X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=35ada0dc2d26b65aa36468b3eefeb32b8812bed1;hb=2b3edc77ed89937505a6c1297b4264cd8b820b8b;hp=75e0cc89b7b7f43044f2239fc0cafe050c57190d;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 75e0cc8..35ada0d 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -1,23 +1,138 @@
-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
+ * 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="";
+  /**
+   * 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);
+  }
+  public DBRefEntry(String source, String version, String accessionId, Mapping map) {
+    this.source = source;
+    this.version = version;
+    this.accessionId = accessionId;
+    this.map = map;
+  }
+  public DBRefEntry(DBRefEntry entry)
+  {
+    this(new String(entry.source), new String(entry.version), new String(entry.accessionId), 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.equals(entry.source))
+            &&
+            (accessionId!=null && entry.accessionId!=null && accessionId.equals(entry.accessionId))
+            &&
+            (version!=null && entry.version!=null && version.equals(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 : "");
+}
+}