simple" ?
+    {
+      for (EmblFeatureLocElement loce : locElements)
+      {
+        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());
+          }
+        }
+      }
+    }
+    else if (locationType.equalsIgnoreCase("join"))
+    {
+      for (EmblFeatureLocElement loce : locElements)
+      {
+        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());
+          }
+        }
+      }
+      return se;
+    }
+    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)
+    {
+      int[] trimmed = new int[sepos];
+      System.arraycopy(se, 0, trimmed, 0, sepos);
+      se = trimmed;
+    }
+    return se;
+  }
+}