From 5c0c34895c290164caad28e0aeac86b5a52ee655 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 14 Dec 2006 16:40:55 +0000 Subject: [PATCH] remove old ebi packages git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@260 be28352e-c001-0410-b1a7-c7978e42abec --- src/uk/ac/ebi/msd/vamsas/vamav/VAMAVClient.java | 195 --- .../vamsas/vamav/documentmanagement/PDBUtil.java | 425 ------ .../VamsasDocumentProcessor.java | 1380 -------------------- .../exceptions/IncorrectDocumentException.java | 61 - .../exceptions/UnableToProcessException.java | 63 - .../grouping/SequenceGrouping.java | 1169 ----------------- .../grouping/SequenceGrouping_domain.java | 272 ---- .../grouping/SequenceGrouping_structure.java | 298 ----- .../UnableToGroupSequencesException.java | 61 - .../msd/vamsas/vamav/session/SessionManager.java | 983 -------------- .../ebi/msd/vamsas/vamav/session/VAMAVSession.java | 462 ------- .../session/exceptions/UnableToOpenSession.java | 50 - 12 files changed, 5419 deletions(-) delete mode 100755 src/uk/ac/ebi/msd/vamsas/vamav/VAMAVClient.java delete mode 100755 src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/PDBUtil.java delete mode 100755 src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/VamsasDocumentProcessor.java delete mode 100755 src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/exceptions/IncorrectDocumentException.java delete mode 100755 src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/exceptions/UnableToProcessException.java delete mode 100755 src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/SequenceGrouping.java delete mode 100755 src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/SequenceGrouping_domain.java delete mode 100755 src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/SequenceGrouping_structure.java delete mode 100755 src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/exceptions/UnableToGroupSequencesException.java delete mode 100755 src/uk/ac/ebi/msd/vamsas/vamav/session/SessionManager.java delete mode 100755 src/uk/ac/ebi/msd/vamsas/vamav/session/VAMAVSession.java delete mode 100755 src/uk/ac/ebi/msd/vamsas/vamav/session/exceptions/UnableToOpenSession.java diff --git a/src/uk/ac/ebi/msd/vamsas/vamav/VAMAVClient.java b/src/uk/ac/ebi/msd/vamsas/vamav/VAMAVClient.java deleted file mode 100755 index 3734057..0000000 --- a/src/uk/ac/ebi/msd/vamsas/vamav/VAMAVClient.java +++ /dev/null @@ -1,195 +0,0 @@ -/* - *============================================================================= -* EMBL - European Bioinformatics institute -* MSD Group -* VAMSAS Project -* -* Copyright (c) 2005 The European Bioinformatics Institute. All rights reserved. -* -* Redistribution and use in source and binary forms, with or without -* modification. -* -*The European Bioinformatics Institute may publish revised and/or new -*versions of this license with new releases of VAMSAS software. -*============================================================================== - * - * - * Created on Feb 22, 2006 - * - * @author Pierre MARGUERITE - * @version 2 - * @since 22 Feb. 2006 - */ -package uk.ac.ebi.msd.vamsas.vamav; - -import java.io.File; - -import org.vamsas.client.ClientHandle; -import org.vamsas.client.Events; -import org.vamsas.client.IClientDocument; -import org.vamsas.client.InvalidSessionUrnException; -import org.vamsas.client.UserHandle; -import org.vamsas.client.simpleclient.SimpleClient; -import org.vamsas.client.simpleclient.VamsasSession; - -import uk.ac.ebi.msd.vamsas.vamav.communication.astexviewer.AVClientIntf; -import uk.ac.ebi.msd.vamsas.vamav.session.VAMAVSession; -import uk.ac.ebi.msd.vamsas.vamav.util.logger.VAMAVLogger; -import uk.ac.ebi.msd.vamsas.vamav.util.logger.VAMAVLoggerImpl; - - -/** - * This class represents a VAMSAS client in the VAMSAS workflow (VAMSAS Client API), - * - * @author Pierre MARGUERITE - * @since 22 Feb. 2006 - * @version 2 - * - */ -public class VAMAVClient extends SimpleClient { - - - private String lastStatus = Events.DOCUMENT_CREATE; - private final VAMAVLogger logger = new VAMAVLoggerImpl(this.getClass()); - private VAMAVSession vamavSession = null; - private AVClientIntf avclient = null; - private VamsasSession sess = null; - private IClientDocument document = null; - - - /** - * Should not be used - * @param applicationHandle application handle for the current application - * @throws InvalidSessionUrnException if a error occurs during the creation of the client and the session. - */ - @Deprecated - public VAMAVClient (ClientHandle applicationHandle)throws InvalidSessionUrnException - { - super(null, applicationHandle, null); - this.client = applicationHandle; - - } - /** - * Inits a client with a given user and a given Client handle in a given session - * @param user information, of the user opening the session - * @param client the clientHandle - * @param sess Session in which is opened the client. - * @throws InvalidSessionUrnException if a error occurs during the creation of the client and the session. - - */ - public VAMAVClient ( - UserHandle user, - ClientHandle client, - VamsasSession _sess) throws InvalidSessionUrnException{ - super(user, client, _sess); - this.sess = _sess; - } - - /** - * Inits a client with a given user and a given Client handle in a given session - * and an archive file from a previous session/treatment - * @param user information, of the user opening the session - * @param client the clientHandle - * @param _sess Session in which is opened the client. - * @param importingArchive - * - * @throws Exception raises if an error occurs during the creation of the client (archive reading, incorrect session, ...) - */ - public VAMAVClient( - UserHandle user, - ClientHandle client, - VamsasSession _sess, - File importingArchive) - throws Exception { - super(user, client, _sess, importingArchive); - this.sess = _sess; - } - - /** - * @see org.vamsas.client.IClient#getAbout() - */ - public String getAbout() { - return new String("VAMAV Client version $version$ build $build$"); - } - - /** - * a clone the current VAMSASClient object - * @return a clone object of the current object - */ - public Object clone() - { - VAMAVClient client = null; - try - { - client = new VAMAVClient(this.user, this.client, this.sess);//this.SessionUrn); - //client.setVAMAVDocument(this.getClientDocument()); - } - catch (InvalidSessionUrnException isuE) - { - this.logger.appliError("Unable to clone client."); - this.logger.sessionError("Unable to clone client."); - client = null; - } - return client; - } - - /** - * Retrieves the vAMAVSession attribut - * - * @return Returns the vAMAVSession. - */ - public VAMAVSession getVAMAVSession() - { - return this.vamavSession; - } - - /** - *Sets session attribut - * - * @param session The vAMAVSession to set. - */ - public void setVAMAVSession(VAMAVSession session) - { - this.vamavSession = session; - this.logger.setSession(session); - } - - /** - * Retrieves the avclient attribut - * - * @return Returns the avclient. - */ - public AVClientIntf getAvclient() - { - return this.avclient; - } - - /** - *Sets avclient attribut - * - * @param avclient The avclient to set. - */ - public void setAvclient(AVClientIntf avclient) - { - this.avclient = avclient; - } -/** - * Set current document associated to the current client - * @param document the document object to associate to the client - */ - public void setVAMAVDocument(IClientDocument document) - { - if (document != null) - { - this.document = document; - } - } - - public void setUser(UserHandle _user) - { - if (_user !=null) - { - this.user = _user; - } - } -} diff --git a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/PDBUtil.java b/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/PDBUtil.java deleted file mode 100755 index bb876e5..0000000 --- a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/PDBUtil.java +++ /dev/null @@ -1,425 +0,0 @@ -/* - * EMBL - European Bioinformatics institute - * MSD Group - * VAMSAS Project - * - *Created on 28 oct. 2005 - * @author Pierre MARGUERITE - * @version 1 - * @since 28 oct. 2005 - */ -package uk.ac.ebi.msd.vamsas.vamav.documentmanagement; - - -import uk.ac.ebi.msd.vamsas.vamav.session.VAMAVSession; -import uk.ac.ebi.msd.vamsas.vamav.util.data.DataBuffer; -import uk.ac.ebi.msd.vamsas.vamav.util.data.PDBEntry; -import uk.ac.ebi.msd.vamsas.vamav.util.file.PlainTextFileReader; -import uk.ac.ebi.msd.vamsas.vamav.util.logger.VAMAVLogger; -import uk.ac.ebi.msd.vamsas.vamav.util.logger.VAMAVLoggerImpl; -import uk.ac.ebi.msd.vamsas.vamav.util.pool.DataBufferPool; -import uk.ac.ebi.msd.vamsas.vamav.util.pool.StringBufferPool; - -import java.io.File; -import java.io.IOException; -import java.util.ArrayList; -import java.util.Enumeration; -import java.util.Hashtable; - -/** - * Convenient methods for PDB entry manipulation - * - * @author Pierre MARGUERITE - * @version 1 - * @since 28 oct. 2005 - * - */ -public class PDBUtil - { - private VAMAVLogger logger = new VAMAVLoggerImpl(this.getClass()); - - private static Hashtable AminoAcids = null; - - /** - * Constructor - * - */ - public PDBUtil(String session) - { - super(); - logger.setSession(session); - - } - - /** - * Constructor - * - */ - public PDBUtil(VAMAVSession session) - { - super(); - logger.setSession(session); - - } - /** - * PDB Format - * http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_35.html - * - * @param entry - * @return - */ - public ArrayList GetChain(PDBEntry entry) - { - if( entry == null) return null; - File pdbFile = entry.getPdbFile(); - if (pdbFile == null || !pdbFile.exists() ) - { - return null; - } - logger.sessionInfo("Retrieving PDB sequence from PDB file."); - ArrayList chains = null; - PlainTextFileReader reader = new PlainTextFileReader(pdbFile); - try - { - reader.openFile(); - DataBuffer line = null; - Hashtable retrievingChains = new Hashtable(); - while (( line = reader.getLine()) !