-/**\r
- * \r
- */\r
-package jalview.ws.dbsources;\r
-\r
-import java.io.File;\r
-import java.io.FileReader;\r
-import java.io.IOException;\r
-import java.util.Enumeration;\r
-import java.util.Hashtable;\r
-import java.util.Vector;\r
-\r
-import org.exolab.castor.xml.Unmarshaller;\r
-\r
-import com.stevesoft.pat.Regex;\r
-\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.DBRefEntry;\r
-import jalview.datamodel.DBRefSource;\r
-import jalview.datamodel.PDBEntry;\r
-import jalview.datamodel.SequenceFeature;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.datamodel.UniprotEntry;\r
-import jalview.datamodel.UniprotFile;\r
-import jalview.io.FormatAdapter;\r
-import jalview.io.IdentifyFile;\r
-import jalview.ws.DBRefFetcher;\r
-import jalview.ws.ebi.EBIFetchClient;\r
-import jalview.ws.seqfetcher.DbSourceProxy;\r
-import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
-\r
-/**\r
- * @author JimP\r
- * \r
- */\r
-public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy\r
-{\r
- public Uniprot() {\r
- super();\r
- addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);\r
- addDbSourceProperty(DBRefSource.PROTSEQDB);\r
-// addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
- */\r
- public String getAccessionSeparator()\r
- {\r
- return null; // ";";\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getAccessionValidator()\r
- */\r
- public Regex getAccessionValidator()\r
- {\r
- return null;\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getDbSource()\r
- */\r
- public String getDbSource()\r
- {\r
- return DBRefSource.UNIPROT;\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getDbVersion()\r
- */\r
- public String getDbVersion()\r
- {\r
- return "0"; // we really don't know what version we're on.\r
- }\r
-\r
- private EBIFetchClient ebi = null;\r
-\r
- public Vector getUniprotEntries(File file)\r
- {\r
- UniprotFile uni = new UniprotFile();\r
- try\r
- {\r
- // 1. Load the mapping information from the file\r
- org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(uni.getClass().getClassLoader());\r
- java.net.URL url = getClass().getResource("/uniprot_mapping.xml");\r
- map.loadMapping(url);\r
-\r
- // 2. Unmarshal the data\r
- Unmarshaller unmar = new Unmarshaller(uni);\r
- unmar.setIgnoreExtraElements(true);\r
- unmar.setMapping(map);\r
-\r
- uni = (UniprotFile) unmar.unmarshal(new FileReader(file));\r
- }\r
- catch (Exception e)\r
- {\r
- System.out.println("Error getUniprotEntries() " + e);\r
- }\r
-\r
- return uni.getUniprotEntries();\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])\r
- */\r
- public AlignmentI getSequenceRecords(String queries) throws Exception\r
- {\r
- startQuery();\r
- try\r
- {\r
- Alignment al=null;\r
- ebi = new EBIFetchClient();\r
- StringBuffer result=new StringBuffer();\r
- // uniprotxml parameter required since december 2007\r
- File file = ebi.fetchDataAsFile("uniprot:" + queries, "uniprotxml", null);\r
- Vector entries = getUniprotEntries(file);\r
-\r
- if (entries != null)\r
- {\r
- // First, make the new sequences\r
- Enumeration en = entries.elements();\r
- while (en.hasMoreElements())\r
- {\r
- UniprotEntry entry = (UniprotEntry) en.nextElement();\r
-\r
- StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");\r
- Enumeration en2 = entry.getAccession().elements();\r
- while (en2.hasMoreElements())\r
- {\r
- name.append("|");\r
- name.append(en2.nextElement());\r
- }\r
- en2 = entry.getName().elements();\r
- while (en2.hasMoreElements())\r
- {\r
- name.append("|");\r
- name.append(en2.nextElement());\r
- }\r
-\r
- if (entry.getProtein() != null)\r
- {\r
- name.append(" " + entry.getProtein().getName().elementAt(0));\r
- }\r
-\r
- result.append(name + "\n"\r
- + entry.getUniprotSequence().getContent() + "\n");\r
-\r
- }\r
-\r
- // Then read in the features and apply them to the dataset\r
- al = parseResult(result.toString());\r
- if (al!=null)\r
- {\r
- // Decorate the alignment with database entries.\r
- addUniprotXrefs(al, entries);\r
- } else {\r
- results = result;\r
- }\r
- }\r
- stopQuery();\r
- return al;\r
- } catch (Exception e)\r
- {\r
- stopQuery();\r
- throw(e);\r
- }\r
- }\r
-\r
- /**\r
- * add an ordered set of UniprotEntry objects to an ordered set of seuqences.\r
- * \r
- * @param al -\r
- * a sequence of n sequences\r
- * @param entries\r
- * a seuqence of n uniprot entries to be analysed.\r
- */\r
- public void addUniprotXrefs(Alignment al, Vector entries)\r
- {\r
- for (int i = 0; i < entries.size(); i++)\r
- {\r
- UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
- Enumeration e = entry.getDbReference().elements();\r
- Vector onlyPdbEntries = new Vector();\r
- while (e.hasMoreElements())\r
- {\r
- PDBEntry pdb = (PDBEntry) e.nextElement();\r
- if (!pdb.getType().equals("PDB"))\r
