/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
public class PDBEntry
{
- String file;
+ private String file;
- String type;
+ private String type;
- String id;
+ 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;
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)))
+ 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)));
+
}
/**
*
* @param filePath
*/
- public PDBEntry(String filePath, String pdbId)
+ // public PDBEntry(String filePath, String pdbId)
+ // {
+ // this.file = filePath;
+ // this.id = pdbId;
+ // }
+
+ public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
+ String filePath)
{
- this.file = filePath;
this.id = pdbId;
+ this.type = type == null ? null : type.toString();
+ this.file = filePath;
+ setChainCode(chain);
}
-
+
/**
* Copy constructor.
*
return file;
}
- public void setType(String type)
+ public void setType(String t)
{
- this.type = type;
+ this.type = t;
+ }
+
+ public void setType(PDBEntry.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;
+ }
+
+ /**
+ * 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<String,String>
+ 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;
+ }
}