=null) - { - /*System.out.println("line "+line);*/ - if( line.toString().startsWith("SEQRES"))//.matches("^SEQRES*")) - {//chain line found - /*System.out.println("SEQRES found "); - System.out.println("line "+line);*/ - //12 Character chainID - char chainID = line.charAt(12 -1); - String chainName = String.valueOf(chainID); - /*System.out.println("chainName "+chainName);*/ - StringBuffer seq = retrievingChains.get(chainName.intern()); - if (seq == null) - { - seq = StringBufferPool.getString(); - } - - /* System.out.println("chain retrieves.");*/ -// 20 23 Residue name resName Residue name. - if(line.length()>=23 ) - { - String aa = line.substring(20-1, 23-1); - if( aa != null) - { - aa = aa.trim(); - if(aa.length()>0) - seq.append(get1LetterCodeFrom3LettersCode(aa)); - - } - } - //24 - 27 Residue name resName Residue name. - if(line.length()>=27 ) - { - String aa = line.substring(24-1, 27-1); - if( aa != null) - { - aa = aa.trim(); - if( aa.length()>0) - seq.append(get1LetterCodeFrom3LettersCode(aa)); - } - } - //28 - 30 Residue name resName Residue name. - if(line.length()>=31 ) - { - String aa = line.substring(28-1, 31-1); - if( aa != null) - { - aa = aa.trim(); - if( aa.length()>0) - seq.append(get1LetterCodeFrom3LettersCode(aa)); - } - } - //32 - 34 Residue name resName Residue name. - if(line.length()>=35 ) - { - String aa = line.substring(32-1, 35-1); - if( aa != null) - { - aa = aa.trim(); - if( aa.length()>0) - seq.append(get1LetterCodeFrom3LettersCode(aa)); - } - } - //36 - 38 Residue name resName Residue name. - if(line.length()>=39 ) - { - String aa = line.substring(36-1, 39-1); - if( aa != null) - { - aa = aa.trim(); - if( aa.length()>0) - seq.append(get1LetterCodeFrom3LettersCode(aa)); - } - } - //40 - 42 Residue name resName Residue name. - if(line.length()>=42 ) - { - String aa = line.substring(40-1, 43-1); - if( aa != null) - { - aa = aa.trim(); - if( aa.length()>0) - seq.append(get1LetterCodeFrom3LettersCode(aa)); - } - } - //44 - 46 Residue name resName Residue name. - if(line.length()>=47 ) - { - String aa = line.substring(44-1, 47-1); - if( aa != null) - { - aa = aa.trim(); - if( aa.length()>0) - seq.append(get1LetterCodeFrom3LettersCode(aa)); - } - } - //48 - 50 Residue name resName Residue name. - if(line.length()>=51 ) - { - String aa = line.substring(48-1, 51-1); - if( aa != null) - { - aa = aa.trim(); - if( aa.length()>0) - seq.append(get1LetterCodeFrom3LettersCode(aa)); - } - } - //52 - 54 Residue name resName Residue name. - if(line.length()>=55 ) - { - String aa = line.substring(52-1, 55-1); - if( aa != null) - { - aa = aa.trim(); - if( aa.length()>0) - seq.append(get1LetterCodeFrom3LettersCode(aa)); - } - } - //56 - 58 Residue name resName Residue name. - if(line.length()>=59 ) - { - String aa = line.substring(56-1, 59-1); - if( aa != null) - { - aa = aa.trim(); - if( aa.length()>0) - seq.append(get1LetterCodeFrom3LettersCode(aa)); - } - } - //60 - 62 Residue name resName Residue name. - if(line.length()>=63 ) - { - String aa = line.substring(60-1, 63-1); - if( aa != null) - { - aa = aa.trim(); - if( aa.length()>0) - seq.append(get1LetterCodeFrom3LettersCode(aa)); - } - } - //64 - 66 Residue name resName Residue name. - if(line.length()>=67 ) - { - String aa = line.substring(64-1, 67-1); - if( aa != null) - { - aa = aa.trim(); - if( aa.length()>0) - seq.append(get1LetterCodeFrom3LettersCode(aa)); - } - } - //68 - 70 Residue name resName Residue name. - if(line.length()>=71 ) - { - String aa = line.substring(68-1, 71-1); - if( aa != null) - { - aa = aa.trim(); - if( aa.length()>0) - seq.append(get1LetterCodeFrom3LettersCode(aa)); - } - } - retrievingChains.put(chainName.intern(), seq); - - //System.out.println("seq "+seq.toString()); - - //StringBufferPool.returnString(seq); - } - - //cleaning - DataBufferPool.returnString(line); - - - } - reader.closeFile(); - //cleaning - if( retrievingChains !=null) - { - if( chains == null) - - chains = new ArrayList(); - for (Enumeration elements = retrievingChains.keys() ; elements.hasMoreElements(); ) - { - String chainID = (String)elements.nextElement(); - if( chainID == null|| chainID.length()<1) continue; - StringBuffer seq = retrievingChains.get(chainID); - if(seq == null || seq.length()<1) continue; - chains.add(new PDBUtil.Chain(entry.getPdbID()+"_"+chainID, seq.toString())); - - StringBufferPool.returnString(seq); - } - retrievingChains.clear(); - retrievingChains = null; - } - - } - catch (IOException ioe) - { - logger.sessionError("error access to PDB file "+pdbFile.getName()+".",ioe); - } - if (!this.logger.isProduction()) logger.sessionDebug("retrieved chain for PDBID: "+entry.getPdbID()+" "+chains.get(0).getSequence()); - return chains; - } - -/** - * Converts a three letter code of AminoAcid to the one letter code of AminoAcid. - * @param threeLettersCode the three letter code to convert - * @return the one letter code associated to the three letter code, if found. null otherwise - */ - private static String get1LetterCodeFrom3LettersCode(String threeLettersCode) - { - /*System.out.println("threeLettersCode to convert |"+threeLettersCode+"|");*/ - if (threeLettersCode == null || threeLettersCode.length()!=3) - { - /*System.out.println("incorrect threeLettersCode "+threeLettersCode);*/ - if( threeLettersCode.length() ==1 ) return threeLettersCode; - return null; - } - String oneLetterCode = getAminoAcids().get(threeLettersCode.toLowerCase()); - if(oneLetterCode == null || oneLetterCode.length()!