X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=115ef886389aa8ddca4b109525bcab130c8aef19;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=35ada0dc2d26b65aa36468b3eefeb32b8812bed1;hpb=4cc8dcf14fd3879de220311a3b091ddf87d6d6b0;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 35ada0d..115ef88 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -1,83 +1,112 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
  */
 package jalview.datamodel;
 
 public class DBRefEntry
 {
-  String source="", version="", accessionId="";
+  String source = "", version = "", accessionId = "";
+
   /**
    * maps from associated sequence to the database sequence's coordinate system
    */
-  Mapping map=null;
-  public DBRefEntry() {
-      
+  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;
+
+  /**
+   * 
+   * @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(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;
-          }
+    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 
+   * 
+   * @param entry
    * @return true if source, accession and version are equal with those of entry
    */
   public boolean equalRef(DBRefEntry entry)
   {
-    if (entry==null)
+    if (entry == null)
     {
       return false;
     }
-    if (entry==this)
+    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))
-            )
+    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;
@@ -92,47 +121,63 @@ public class DBRefEntry
   {
     return accessionId;
   }
-/**
- * @param accessionId the accessionId to set
- */
-public void setAccessionId(String 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) {
+  }
+
+  /**
+   * @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) {
+  }
+
+  /**
+   * @param version
+   *          the version to set
+   */
+  public void setVersion(String version)
+  {
     this.version = version;
-}
-/**
- * @return the map
- */
-public Mapping getMap() {
+  }
+
+  /**
+   * @return the map
+   */
+  public Mapping getMap()
+  {
     return map;
-}
-/**
- * @param map the map to set
- */
-public void setMap(Mapping 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 : "");
-}
+  }
+
+  public boolean hasMap()
+  {
+    return map != null;
+  }
+
+  /**
+   * 
+   * @return source+":"+accessionId
+   */
+  public String getSrcAccString()
+  {
+    return ((source != null) ? source : "") + ":"
+            + ((accessionId != null) ? accessionId : "");
+  }
 }