- {\r
- continue;\r
- }\r
-\r
- onlyPdbEntries.addElement(pdb);\r
- }\r
- SequenceI sq = al.getSequenceAt(i);\r
- while (sq.getDatasetSequence()!=null)\r
- {\r
- sq = sq.getDatasetSequence();\r
- }\r
-\r
- Enumeration en2 = entry.getAccession().elements();\r
- while (en2.hasMoreElements())\r
- {\r
- // we always add as uniprot if we retrieved from uniprot or uniprot name\r
- sq.addDBRef(\r
- new DBRefEntry(DBRefSource.UNIPROT, getDbVersion(), en2.nextElement()\r
- .toString()));\r
- }\r
- sq.setPDBId(onlyPdbEntries);\r
- if (entry.getFeature() != null)\r
- {\r
- e = entry.getFeature().elements();\r
- while (e.hasMoreElements())\r
- {\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- sf.setFeatureGroup("Uniprot");\r
- sq.addSequenceFeature(sf);\r
- }\r
- }\r
- }\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)\r
- */\r
- public boolean isValidReference(String accession)\r
- {\r
- return true;\r
- }\r
- /**\r
- * return LDHA_CHICK uniprot entry\r
- */\r
- public String getTestQuery()\r
- {\r
- return "P00340";\r
- }\r
- public String getDbName()\r
- {\r
- return getDbSource();\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.UniprotEntry;
+import jalview.datamodel.UniprotFile;
+import jalview.ws.ebi.EBIFetchClient;
+import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.ws.seqfetcher.DbSourceProxyImpl;
+
+import java.io.File;
+import java.io.FileReader;
+import java.io.Reader;
+import java.util.Vector;
+
+import org.exolab.castor.xml.Unmarshaller;
+
+import com.stevesoft.pat.Regex;
+
+/**
+ * @author JimP
+ *
+ */
+public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
+{
+
+ private static final String BAR_DELIMITER = "|";
+
+ private static final String NEWLINE = "\n";
+
+ private static org.exolab.castor.mapping.Mapping map;
+
+ /**
+ * Constructor
+ */
+ public Uniprot()
+ {
+ super();
+ addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);
+ addDbSourceProperty(DBRefSource.PROTSEQDB);
+ // addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
+ */
+ public String getAccessionSeparator()
+ {
+ return null; // ";";
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionValidator()
+ */
+ public Regex getAccessionValidator()
+ {
+ return new Regex("([A-Z]+[0-9]+[A-Z0-9]+|[A-Z0-9]+_[A-Z0-9]+)");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbSource()
+ */
+ public String getDbSource()
+ {
+ return DBRefSource.UNIPROT;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbVersion()
+ */
+ public String getDbVersion()
+ {
+ return "0"; // we really don't know what version we're on.
+ }
+
+ /**
+ * Reads a file containing the reply to the EBI Fetch Uniprot data query,
+ * unmarshals it to a UniprotFile object, and returns the list of UniprotEntry
+ * data models (mapped from <entry> elements)
+ *
+ * @param fileReader
+ * @return
+ */
+ public Vector<UniprotEntry> getUniprotEntries(Reader fileReader)
+ {
+ UniprotFile uni = new UniprotFile();
+ try
+ {
+ if (map == null)
+ {
+ // 1. Load the mapping information from the file
+ map = new org.exolab.castor.mapping.Mapping(uni.getClass()
+ .getClassLoader());
+ java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
+ map.loadMapping(url);
+ }
+
+ // 2. Unmarshal the data
+ Unmarshaller unmar = new Unmarshaller(uni);
+ unmar.setIgnoreExtraElements(true);
+ unmar.setMapping(map);
+ if (fileReader != null)
+ {
+ uni = (UniprotFile) unmar.unmarshal(fileReader);
+ }
+ } catch (Exception e)
+ {
+ System.out.println("Error getUniprotEntries() " + e);
+ }
+
+ return uni.getUniprotEntries();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
+ */
+ public AlignmentI getSequenceRecords(String queries) throws Exception
+ {
+ startQuery();
+ try
+ {
+ queries = queries.toUpperCase().replaceAll(
+ "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
+ AlignmentI al = null;
+ EBIFetchClient ebi = new EBIFetchClient();
+ // uniprotxml parameter required since december 2007
+ // uniprotkb dbname changed introduced december 2008
+ File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
+ null);
+ Vector<UniprotEntry> entries = getUniprotEntries(new FileReader(file));
+
+ if (entries != null)
+ {
+ /*
+ * If Castor binding included sequence@length, we could guesstimate the
+ * size of buffer to hold the alignment
+ */
+ StringBuffer result = new StringBuffer(128);
+ // First, make the new sequences
+ for (UniprotEntry entry : entries)
+ {
+ StringBuilder name = constructSequenceFastaHeader(entry);
+
+ result.append(name).append(NEWLINE)
+ .append(entry.getUniprotSequence().getContent())
+ .append(NEWLINE);
+ }
+
+ // Then read in the features and apply them to the dataset
+ al = parseResult(result.toString());
+ if (al != null)
+ {
+ // Decorate the alignment with database entries.