=1 ) oneLetterCode ="X"; - return oneLetterCode; - } - - /** - * Represents a chain contains in a PDB entry/file - * - * @author Pierre MARGUERITE - * @version 1 - * @since 28 oct. 2005 - * - */ - public static class Chain - { - /** - * name of the chain - */ - private String name = null; - private String sequence = null; - - /** - * - * Constructor for chain - * - * @param _name name of the chain - * @param _sequence sequence of the chain - */ - public Chain (String _name, String _sequence) - { - this.name = _name; - this.sequence = _sequence; - } - - /** - * Retrieves the name attribut - * - * @return Returns the name. - */ - public String getName() - { - return this.name; - } - - /** - * Retrieves the sequence attribut - * - * @return Returns the sequence. - */ - public String getSequence() - { - return this.sequence; - } - - - } - - /** - * Retrieves the aminoAcids attribut - * - *AAs = Hashtable(); - AAsAla A hydrophobic - Arginine Arg R free amino group makes it basic and hydrophilic - Asparagine Asn N carbohydrate can be covalently linked ("N-linked) to its -NH - Aspartic acid Asp D free carboxyl group makes it acidic and hydrophilic - Cysteine Cys C oxidation of their sulfhydryl (-SH) groups link 2 Cys (S-S) - Glutamic acid Glu E free carboxyl group makes it acidic and hydrophilic - Glutamine Gln Q moderately hydrophilic - Glycine Gly G so small it is amphiphilic (can exist in any surroundings) - Histidine His H basic and hydrophilic - Isoleucine Ile I hydrophobic - Leucine Leu L hydrophobic - Lysine Lys K strongly basic and hydrophilic - Methionine Met M hydrophobic - Phenylalanine Phe F very hydrophobic - Proline Pro P causes kinks in the chain - Serine Ser S carbohydrate can be covalently linked ("O-linked") to its -OH - Threonine Thr T carbohydrate can be covalently linked ("O-linked") to its -OH - Tryptophan Trp W scarce in most plant proteins - Tyrosine Tyr Y a phosphate or sulfate group can be covalently attached to its -OH - Valine Val V - - A R D N B C E Z Q G H I L K M F P S T W Y V X - * - * @return Returns the aminoAcids. - */ - private static Hashtable getAminoAcids() - { - if( AminoAcids == null) - {//lazy initialisation - AminoAcids = new Hashtable(); - AminoAcids.put("Ala".toLowerCase(), "A"); - AminoAcids.put("Arg".toLowerCase(), "R"); - AminoAcids.put("Asp".toLowerCase(), "D"); - AminoAcids.put("Asn".toLowerCase(), "N"); - AminoAcids.put("Asx".toLowerCase(), "B");// Aspartic acid or Asparagine - AminoAcids.put("Cys".toLowerCase(), "C"); - AminoAcids.put("Glu".toLowerCase(), "E"); - AminoAcids.put("Glx".toLowerCase(), "Z");// Glutamine or Glutamic acid. - AminoAcids.put("Gln".toLowerCase(), "Q"); - AminoAcids.put("Gly".toLowerCase(), "G"); - AminoAcids.put("His".toLowerCase(), "H"); - AminoAcids.put("Ile".toLowerCase(), "I"); - AminoAcids.put("Leu".toLowerCase(), "L"); - AminoAcids.put("Lys".toLowerCase(), "K"); - AminoAcids.put("Met".toLowerCase(), "M"); - AminoAcids.put("Phe".toLowerCase(), "F"); - AminoAcids.put("Pro".toLowerCase(), "P"); - AminoAcids.put("Ser".toLowerCase(), "S"); - AminoAcids.put("Thr".toLowerCase(), "T"); - AminoAcids.put("Trp".toLowerCase(), "W"); - AminoAcids.put("Tyr".toLowerCase(), "Y"); - AminoAcids.put("Val".toLowerCase(), "V"); - AminoAcids.put("Xaa".toLowerCase(), "X");// Any amino acid. - - - } - return AminoAcids; - } - - } diff --git a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/VamsasDocumentProcessor.java b/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/VamsasDocumentProcessor.java deleted file mode 100755 index 0487002..0000000 --- a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/VamsasDocumentProcessor.java +++ /dev/null @@ -1,1380 +0,0 @@ - -package uk.ac.ebi.msd.vamsas.vamav.documentmanagement; - -import uk.ac.ebi.msd.vamsas.vamav.VAMAVClient; -import uk.ac.ebi.msd.vamsas.vamav.documentmanagement.exceptions.IncorrectDocumentException; -import uk.ac.ebi.msd.vamsas.vamav.documentmanagement.exceptions.UnableToProcessException; -import uk.ac.ebi.msd.vamsas.vamav.documentmanagement.grouping.SequenceGrouping; -import uk.ac.ebi.msd.vamsas.vamav.documentmanagement.grouping.SequenceGrouping_domain; -import uk.ac.ebi.msd.vamsas.vamav.documentmanagement.grouping.SequenceGrouping_structure; -import uk.ac.ebi.msd.vamsas.vamav.documentmanagement.grouping.exceptions.UnableToGroupSequencesException; -import uk.ac.ebi.msd.vamsas.vamav.exceptions.IncorrectVamavModuleInitialisation; -import uk.ac.ebi.msd.vamsas.vamav.util.logger.VAMAVLogger; -import uk.ac.ebi.msd.vamsas.vamav.util.logger.VAMAVLoggerImpl; -import uk.ac.ebi.msd.vamsas.vamav.util.mapping.MappingManager; -import uk.ac.ebi.msd.vamsas.vamav.util.properties.PropertyManager; -import org.vamsas.objects.core.Alignment; -import org.vamsas.objects.core.AlignmentAnnotations; -import org.vamsas.objects.core.AlignmentSequence; -import org.vamsas.objects.core.AnnotationElement; -import org.vamsas.objects.core.ApplicationData; -import org.vamsas.objects.core.DataSet; -import org.vamsas.objects.core.DbRef; -import org.vamsas.objects.core.Entry; -import org.vamsas.objects.core.Provenance; -import org.vamsas.objects.core.Sequence; -import org.vamsas.objects.core.SequenceType; -import org.vamsas.objects.core.Tree; -import org.vamsas.objects.core.User; -import org.vamsas.objects.core.VAMSAS; -import org.vamsas.objects.core.VamsasDocument; - -import org.vamsas.client.IClient; -import org.vamsas.client.IClientDocument; -import org.vamsas.client.simpleclient.IdFactory; -import org.vamsas.client.simpleclient.SimpleDocument; -import org.vamsas.client.simpleclient.VamsasArchive; -import org.vamsas.client.simpleclient.ClientDocument; - -import java.io.File; -import java.io.IOException; -import java.util.ArrayList; -import java.util.Calendar; -import java.util.Collection; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.Iterator; -import java.util.Properties; -import java.util.TimeZone; - -import MSD.vamav.common.AVActiveSite; -import MSD.vamav.common.AVSequence; -import MSD.vamav.common.Highlight; -import MSD.vamav.common.ResidueAnnotation; - -/** - *

