X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=6dc6641a9043fc9dfc0a22f6bcd29cec0eeb56f9;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=c35c8c26d4e8a94c5da9c9be4cc0dab036565d7d;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index c35c8c2..6dc6641 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -1,47 +1,184 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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 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.
- *
- * 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
- */
-package jalview.datamodel;
-
-public class DBRefEntry
-{
-  String source, version, accessionId;
-
-  public DBRefEntry(String source, String version, String accessionId)
-  {
-    this.source = source;
-    this.version = version;
-    this.accessionId = accessionId;
-  }
-
-  public String getSource()
-  {
-    return source;
-  }
-
-  public String getVersion()
-  {
-    return version;
-  }
-
-  public String getAccessionId()
-  {
-    return accessionId;
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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;
+
+public class DBRefEntry
+{
+  String source = "", version = "", accessionId = "";
+
+  /**
+   * maps from associated sequence to the database sequence's coordinate system
+   */
+  Mapping map = null;
+
+  public DBRefEntry()
+  {
+
+  }
+
+  public DBRefEntry(String source, String version, String accessionId)
+  {
+    this(source, version, accessionId, null);
+  }
+
+  /**
+   * 
+   * @param source
+   *          canonical source (uppercase only)
+   * @param version
+   *          (source dependent version string)
+   * @param accessionId
+   *          (source dependent accession number string)
+   * @param map
+   *          (mapping from local sequence numbering to source accession
+   *          numbering)
+   */
+  public DBRefEntry(String source, String version, String accessionId,
+          Mapping map)
+  {
+    this.source = source.toUpperCase();
+    this.version = version;
+    this.accessionId = accessionId;
+    this.map = map;
+  }
+
+  public DBRefEntry(DBRefEntry 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)));
+  }
+
+  public boolean equals(DBRefEntry entry)
+  {
+    if (entry == this)
+      return true;
+    if (entry == null)
+      return false;
+    if (equalRef(entry)
+            && ((map == null && entry.map == null) || (map != null
+                    && entry.map != null && map.equals(entry.map))))
+    {
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * test for similar DBRef attributes, except for the map object.
+   * 
+   * @param entry
+   * @return true if source, accession and version are equal with those of entry
+   */
+  public boolean equalRef(DBRefEntry entry)
+  {
+    if (entry == null)
+    {
+      return false;
+    }
+    if (entry == this)
+      return true;
+    if ((source != null && entry.source != null && source
+            .equalsIgnoreCase(entry.source))
+            && (accessionId != null && entry.accessionId != null && accessionId
+                    .equalsIgnoreCase(entry.accessionId))
+            && (version != null && entry.version != null && version
+                    .equalsIgnoreCase(entry.version)))
+    {
+      return true;
+    }
+    return false;
+  }
+
+  public String getSource()
+  {
+    return source;
+  }
+
+  public String getVersion()
+  {
+    return version;
+  }
+
+  public String getAccessionId()
+  {
+    return accessionId;
+  }
+
+  /**
+   * @param accessionId
+   *          the accessionId to set
+   */
+  public void setAccessionId(String accessionId)
+  {
+    this.accessionId = accessionId;
+  }
+
+  /**
+   * @param source
+   *          the source to set
+   */
+  public void setSource(String source)
+  {
+    this.source = source;
+  }
+
+  /**
+   * @param version
+   *          the version to set
+   */
+  public void setVersion(String version)
+  {
+    this.version = version;
+  }
+
+  /**
+   * @return the map
+   */
+  public Mapping getMap()
+  {
+    return map;
+  }
+
+  /**
+   * @param map
+   *          the map to set
+   */
+  public void setMap(Mapping map)
+  {
+    this.map = map;
+  }
+
+  public boolean hasMap()
+  {
+    return map != null;
+  }
+
+  /**
+   * 
+   * @return source+":"+accessionId
+   */
+  public String getSrcAccString()
+  {
+    return ((source != null) ? source : "") + ":"
+            + ((accessionId != null) ? accessionId : "");
+  }
+}