-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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
-import java.util.*;\r
-public class PDBEntry\r
-{\r
- String file;\r
- String type;\r
- String id;\r
- Hashtable properties;\r
-\r
- public PDBEntry()\r
- { }\r
-\r
- public void setFile(String file)\r
- { this.file = file; }\r
-\r
- public String getFile()\r
- { return file; }\r
-\r
- public void setType(String type)\r
- { this.type = type; }\r
-\r
- public String getType()\r
- { return type; }\r
-\r
- public void setId(String id)\r
- { this.id = id; }\r
-\r
- public String getId()\r
- { return id; }\r
-\r
- public void setProperty(Hashtable property)\r
- {\r
- this.properties = property;\r
- }\r
-\r
- public Hashtable getProperty()\r
- {\r
- return properties;\r
- }\r
-\r
-\r
-}\r
+/*
+ * 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.
+ *
+ * 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;
+
+import jalview.util.CaseInsensitiveString;
+
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Map.Entry;
+
+public class PDBEntry
+{
+
+ /**
+ * constant for storing chain code in properties table
+ */
+ private static final String CHAIN_ID = "chain_code";
+
+ Hashtable<String, Object> properties;
+
+ 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));
+ }
+ }
+
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.lang.Object#equals(java.lang.Object)
+ */
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == null || !(obj instanceof PDBEntry))
+ {
+ return false;
+ }
+ if (obj == this)
+ {
+ return true;
+ }
+ PDBEntry o = (PDBEntry) obj;
+ 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()
+ {
+ }
+
+ /**
+ * 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)
+ {
+ properties = (Hashtable<String, Object>) entry.properties.clone();
+ }
+ }
+
+ public void setFile(String f)
+ {
+ this.file = f;
+ }
+
+ public String getFile()
+ {
+ return file;
+ }
+
+ public void setType(String t)
+ {
+ this.type = t;
+ }
+
+ public void setType(PDBEntry.Type type)
+ {
+ this.type = type == null ? null : type.toString();
+ }
+
+ public String getType()
+ {
+ return type;
+ }
+
+ public void setId(String id)
+ {
+ this.id = id;
+ }
+
+ public String getId()
+ {
+ return id;
+ }
+
+ public void setProperty(String key, Object value)
+ {
+ if (this.properties == null)
+ {
+ this.properties = new Hashtable<String, Object>();
+ }
+ properties.put(key, value);
+ }
+
+ public Object getProperty(String key)
+ {
+ return properties == null ? null : properties.get(key);
+ }
+
+ /**
+ * Returns an enumeration of the keys of this object's properties (or an empty
+ * enumeration if it has no properties)
+ *
+ * @return
+ */
+ public Enumeration<String> getProperties()
+ {
+ if (properties == null)
+ {
+ return Collections.emptyEnumeration();
+ }
+ return properties.keys();
+ }
+
+ /**
+ *
+ * @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();
+ }
+
+ /**
+ * Sets a non-case-sensitive property for the given chain code. Two PDBEntry
+ * objects which differ only in the case of their chain code are considered
+ * equal. This avoids duplication of objects in lists of PDB ids.
+ *
+ * @param chainCode
+ */
+ public void setChainCode(String chainCode)
+ {
+ if (chainCode == null)
+ {
+ deleteProperty(CHAIN_ID);
+ }
+ else
+ {
+ setProperty(CHAIN_ID, new CaseInsensitiveString(chainCode));
+ }
+ }
+
+ /**
+ * Deletes the property with the given key, and returns the deleted value (or
+ * null)
+ */
+ Object deleteProperty(String key)
+ {
+ Object result = null;
+ if (properties != null)
+ {
+ result = properties.remove(key);
+ }
+ return result;
+ }
+
+ @Override
+ public String toString()
+ {
+ return id;
+ }
+
+ /**
+ * Getter provided for Castor binding only. Application code should call
+ * getProperty() or getProperties() instead.
+ *
+ * @deprecated
+ * @see #getProperty(String)
+ * @see #getProperties()
+ * @see jalview.ws.dbsources.Uniprot#getUniprotEntries
+ * @return
+ */
+ @Deprecated
+ public Hashtable<String, Object> getProps()
+ {
+ return properties;
+ }
+
+ /**
+ * Setter provided for Castor binding only. Application code should call
+ * setProperty() instead.
+ *
+ * @deprecated
+ * @return
+ */
+ @Deprecated
+ public void setProps(Hashtable<String, Object> props)
+ {
+ properties = props;
+ }
+
+ /**
+ * update entry with details from another entry concerning the same PDB
+ * ID/file spec.
+ *
+ * @param newEntry
+ * @return true if modifications were made
+ */
+ public boolean updateFrom(PDBEntry newEntry)
+ {
+ boolean modified = false;
+
+ if (getFile() == null)
+ {
+ // update file and type of file
+ modified = newEntry.getFile() != null;
+ setFile(newEntry.getFile());
+ }
+ if (newEntry.getType() != null && newEntry.getFile() != null
+ && newEntry.getFile().equals(getFile()))
+ {
+ setType(newEntry.getType());
+ }
+ if (getChainCode() == null
+ || (getChainCode() != null && getChainCode().length() == 0 && newEntry
+ .getChainCode() != null))
+ {
+ modified |= (getChainCode() == null || !newEntry.getChainCode()
+ .equals(getChainCode()));
+ setChainCode(newEntry.getChainCode());
+ }
+ if (newEntry.properties != null)
+ {
+ for (Entry<String, Object> entry : newEntry.properties.entrySet())
+ {
+ if (!entry.getValue().equals(getProperty(entry.getKey())))
+ {
+ modified = true;
+ }
+ setProperty(entry.getKey(), entry.getValue());
+ }
+ }
+ return modified;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff