/*
- * 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);
}
+
/**
*
- * @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)
+ * @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) {
+ 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;
- }
+ 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.equalsIgnoreCase(entry.source))
- &&
- (accessionId!=null && entry.accessionId!=null && accessionId.equalsIgnoreCase(entry.accessionId))
- &&
- (version!=null && entry.version!=null && version.equalsIgnoreCase(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;
{
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 : "");
+ }
}
git://source.jalview.org / jalview.git / blobdiff