X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FPDBEntry.java;h=741ef0774cd9ed2ec3ed9463089215f51ff61e42;hb=584ab9644955bec02d96448361b8aac5b9542599;hp=39d491bb8640caa49ded290a09cd98d33f058c1b;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java index 39d491b..741ef07 100755 --- a/src/jalview/datamodel/PDBEntry.java +++ b/src/jalview/datamodel/PDBEntry.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 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. * @@ -22,12 +22,31 @@ package jalview.datamodel; import jalview.util.CaseInsensitiveString; +import java.util.Collections; +import java.util.Enumeration; import java.util.Hashtable; public class PDBEntry { + + /** + * constant for storing chain code in properties table + */ + private static final String CHAIN_ID = "chain_code"; + + private Hashtable properties; + private static final int PDB_ID_LENGTH = 4; + /** + * property set when id is a 'manufactured' identifier from the structure data's filename + */ + private static final String FAKED_ID = "faked_pdbid"; + /** + * property set when the id is authoritative, and should be used in preference to any identifiers in the structure data + */ + private static final String AUTHORITATIVE_ID = "authoritative_pdbid"; + private String file; private String type; @@ -36,7 +55,39 @@ public class PDBEntry public enum Type { - PDB, MMCIF, FILE; + // TODO is FILE needed; if not is this enum needed, or can we + // use FileFormatI for PDB, MMCIF? + PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), BCIF("bcif","bcif"),FILE("?", "?"); + + /* + * file extension for cached structure file; must be one that + * is recognised by Chimera 'open' command + * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html + */ + String ext; + + /* + * format specifier used in dbfetch request + * @see http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#pdb + */ + String format; + + private Type(String fmt, String ex) + { + format = fmt; + ext = ex; + } + + public String getFormat() + { + return format; + } + + public String getExtension() + { + return ext; + } + /** * case insensitive matching for Type enum * @@ -68,13 +119,6 @@ public class PDBEntry } /** - * 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 */ @@ -117,17 +161,6 @@ public class 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) { @@ -137,13 +170,14 @@ public class PDBEntry /** * @param pdbId * @param chain - * @param type + * @param entryType * @param filePath */ - void init(String pdbId, String chain, PDBEntry.Type type, String filePath) + void init(String pdbId, String chain, PDBEntry.Type entryType, + String filePath) { this.id = pdbId; - this.type = type == null ? null : type.toString(); + this.type = entryType == null ? null : entryType.toString(); this.file = filePath; setChainCode(chain); } @@ -160,7 +194,7 @@ public class PDBEntry id = entry.id; if (entry.properties != null) { - properties = (Hashtable) entry.properties.clone(); + properties = (Hashtable) entry.properties.clone(); } } @@ -175,8 +209,8 @@ public class PDBEntry { if (!DBRefSource.PDB.equals(dbr.getSource())) { - throw new IllegalArgumentException("Invalid source: " - + dbr.getSource()); + throw new IllegalArgumentException( + "Invalid source: " + dbr.getSource()); } String pdbId = dbr.getAccessionId(); @@ -193,9 +227,9 @@ public class PDBEntry init(pdbId, chainCode, null, null); } - public void setFile(String file) + public void setFile(String f) { - this.file = file; + this.file = f; } public String getFile() @@ -228,14 +262,33 @@ public class PDBEntry return id; } - public void setProperty(Hashtable property) + public void setProperty(String key, Object value) { - this.properties = property; + if (this.properties == null) + { + this.properties = new Hashtable(); + } + properties.put(key, value); } - public Hashtable getProperty() + public Object getProperty(String key) { - return properties; + 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 getProperties() + { + if (properties == null) + { + return Collections.emptyEnumeration(); + } + return properties.keys(); } /** @@ -248,24 +301,37 @@ public class PDBEntry : 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 (properties == null) + if (chainCode == null) { - if (chainCode == null) - { - // nothing to do. - return; - } - properties = new Hashtable(); + deleteProperty(CHAIN_ID); } - if (chainCode == null) + else { - properties.remove(CHAIN_ID); - return; + setProperty(CHAIN_ID, new CaseInsensitiveString(chainCode)); } - // update property for non-null chainCode - properties.put(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 @@ -275,6 +341,35 @@ public class PDBEntry } /** + * 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 getProps() + { + return properties; + } + + /** + * Setter provided for Castor binding only. Application code should call + * setProperty() instead. + * + * @deprecated + * @return + */ + @Deprecated + public void setProps(Hashtable props) + { + properties = props; + } + + /** * Answers true if this object is either equivalent to, or can be 'improved' * by, the given entry. *