Processor for Vamsas Document, to extract data for calling an AstexViewer@MSD-EBI, for displaying the provided data

- * - *

Grouping mode :

- *
    - *
  • 1. per structure
    • - *
  • 2. per PFAM domain
    • - *
- * - */ -public class VamsasDocumentProcessor implements uk.ac.ebi.msd.vamsas.vamav.VamaVModule { - - - //private IClientDocument doc = null; - private IClient client = null; - private VAMAVLogger logger = new VAMAVLoggerImpl(this.getClass()); - - private final String modulePrefix = "documentprocessor"; - private SequenceGrouping groupingManager = null; - private int moleculeNumber = 1; - private int highlightNumber = 0; - private boolean hasAlignmentSequences = false; - private MappingManager mappingManager = null; - private String activeSiteDescription = "Active Site"; - - /** - * Retrieves the modulePrefix attribut - * - * @return Returns the modulePrefix. - */ - public String getModulePrefix() - { - return this.modulePrefix; - } - - public void init(Properties moduleProperties) throws IncorrectVamavModuleInitialisation - { - PropertyManager propManager = new PropertyManager(); - Properties props = propManager.getModuleProperties(moduleProperties, this.groupingManager.getModulePrefix()); - this.groupingManager.init(props); - propManager = null; - } - - /** - * - * Constructor for a given document - * @param document Vamsas Document to process. - * @param _mappingManager mapping manager - * @throws IncorrectDocumentException if the given document is incorrect - */ - public VamsasDocumentProcessor (IClient _client, MappingManager _mappingManager ) throws IncorrectDocumentException - { - if(_client == null ) throw new IncorrectDocumentException(); - - this.client = _client; - this.logger.setSession(this.client.getSessionUrn()); - this.mappingManager = _mappingManager; - this.mappingManager.setSession(((VAMAVClient)this.client).getVAMAVSession()); - this.groupingManager = new SequenceGrouping_structure(this.mappingManager, ((VAMAVClient)this.client).getVAMAVSession()); - //this.logger = new VAMAVLoggerImpl(this.getClass(),this.client.getSessionUrn() ); - - //this.groupingManager.load(); - } - - /** - * - * Constructor for a given document - * @param document Vamsas Document to process. - * @param _mappingManager mapping manager - * @param groupingMode grouping Mode number, for sequence grouping (structure, domain) - * @throws IncorrectDocumentException if the given document is incorrect - */ - public VamsasDocumentProcessor (IClient _client, MappingManager _mappingManager, int groupingMode) throws IncorrectDocumentException - { - if(_client == null ) throw new IncorrectDocumentException(); - - this.client = _client; - this.logger.setSession(this.client.getSessionUrn()); - - - ((VAMAVClient)this.client).getVAMAVSession().setGroupingMode(groupingMode); - this.mappingManager = _mappingManager; - this.mappingManager.setSession(((VAMAVClient)this.client).getVAMAVSession()); - this.mappingManager.setSession(((VAMAVClient)this.client).getVAMAVSession()); - if( groupingMode == 0) - { - this.groupingManager = new SequenceGrouping_structure(this.mappingManager, ((VAMAVClient)this.client).getVAMAVSession()); - } - else - if( groupingMode == 1) - { - this.groupingManager = new SequenceGrouping_domain(this.mappingManager, ((VAMAVClient)this.client).getVAMAVSession()); - } - else - // default - this.groupingManager = new SequenceGrouping_structure(this.mappingManager, ((VAMAVClient)this.client).getVAMAVSession()); - - - //this.logger = new VAMAVLoggerImpl(this.getClass(),this.client.getSessionUrn() ); - - //this.groupingManager.load(); - } -/** - *

Process a document to extract element for AstexViewer@MSD-EBI

- * - */ - public Hashtable process( ) throws IncorrectDocumentException, UnableToProcessException - { - Hashtable parameters = new Hashtable(); - //int moleculeNumber = 1; - IClientDocument doc = null; - try - { - doc = this.client.getClientDocument(); - } - catch (IOException ioe) - { - this.logger.sessionError("Unable to access to the VAMSAS document. Can not process.",ioe); - throw new IncorrectDocumentException(ioe); - } - if( doc == null) - { - this.logger.sessionError("The document is null. Can not process it."); - throw new IncorrectDocumentException(); - } - this.logger.sessionInfo("The processing vamsas document."); - try - { - VAMSAS[] roots = doc.getVamsasRoots(); - if( roots != null && roots.length>0) - for (int rootNumber = roots.length-1; rootNumber>=0; rootNumber--) - { - VAMSAS root = roots[rootNumber]; - if (root == null) continue; - Tree [] trees = root.getTree(); - //treating Trees - if (trees !=null) - { - for (int treeNumber=0; treeNumber< trees.length; treeNumber++) - { - Tree aTree = trees[treeNumber]; - if( aTree == null) continue; - parameters = this.addParameters(this.processTree(aTree), parameters); - } - } - else - { - this.logger.sessionDebug("No Tree found."); - } - int setCount = root.getDataSetCount(); - this.logger.sessionDebug("DataSet "+setCount); - if (setCount>0) - { - this.hasAlignmentSequences = false; - for (int setNumber=0; setNumber< setCount; setNumber++) - { - // treating DataSet - this.logger.sessionDebug("DataSet " +setNumber ); - DataSet set = root.getDataSet(setNumber); - if (set == null) - { - this.logger.sessionDebug("data set is null?? "+setNumber); - continue; - } - parameters = this.addParameters(this.processDataSet(set), parameters); - } - } - } - } - catch (Exception e) - { - this.logger.sessionError("VamsasDocumentProcessor process- Error during Document processing.",e); - parameters = null; - } - if (parameters!