merge

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

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 142d996..738c4dc 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -37,6 +37,7 @@ public class DBRefEntry implements DBRefEntryI
 
   }
 
+
   public DBRefEntry(String source, String version, String accessionId)
   {
     this(source, version, accessionId, null);
@@ -63,13 +64,14 @@ public class DBRefEntry implements DBRefEntryI
     this.map = map;
   }
 
-  public DBRefEntry(DBRefEntry entry)
+  public DBRefEntry(DBRefEntryI entry)
   {
-    this(
-            (entry.source == null ? "" : new String(entry.source)),
-            (entry.version == null ? "" : new String(entry.version)),
-            (entry.accessionId == null ? "" : new String(entry.accessionId)),
-            (entry.map == null ? null : new Mapping(entry.map)));
+    this((entry.getSource() == null ? "" : new String(entry.getSource())),
+            (entry.getVersion() == null ? "" : new String(
+                    entry.getVersion())),
+            (entry.getAccessionId() == null ? "" : new String(
+                    entry.getAccessionId())),
+            (entry.getMap() == null ? null : new Mapping(entry.getMap())));
   }
 
   @Override
@@ -96,6 +98,82 @@ public class DBRefEntry implements DBRefEntryI
   }
 
   /**
+   * Answers true if this object is either equivalent to, or can be 'improved'
+   * by, the given entry. Specifically, answers true if
+   * <ul>
+   * <li>source and accession are identical (ignoring case)</li>
+   * <li>version is identical (ignoring case), or this version is of the format
+   * "someSource:0", in which case the version for the other entry replaces it</li>
+   * <li>mappings are not compared but if this entry has no mapping, replace
+   * with that for the other entry</li>
+   * </ul>
+   * 
+   * @param other
+   * @return
+   */
+  @Override
+  public boolean updateFrom(DBRefEntry other)
+  {
+    if (other == null)
+    {
+      return false;
+    }
+    if (other == this)
+    {
+      return true;
+    }
+
+    /*
+     * source must either match or be both null
+     */
+    String otherSource = other.getSource();
+    if ((source == null && otherSource != null)
+            || (source != null && otherSource == null)
+            || (source != null && !source.equalsIgnoreCase(otherSource)))
+    {
+      return false;
+    }
+
+    /*
+     * accession id must either match or be both null
+     */
+    String otherAccession = other.getAccessionId();
+    if ((accessionId == null && otherAccession != null)
+            || (accessionId != null && otherAccession == null)
+            || (accessionId != null && !accessionId.equalsIgnoreCase(otherAccession)))
+    {
+      return false;
+    }
+
+    /*
+     * if my version is null, "0" or "source:0" then replace with other version,
+     * otherwise the versions have to match
+     */
+    String otherVersion = other.getVersion();
+    if ((version == null || version.equals("0") || version.endsWith(":0"))
+            && otherVersion != null)
+    {
+      setVersion(otherVersion);
+    }
+    else
+    {
+      if (!version.equalsIgnoreCase(otherVersion))
+      {
+        return false;
+      }
+    }
+
+    /*
+     * if I have no mapping, take that of the other dbref
+     */
+    if (map == null)
+    {
+      setMap(other.getMap());
+    }
+    return true;
+  }
+
+  /**
    * test for similar DBRef attributes, except for the map object.
    * 
    * @param entry
@@ -104,6 +182,7 @@ public class DBRefEntry implements DBRefEntryI
   @Override
   public boolean equalRef(DBRefEntryI entry)
   {
+    // TODO is this method and equals() not needed?
     if (entry == null)
     {
       return false;
@@ -143,39 +222,29 @@ public class DBRefEntry implements DBRefEntryI
     return accessionId;
   }
 
-  /**
-   * @param accessionId
-   *          the accessionId to set
-   */
+
   @Override
   public void setAccessionId(String accessionId)
   {
     this.accessionId = accessionId;
   }
 
-  /**
-   * @param source
-   *          the source to set
-   */
+
   @Override
   public void setSource(String source)
   {
     this.source = source;
   }
 
-  /**
-   * @param version
-   *          the version to set
-   */
+
   @Override
   public void setVersion(String version)
   {
     this.version = version;
   }
 
-  /**
-   * @return the map
-   */
+
+  @Override
   public Mapping getMap()
   {
     return map;
@@ -211,21 +280,25 @@ public class DBRefEntry implements DBRefEntryI
     return getSrcAccString();
   }
 
+  @Override
   public int getStartRes()
   {
     return startRes;
   }
 
+  @Override
   public void setStartRes(int startRes)
   {
     this.startRes = startRes;
   }
 
+  @Override
   public int getEndRes()
   {
     return endRes;
   }
 
+  @Override
   public void setEndRes(int endRes)
   {
     this.endRes = endRes;