@@ -285,7 +380,7 @@ public class PDBEntry * @param newEntry * @return true if modifications were made */ - protected boolean updateFrom(PDBEntry newEntry) + public boolean updateFrom(PDBEntry newEntry) { if (this.equals(newEntry)) { @@ -298,21 +393,40 @@ public class PDBEntry return false; // shouldn't happen } - /* - * id (less any chain code) has to match (ignoring case) - */ - if (!getId().equalsIgnoreCase(newId)) - { - return false; - } + boolean idMatches = getId().equalsIgnoreCase(newId); /* * Don't update if associated with different structure files */ String newFile = newEntry.getFile(); - if (newFile != null && getFile() != null && !newFile.equals(getFile())) + if (newFile != null && getFile() != null) { - return false; + if (!newFile.equals(getFile())) + { + return false; + } + else + { + // files match. + if (!idMatches) + { + // this shouldn't happen, but could do if the id from the + // file is not the same as the id from the authority that provided + // the file + if (!newEntry.fakedPDBId() && !isAuthoritative()) + { + return false; + } // otherwise we can update + } + } + } + else + { + // one has data, one doesn't .. + if (!idMatches) + { + return false; + } // otherwise maybe can update } /* @@ -356,28 +470,153 @@ public class PDBEntry } /* - * copy any new properties; notice this may include chain_code, - * but we excluded differing chain codes earlier + * copy any new or modified properties */ - if (newEntry.getProperty() != null) + Enumeration newProps = newEntry.getProperties(); + while (newProps.hasMoreElements()) { - if (properties == null) + /* + * copy properties unless value matches; this defends against changing + * the case of chain_code which is wrapped in a CaseInsensitiveString + */ + String key = newProps.nextElement(); + Object value = newEntry.getProperty(key); + if (FAKED_ID.equals(key) || AUTHORITATIVE_ID.equals(key)) { - properties = new Hashtable(); + // we never update the fake ID property + continue; } - for (Object p : newEntry.getProperty().keySet()) + if (!value.equals(getProperty(key))) { - /* - * 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)); - } + setProperty(key, value); } } return true; } + + public void setAuthoritative(boolean isAuthoritative) + { + setProperty(AUTHORITATIVE_ID, Boolean.valueOf(isAuthoritative)); + } + + /** + * + * @return true if the identifier should be preferred over any identifiers + * embedded in the structure data + */ + public boolean isAuthoritative() + { + if (_hasProperty(AUTHORITATIVE_ID)) + { + return ((Boolean)getProperty(AUTHORITATIVE_ID)); + } + return false; + } + + /** + * set when Jalview has manufactured the ID using a local filename + * @return + */ + public boolean fakedPDBId() + { + if (_hasProperty(FAKED_ID)) + { + return true; + } + return false; + } + public void setFakedPDBId(boolean faked) + { + if (faked) + { + setProperty(FAKED_ID, Boolean.TRUE); + } + else + { + if (properties!=null) { + properties.remove(FAKED_ID); + } + } + } + + private boolean _hasProperty(final String key) + { + return (properties != null && properties.containsKey(key)); + } + + private static final String RETRIEVE_FROM = "RETRIEVE_FROM"; + + private static final String PROVIDER = "PROVIDER"; + + private static final String MODELPAGE = "PROVIDERPAGE"; + + /** + * Permanent URI for retrieving the original structure data + * + * @param urlStr + */ + public void setRetrievalUrl(String urlStr) + { + setProperty(RETRIEVE_FROM, urlStr); + } + + public boolean hasRetrievalUrl() + { + return _hasProperty(RETRIEVE_FROM); + } + + /** + * get the Permanent URI for retrieving the original structure data + */ + public String getRetrievalUrl() + { + return (String) getProperty(RETRIEVE_FROM); + } + + /** + * Data provider name - from 3D Beacons + * + * @param provider + */ + public void setProvider(String provider) + { + setProperty(PROVIDER, provider); + } + + /** + * Get Data provider name - from 3D Beacons + * + */ + public String getProvider() + { + return (String) getProperty(PROVIDER); + } + + /** + * Permanent URI for retrieving the original structure data + * + * @param urlStr + */ + public void setProviderPage(String urlStr) + { + setProperty(MODELPAGE, urlStr); + } + + /** + * get the Permanent URI for retrieving the original structure data + */ + public String getProviderPage() + { + return (String) getProperty(MODELPAGE); + } + + public boolean hasProviderPage() + { + return _hasProperty(MODELPAGE); + } + + public boolean hasProvider() + { + return _hasProperty(PROVIDER); + } }