X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FPDBEntry.java;h=db792e270fd7d6042eac33df4b026f84cc00ad3f;hb=8edebdd9789b2d93fb8f9db24b8be2c1e6317690;hp=d65293fc0274a6ce679316738394d47409f8a7b4;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index d65293f..db792e2 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -1,32 +1,41 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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 .
+ * 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.*;
+import java.util.Hashtable;
public class PDBEntry
{
- String file;
+ private String file;
+
+ private String type;
- String type;
+ private String id;
- String id;
+ private String chainCode;
+ public enum Type
+ {
+ PDB, FILE
+ }
Hashtable properties;
/*
@@ -34,6 +43,7 @@ public class PDBEntry
*
* @see java.lang.Object#equals(java.lang.Object)
*/
+ @Override
public boolean equals(Object obj)
{
if (obj == null || !(obj instanceof PDBEntry))
@@ -41,28 +51,62 @@ public class PDBEntry
return false;
}
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
+ 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)))
+ && (chainCode == o.chainCode || (chainCode != null
+ && o.chainCode != null && o.chainCode
+ .equalsIgnoreCase(chainCode)))
&& (properties == o.properties || (properties != null
&& o.properties != null && properties
- .equals(o.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.chainCode = chain;
+ this.type = type == null ? null : type.toString();
+ this.file = filePath;
+ }
+
+ /**
+ * Copy constructor.
+ *
+ * @param entry
+ */
public PDBEntry(PDBEntry entry)
{
file = entry.file;
type = entry.type;
id = entry.id;
+ chainCode = entry.chainCode;
if (entry.properties != null)
{
properties = (Hashtable) entry.properties.clone();
@@ -79,9 +123,13 @@ public class PDBEntry
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()
@@ -109,4 +157,14 @@ public class PDBEntry
return properties;
}
+ public String getChainCode()
+ {
+ return chainCode;
+ }
+
+ public void setChainCode(String chainCode)
+ {
+ this.chainCode = chainCode;
+ }
+
}