=null) this.logger.sessionDebug("parameter count "+parameters.size()); - //store PDB - //this.logger.sessionInfo("Save computed data"); - try - { - File atrFile = this.groupingManager.storeGroups(); - // this.groupingManager.getSequenceFiles() - // add atribute file parameter - if(atrFile != null) - { - this.logger.sessionDebug("Atribute file "+atrFile.getName()); - parameters.put("attribute", atrFile); - } - else - this.logger.sessionError("No atribute file created."); - - //addsequenceFile - ArrayListseqFiles = this.groupingManager.getSequenceFiles(); - if(seqFiles != null && seqFiles.size()>0) - { - for (int fileNumber = seqFiles.size() - 1;fileNumber >=0; fileNumber -- ) - { - File file = seqFiles.get(fileNumber); - if( file == null) continue; - this.logger.sessionDebug("VAMSASSequence"+(fileNumber+1)+": add sequence file to parameter "+file.getName()); - parameters.put("VAMSASSequence"+(fileNumber+1), file); - } - } - } - catch (UnableToGroupSequencesException ue) - { - this.logger.sessionError("VamsasDocumentProcessor StoreGroups - Unable to group sequences.", ue); - throw new UnableToProcessException(ue); - } - - this.groupingManager = null; - this.logger.sessionDebug("process "+(parameters==null?0:parameters.size())); - return parameters; - } - - /** - * Process Vamsas Tree object - * Currently do nothing - * @param atree the tree to process - * @return a list of parameters to call an AstexViewer@MSD-EBI client - */ - private Hashtable processTree(Tree atree) - { - return null; - } - - - private Hashtable processDataSet(DataSet aDataSet) throws UnableToGroupSequencesException - { - if (aDataSet == null) - { - this.logger.sessionDebug("data set is null??"); - return null; - } - Hashtable parameters = new Hashtable (); - int alignCount = aDataSet.getAlignmentCount(); - if (alignCount>0) - { - for (int algNumber=0; algNumber< alignCount; algNumber++) - { - this.logger.sessionDebug("Alignment " +algNumber ); - Alignment align = aDataSet.getAlignment(algNumber); - if (align == null) continue; //should not happen - Hashtable newparameters =this.ProcessAlignment(align); - this.logger.sessionDebug("end ab aligment "+(newparameters==null?0:newparameters.size())); - parameters = this.addParameters(newparameters, parameters); - this.logger.sessionDebug("end ab aligment "+(parameters==null?0:parameters.size())); - } - this.logger.sessionDebug("end aligments "+(parameters==null?0:parameters.size())); - } - int sequenceCount = aDataSet.getSequenceCount(); - if (!this.hasAlignmentSequences && sequenceCount > 0 ) - { - this.logger.sessionInfo("No alignment has been found. Process DataSet sequences."+sequenceCount); - for (int seqNumber=0; seqNumber< sequenceCount; seqNumber++) - { - Sequence seq = aDataSet.getSequence(seqNumber); - if (seq == null) - { - this.logger.sessionDebug("sequence is null??"); - continue; - } - - this.logger.sessionDebug(seq.getId()); - DbRef[] dbRefs = seq.getDbRef(); - boolean idFound = false; - if( dbRefs != null && dbRefs.length >0) - { - for (int dbRefNumber = dbRefs.length - 1; dbRefNumber >=0; dbRefNumber-- ) - { - DbRef ref = dbRefs[dbRefNumber]; - if( ref == null) continue; - - String acID = ref.getAccessionId(); - if( acID == null) - { - continue; - } - String source = ref.getSource() ; - if( source== null || source.length()<1 ) - { - continue; - } - - Hashtable tempParameters = this.groupingManager.addSequence(seq.getSequence(), seq.getName(), acID, source); - if (tempParameters != null && tempParameters.size()>0) - { - this.logger.sessionDebug("parameter count "+parameters.size()); - String pdbids = (String) tempParameters.remove(this.groupingManager.getPdbidsproperty()); - - if(pdbids!=null && pdbids.length()>0) - { - //TODO check if the ref does not have already the new DB reference - this.logger.sessionDebug("Adding pdb IDs to doc "+pdbids ); - DbRef dbref = new DbRef(); - dbref.setSource("PDB"); - dbref.setAccessionId(pdbids); - seq.addDbRef(dbref); - //seq.setRefid(ref) - } - parameters = addParameters(tempParameters, parameters); - this.logger.sessionDebug("end add sequence "+(parameters==null?0:parameters.size())); - idFound = true; - this.hasAlignmentSequences = true; - } - - /*String pdbids = (String) tempParameters.remove(this.groupingManager.getPdbidsproperty()); - String id = ref.getAccessionId(); - if(id == null || id.length()<1 ) continue; - //suppose it is a PDB ID (should be like PDBID:CHAIN) - //We don t handle chain name , remove id - int pos = id.indexOf(":"); - if (pos>=0) - {//there is a match - id = id.substring(0,pos); - } - PDBEntry entry = SequenceToPDB_MSDLite.getPDBFileFromPDBID(id); - if( entry != null) - { - idFound = true; - if( !parameters.containsValue(entry)) - /*parameters.add(entry);*/ - /* { - parameters.put("molecule"+moleculeNumber,entry); - parameters.put("name"+moleculeNumber, entry.getPdbID()); - moleculeNumber++; - } - Grouping.addSequenceToGroup(entry.getPdbID(), seq);*/ - - } - } - if (!idFound) - { - HashtabletempParameters = this.processSequence(seq); - if (tempParameters != null) - { - //parameters = this.addParameters(this.processSequence(seq), parameters); - String pdbids = (String) tempParameters.remove(this.groupingManager.getPdbidsproperty()); - if(pdbids!