+ addUniprotXrefs(al, entries);
+ }
+ else
+ {
+ results = result;
+ }
+ }
+ stopQuery();
+ return al;
+ } catch (Exception e)
+ {
+ stopQuery();
+ throw (e);
+ }
+ }
+
+ /**
+ * Construct a Fasta-format sequence header by concatenating the source,
+ * accession id(s) and name(s), delimited by '|', plus any protein names, now
+ * with space rather than bar delimiter
+ *
+ * @param entry
+ * @return
+ */
+ public static StringBuilder constructSequenceFastaHeader(
+ UniprotEntry entry)
+ {
+ StringBuilder name = new StringBuilder(32);
+ name.append(">UniProt/Swiss-Prot");
+ for (String accessionId : entry.getAccession())
+ {
+ name.append(BAR_DELIMITER);
+ name.append(accessionId);
+ }
+ for (String n : entry.getName())
+ {
+ name.append(BAR_DELIMITER);
+ name.append(n);
+ }
+
+ if (entry.getProtein() != null && entry.getProtein().getName() != null)
+ {
+ for (String nm : entry.getProtein().getName())
+ {
+ name.append(" ").append(nm);
+ }
+ }
+ return name;
+ }
+
+ /**
+ * add an ordered set of UniprotEntry objects to an ordered set of seuqences.
+ *
+ * @param al
+ * - a sequence of n sequences
+ * @param entries
+ * a list of n uniprot entries to be analysed.
+ */
+ public void addUniprotXrefs(AlignmentI al, Vector<UniprotEntry> entries)
+ {
+ final String dbVersion = getDbVersion();
+
+ for (int i = 0; i < entries.size(); i++)
+ {
+ UniprotEntry entry = entries.elementAt(i);
+ Vector<PDBEntry> onlyPdbEntries = new Vector<PDBEntry>();
+ Vector<DBRefEntry> dbxrefs = new Vector<DBRefEntry>();
+
+ for (PDBEntry pdb : entry.getDbReference())
+ {
+ DBRefEntry dbr = new DBRefEntry();
+ dbr.setSource(pdb.getType());
+ dbr.setAccessionId(pdb.getId());
+ dbr.setVersion(DBRefSource.UNIPROT + ":" + dbVersion);
+ dbxrefs.addElement(dbr);
+ if ("PDB".equals(pdb.getType()))
+ {
+ onlyPdbEntries.addElement(pdb);
+ }
+ }
+
+ SequenceI sq = al.getSequenceAt(i);
+ while (sq.getDatasetSequence() != null)
+ {
+ sq = sq.getDatasetSequence();
+ }
+
+ for (String accessionId : entry.getAccession())
+ {
+ /*
+ * add as uniprot whether retrieved from uniprot or uniprot_name
+ */
+ sq.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
+ accessionId));
+ }
+
+ for (DBRefEntry dbRef : dbxrefs)
+ {
+ sq.addDBRef(dbRef);
+ }
+ sq.setPDBId(onlyPdbEntries);
+ if (entry.getFeature() != null)
+ {
+ for (SequenceFeature sf : entry.getFeature())
+ {
+ sf.setFeatureGroup("Uniprot");
+ sq.addSequenceFeature(sf);
+ }
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
+ */
+ public boolean isValidReference(String accession)
+ {
+ // TODO: make the following a standard validator
+ return (accession == null || accession.length() < 2) ? false
+ : getAccessionValidator().search(accession);
+ }
+
+ /**
+ * return LDHA_CHICK uniprot entry
+ */
+ public String getTestQuery()
+ {
+ return "P00340";
+ }
+
+ public String getDbName()
+ {
+ return "Uniprot"; // getDbSource();
+ }
+
+ @Override
+ public int getTier()
+ {
+ return 0;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff