-/*\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 (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 : "");
+ }
+}
git://source.jalview.org / jalview.git / blobdiff