=null && pdbids.length()>0) - { - //TODO check if the ref does not have already the new DB reference - this.logger.sessionDebug("Adding pdb IDs to doc "+pdbids ); - DbRef ref = new DbRef(); - ref.setSource("PDB"); - ref.setAccessionId(pdbids); - seq.addDbRef(ref); - //seq.setRefid(ref) - } - parameters = this.addParameters(tempParameters, parameters); - } - } - } - } - this.logger.sessionDebug("ProcessDataSet "+(parameters==null?0:parameters.size())); - return parameters; - } - - - /** - * Process an alignment to extract sequences for grouping - * - * @param align alignment Object to process - */ - private Hashtable ProcessAlignment(Alignment align) throws UnableToGroupSequencesException - { - if (align == null) return null; //should not happen - int seqCount = align.getAlignmentSequenceCount(); - Hashtable parameters = null; - if( seqCount>0 ) - { - parameters = new Hashtable (); - String sequenceName = null; - for (int seqNumber=0; seqNumber< seqCount; seqNumber++) - { - this.logger.sessionDebug("alig seq " +seqNumber ); - AlignmentSequence seq = align.getAlignmentSequence(seqNumber); - if (seq == null) continue; //should not happen - Sequence refSeq = (Sequence) seq.getRefid(); - boolean notFound = true; - if (refSeq != null) - { - if (refSeq.getDbRefCount()>0) - { - int dbRefNumber = 0; - int refCount = refSeq.getDbRefCount(); - while (notFound && dbRefNumber tempParameters = this.groupingManager.addSequence(seq.getSequence(), seq.getName(), acID, source); - - if (tempParameters != null && tempParameters.size()>0) - { - this.logger.sessionDebug("parameter count "+parameters.size()); - String pdbids = (String) tempParameters.remove(this.groupingManager.getPdbidsproperty()); - if(pdbids!=null && pdbids.length()>0) - { - //TODO check if the ref does not have already the new DB reference - this.logger.sessionDebug("Adding pdb IDs to doc "+pdbids ); - DbRef ref = new DbRef(); - ref.setSource("PDB"); - ref.setAccessionId(pdbids); - refSeq.addDbRef(ref); - //seq.setRefid(ref) - } - parameters = addParameters(tempParameters, parameters); - notFound = false; - hasAlignmentSequences = true; - this.logger.sessionDebug("parameter count "+parameters.size()); - } - //if (sequenceName ==null) sequenceName = entry.getPdbID()+"_"; - } - } - else - { /*System.out.println("No DbRef");*/ - } - } - if (notFound) - { - Hashtable tempParameters = processSequence(seq); - if (tempParameters != null) - { - /* String pdbids = (String) tempParameters.remove(this.groupingManager.getPdbidsproperty()); - if(pdbids!=null && pdbids.length()>0) - { - //TODO check if the ref does not have already the new DB reference - this.logger.sessionDebug("Adding pdb IDs to doc "+pdbids ); - DbRef ref = new DbRef(); - ref.setSource("PDB"); - ref.setAccessionId(pdbids); - seq.addDbRef(ref); - //seq.setRefid(ref) - }*/ - parameters = this.addParameters(tempParameters, parameters); - } - } - } - //treat AnnotationElement for highlight - int annotationCount = align.getAlignmentAnnotationsCount(); - this.logger.sessionDebug("annotationCount "+ annotationCount); - for (int annotationNumber = annotationCount-1; annotationNumber>=0; annotationNumber--) - { - this.logger.sessionDebug("annotationNumber "+annotationNumber); - AlignmentAnnotations annotation = align.getAlignmentAnnotations(annotationNumber); - if (annotation == null) continue; - int elementCount = annotation.getAnnotationElementCount(); - for (int elementNumber = elementCount-1; elementNumber>=0; elementNumber--) - { - this.logger.sessionDebug("annotationElement "+elementNumber); - AnnotationElement elt = annotation.getAnnotationElement(elementNumber); - if (elt == null) continue; - parameters = this.addParameters(this.processAnnotationElement(elt), parameters); - } - } - } - this.logger.sessionDebug("ProcessAlignment "+(parameters==null?0:parameters.size())); - return parameters; - } - - private Hashtable processAnnotationElement( AnnotationElement annotation) - { - if (annotation == null) return null; - int secStructure = -1;//unknown - Hashtable parameters = null; - try - { - secStructure = new Integer(annotation.getSecondaryStructure()).intValue(); - } - catch (NumberFormatException nfExcep) - { - this.logger.sessionWarn("Unknown secondary sequence: "+ annotation.getSecondaryStructure()); - secStructure = -1; - } - if (annotation.getDescription().contains("breakpoint") || annotation.getDescription().contains("Breakpoint")) - { - Highlight hgl = new Highlight (annotation.getDisplayCharacter().charAt(0), annotation.getDescription(), secStructure, null, annotation.getPosition()); - //Hashtable temp - parameters = new Hashtable(); - //temp - parameters.put("highlightT0",hgl); - this.groupingManager.addBreakpoint(annotation); - } - //this.groupingManager.addBreakpoint(annotation); - return parameters; - } - - private Hashtable processSequence(SequenceType sequence) throws UnableToGroupSequencesException - { - if (sequence == null) return null; - Hashtable tempParameters = this.groupingManager.addSequence(sequence.getSequence(), sequence.getName()); - - //return null; - - return tempParameters; - } -/** - *

Does ...

