-/*\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);
+ }
+ 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 ((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))
+ &&
+ ((map==null && entry.map==null) || (map!=null && entry.map!=null && map.equals(entry.map)))) {
+ 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()
+{
+ // TODO Auto-generated method stub
+ return map!=null;
+}
+/**
+ *
+ * @return source+":"+accessionId
+ */
+public String getSrcAccString()
+{
+ return ((source!=null) ? source : "")
+ + ":" + ((accessionId!=null) ? accessionId : "");
+}
+}