safer copy constructor

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

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index c35c8c2..b6c3192 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -1,47 +1,148 @@
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
- */\r
-package jalview.datamodel;\r
-\r
-public class DBRefEntry\r
-{\r
-  String source, version, accessionId;\r
-\r
-  public DBRefEntry(String source, String version, String accessionId)\r
-  {\r
-    this.source = source;\r
-    this.version = version;\r
-    this.accessionId = accessionId;\r
-  }\r
-\r
-  public String getSource()\r
-  {\r
-    return source;\r
-  }\r
-\r
-  public String getVersion()\r
-  {\r
-    return version;\r
-  }\r
-\r
-  public String getAccessionId()\r
-  {\r
-    return accessionId;\r
-  }\r
-\r
-}\r
+/*
+ * 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);
+  }
+  /**
+   * 
+   * @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 : "");
+}
+}