/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
+import java.util.Hashtable;
public class PDBEntry
{
- String file;
- String type;
- String id;
+ private String file;
+
+ private String type;
+
+ private String id;
+
+ public enum Type
+ {
+ PDB, MMCIF, FILE;
+ /**
+ * case insensitive matching for Type enum
+ *
+ * @param value
+ * @return
+ */
+ public static Type getType(String value)
+ {
+ for (Type t : Type.values())
+ {
+ if (t.toString().equalsIgnoreCase(value))
+ {
+ return t;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * case insensitive equivalence for strings resolving to PDBEntry type
+ *
+ * @param t
+ * @return
+ */
+ public boolean matches(String t)
+ {
+ return (this.toString().equalsIgnoreCase(t));
+ }
+ }
+
+ public final class ChainId
+ {
+ String chainId;
+
+ public ChainId(String chainId)
+ {
+ this.chainId = chainId;
+ }
+
+ @Override
+ public String toString()
+ {
+ return chainId;
+ }
+
+ @Override
+ public boolean equals(Object o){
+ if (o==null)
+ {
+ return false;
+ }
+ return chainId.equalsIgnoreCase(o.toString());
+ }
+ }
+
+ /**
+ * constant for storing chain code in properties table
+ */
+ private static final String CHAIN_ID = "chain_code";
+
Hashtable properties;
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see java.lang.Object#equals(java.lang.Object)
*/
+ @Override
public boolean equals(Object obj)
{
- if (obj==null || !(obj instanceof PDBEntry))
+ if (obj == null || !(obj instanceof PDBEntry))
{
- return false;
+ return false;
}
- if (obj==this)
+ if (obj == this)
+ {
return true;
+ }
PDBEntry o = (PDBEntry) obj;
- return (file==o.file || (file!=null && o.file!=null && o.file.equals(file)))
- && (type==o.type || (type!=null && o.type!=null && o.type.equals(type)))
- && (id==o.id || (id!=null && o.id!=null && o.id.equalsIgnoreCase(id)))
- && (properties==o.properties || (properties!=null && o.properties!=null && properties.equals(o.properties)));
+ return (type == o.type || (type != null && o.type != null && o.type
+ .equals(type)))
+ && (id == o.id || (id != null && o.id != null && o.id
+ .equalsIgnoreCase(id)))
+ && (properties == o.properties || (properties != null
+ && o.properties != null && properties
+ .equals(o.properties)));
+
}
+
+ /**
+ * Default constructor
+ */
public PDBEntry()
- {}
- public PDBEntry(PDBEntry entry) {
+ {
+ }
+
+ /**
+ * Constructor given file path and PDB id.
+ *
+ * @param filePath
+ */
+ // public PDBEntry(String filePath, String pdbId)
+ // {
+ // this.file = filePath;
+ // this.id = pdbId;
+ // }
+
+ public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
+ String filePath)
+ {
+ this.id = pdbId;
+ this.type = type == null ? null : type.toString();
+ this.file = filePath;
+ setChainCode(chain);
+ }
+
+ /**
+ * Copy constructor.
+ *
+ * @param entry
+ */
+ public PDBEntry(PDBEntry entry)
+ {
file = entry.file;
type = entry.type;
id = entry.id;
- if (entry.properties!=null)
+ if (entry.properties != null)
{
properties = (Hashtable) entry.properties.clone();
}
}
+
public void setFile(String file)
{
this.file = file;
return file;
}
- public void setType(String type)
+ public void setType(String t)
+ {
+ this.type = t;
+ }
+
+ public void setType(PDBEntry.Type type)
{
- this.type = type;
+ this.type = type == null ? null : type.toString();
}
public String getType()
return properties;
}
+ /**
+ *
+ * @return null or a string for associated chain IDs
+ */
+ public String getChainCode()
+ {
+ return (properties == null || properties.get(CHAIN_ID) == null) ? null
+ : properties.get(CHAIN_ID).toString();
+ }
+
+ public void setChainCode(String chainCode)
+ {
+ if (properties == null)
+ {
+ if (chainCode == null)
+ {
+ // nothing to do.
+ return;
+ }
+ properties = new Hashtable();
+ }
+ if (chainCode == null)
+ {
+ properties.remove(CHAIN_ID);
+ return;
+ }
+ // update property for non-null chainCode
+ properties.put(CHAIN_ID, new ChainId(chainCode));
+ }
+
+ @Override
+ public String toString()
+ {
+ return id;
+ }
}
git://source.jalview.org / jalview.git / blobdiff