X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FPDBEntry.java;h=1c1d192fcbabc754b547bff599aa21408d7af19c;hb=3f12f4932226512316ec113e600695150431fd0a;hp=398eae39bfea2b5e668725b6ca091946e489e8b6;hpb=c9c60ab441d23ab149afe22a739d8376c58b8cec;p=jalview.git
diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 398eae3..1c1d192 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -1,61 +1,298 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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;
-
-import java.util.*;
-public class PDBEntry
-{
- String file;
- String type;
- String id;
- Hashtable properties;
-
- public PDBEntry()
- { }
-
- public void setFile(String file)
- { this.file = file; }
-
- public String getFile()
- { return file; }
-
- public void setType(String type)
- { this.type = type; }
-
- public String getType()
- { return type; }
-
- public void setId(String id)
- { this.id = id; }
-
- public String getId()
- { return id; }
-
- public void setProperty(Hashtable property)
- {
- this.properties = property;
- }
-
- public Hashtable getProperty()
- {
- return properties;
- }
-
-
-}
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import java.util.Hashtable;
+
+public class PDBEntry
+{
+ 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)
+ *
+ * @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) entry.properties.clone();
+ }
+ }
+
+ public void setFile(String file)
+ {
+ this.file = file;
+ }
+
+ 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(Hashtable property)
+ {
+ this.properties = property;
+ }
+
+ public Hashtable getProperty()
+ {
+ 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;
+ }
+
+ /**
+ * 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.getProperty() != null)
+ {
+ if (properties == null)
+ {
+ properties = new Hashtable();
+ }
+ // TODO: getProperty -> Map
+ for (Object p : newEntry.getProperty().keySet())
+ {
+ if (properties.get(p) == null
+ || !properties.get(p).equals(newEntry.getProperty().get(p)))
+ {
+ modified = true;
+ }
+ properties.put(p, newEntry.getProperty().get(p));
+ }
+ }
+ return modified;
+ }
+}