X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FPDBEntry.java;h=14035957fe08c181c99d2580e042f0ac756bcf8e;hb=ee0f6c877392ffc2018ae1a832042fbd364730ab;hp=16f88642f3b71e6d37e109e4a3fbc7b26c2736b0;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 16f8864..1403595 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -1,73 +1,383 @@
-/*
- * 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
- * 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 jalview.util.CaseInsensitiveString;
+
+import java.util.Hashtable;
+
+public class PDBEntry
+{
+ private static final int PDB_ID_LENGTH = 4;
+
+ 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));
+ }
+ }
+
+ /**
+ * constant for storing chain code in properties table
+ */
+ private static final String CHAIN_ID = "chain_code";
+
+ Hashtable properties;
+
+ /**
+ * Answers true if obj is a PDBEntry with the same id and chain code (both
+ * ignoring case), file, type and properties
+ */
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == null || !(obj instanceof PDBEntry))
+ {
+ return false;
+ }
+ if (obj == this)
+ {
+ return true;
+ }
+ PDBEntry o = (PDBEntry) obj;
+
+ /*
+ * note that chain code is stored as a property wrapped by a
+ * CaseInsensitiveString, so we are in effect doing a
+ * case-insensitive comparison of chain codes
+ */
+ boolean idMatches = id == o.id
+ || (id != null && id.equalsIgnoreCase(o.id));
+ boolean fileMatches = file == o.file
+ || (file != null && file.equals(o.file));
+ boolean typeMatches = type == o.type
+ || (type != null && type.equals(o.type));
+ if (idMatches && fileMatches && typeMatches)
+ {
+ return properties == o.properties
+ || (properties != null && properties.equals(o.properties));
+ }
+ return false;
+ }
+
+ /**
+ * 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)
+ {
+ init(pdbId, chain, type, filePath);
+ }
+
+ /**
+ * @param pdbId
+ * @param chain
+ * @param type
+ * @param filePath
+ */
+ void init(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();
+ }
+ }
+
+ /**
+ * Make a PDBEntry from a DBRefEntry. The accession code is used for the PDB
+ * id, but if it is 5 characters in length, the last character is removed and
+ * set as the chain code instead.
+ *
+ * @param dbr
+ */
+ public PDBEntry(DBRefEntry dbr)
+ {
+ if (!DBRefSource.PDB.equals(dbr.getSource()))
+ {
+ throw new IllegalArgumentException("Invalid source: "
+ + dbr.getSource());
+ }
+
+ String pdbId = dbr.getAccessionId();
+ String chainCode = null;
+ if (pdbId.length() == PDB_ID_LENGTH + 1)
+ {
+ char chain = pdbId.charAt(PDB_ID_LENGTH);
+ if (('a' <= chain && chain <= 'z') || ('A' <= chain && chain <= 'Z'))
+ {
+ pdbId = pdbId.substring(0, PDB_ID_LENGTH);
+ chainCode = String.valueOf(chain);
+ }
+ }
+ init(pdbId, chainCode, null, null);
+ }
+
+ 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 CaseInsensitiveString(chainCode));
+ }
+
+ @Override
+ public String toString()
+ {
+ return id;
+ }
+
+ /**
+ * Answers true if this object is either equivalent to, or can be 'improved'
+ * by, the given entry.
+ *
+ * If newEntry has the same id (ignoring case), and doesn't have a conflicting
+ * file spec or chain code, then update this entry from its file and/or chain
+ * code.
+ *
+ * @param newEntry
+ * @return true if modifications were made
+ */
+ protected boolean updateFrom(PDBEntry newEntry)
+ {
+ if (this.equals(newEntry))
+ {
+ return true;
+ }
+
+ String newId = newEntry.getId();
+ if (newId == null || getId() == null)
+ {
+ return false; // shouldn't happen
+ }
+
+ /*
+ * id (less any chain code) has to match (ignoring case)
+ */
+ if (!getId().equalsIgnoreCase(newId))
+ {
+ return false;
+ }
+
+ /*
+ * Don't update if associated with different structure files
+ */
+ String newFile = newEntry.getFile();
+ if (newFile != null && getFile() != null && !newFile.equals(getFile()))
+ {
+ return false;
+ }
+
+ /*
+ * Don't update if associated with different chains (ignoring case)
+ */
+ String newChain = newEntry.getChainCode();
+ if (newChain != null && newChain.length() > 0 && getChainCode() != null
+ && getChainCode().length() > 0
+ && !getChainCode().equalsIgnoreCase(newChain))
+ {
+ return false;
+ }
+
+ /*
+ * set file path if not already set
+ */
+ String newType = newEntry.getType();
+ if (getFile() == null && newFile != null)
+ {
+ setFile(newFile);
+ setType(newType);
+ }
+
+ /*
+ * set file type if new entry has it and we don't
+ * (for the case where file was not updated)
+ */
+ if (getType() == null && newType != null)
+ {
+ setType(newType);
+ }
+
+ /*
+ * set chain if not already set (we excluded differing
+ * chains earlier) (ignoring case change only)
+ */
+ if (newChain != null && newChain.length() > 0
+ && !newChain.equalsIgnoreCase(getChainCode()))
+ {
+ setChainCode(newChain);
+ }
+
+ /*
+ * copy any new properties; notice this may include chain_code,
+ * but we excluded differing chain codes earlier
+ */
+ if (newEntry.getProperty() != null)
+ {
+ if (properties == null)
+ {
+ properties = new Hashtable();
+ }
+ for (Object p : newEntry.getProperty().keySet())
+ {
+ /*
+ * copy properties unless value matches; this defends against changing
+ * the case of chain_code which is wrapped in a CaseInsensitiveString
+ */
+ Object value = newEntry.getProperty().get(p);
+ if (!value.equals(properties.get(p)))
+ {
+ properties.put(p, newEntry.getProperty().get(p));
+ }
+ }
+ }
+ return true;
+ }
+}