- * - */ - public void updateDocument(Hashtable parameters) - { - this.logger.sessionDebug("Updating Document"); - if( parameters == null || parameters.size()<1) - { - this.logger.sessionWarn("UpdateDocument: no object provided: No update."); - return ; - } - VAMSAS[] roots = null; - try - { - roots = this.client.getClientDocument().getVamsasRoots(); - } - catch (IOException ioe) - { - this.logger.sessionWarn("Add active site: The document does not exist. Can not add Active site."); - return; - - } - if (roots == null || roots.length<1) - { - this.logger.sessionWarn("Add active site: The document is empty. Can not add Active site."); - return; - } - for (int rootNumber = roots.length-1; rootNumber >=0 && parameters != null&& parameters.size()>0; rootNumber-- ) - { - VAMSAS root = roots[rootNumber]; - if (root == null) - { - continue; - } - updateVAMSAS(root,parameters); - } - } - - /** - * Updates a VAMSAS entity with the given parameters - * @param parameters list of objects to update into the VAMSAS tree - */ - private void updateVAMSAS(VAMSAS root, Hashtable parameters) - { - this.logger.sessionDebug("Updating Vamsas"); - if( parameters == null || parameters.size()<1) - { - this.logger.sessionWarn("UpdateVAMSAS: no object provided: No update."); - return ; - } - if(root == null ) - { - this.logger.sessionWarn("UpdateVAMSAS: no VAMSAS XML Entity."); - return ; - } - for (int dataSetNumber = root.getDataSetCount() -1; dataSetNumber>=0&& parameters != null&& parameters.size()>0; dataSetNumber--) - { - DataSet set = root.getDataSet(dataSetNumber); - if( set == null) continue; - updateDataSet(set, parameters); - - } - } - - /** - * Updates a DataSet entity with the given parameters - * @param parameters list of objects to update into the DataSet tree - */ - private void updateDataSet(DataSet root, Hashtable parameters) - { - this.logger.sessionDebug("Updating DataSet"); - if( parameters == null || parameters.size()<1) - { - this.logger.sessionWarn("updateDataSet: no object provided: No update."); - return ; - } - if(root == null ) - { - this.logger.sessionWarn("updateDataSet: no DataSet XML Entity."); - return ; - } - for (int alignmentNumber= root.getAlignmentCount()-1; alignmentNumber>=0&& parameters != null&& parameters.size()>0; alignmentNumber-- ) - { - Alignment align = root.getAlignment(alignmentNumber); - if( align != null) - { - updateAlignment(align, parameters); - } - } - } - - /** - * Updates a Alignment entity with the given parameters - * @param parameters list of objects to update into the Alignment tree - */ - private void updateAlignment(Alignment root, Hashtable parameters) - { - this.logger.sessionDebug("Updating ALignment"); - if( parameters == null || parameters.size()<1) - { - this.logger.sessionWarn("updateAlignment: no object provided: No update."); - return ; - } - if(root == null ) - { - this.logger.sessionWarn("updateAlignment: no DataSet XML Entity."); - return ; - } - this.logger.sessionDebug("list of parameters: "+parameters); - Hashtable> sites = (Hashtable>) parameters.get("MSD.vamav.common.AVActiveSite"); - Hashtable> residueAnnotations = (Hashtable>) parameters.get("MSD.vamav.common.ResidueAnnotation"); - try - { - if ((sites != null && sites.size()>0) || (residueAnnotations!= null && residueAnnotations.size()>0)) - { - boolean hasSitesToUpdate = false; - if (sites!= null && sites.size()>0) - { - hasSitesToUpdate = true; - } - boolean hasAnnotationToUpdate = false; - if (residueAnnotations!= null && residueAnnotations.size()>0) - { - hasAnnotationToUpdate = true; - } - for (int seqNumber = root.getAlignmentSequenceCount() -1; seqNumber>=0; seqNumber --) - { - AlignmentSequence seq = root.getAlignmentSequence(seqNumber); - if( seq == null) continue; - String name = seq.getName(); - if( name == null ) continue; - this.logger.sessionDebug("sequence name "+name); - name = name.trim().toLowerCase().intern(); - if (hasSitesToUpdate) - { - if( sites.containsKey(name) ) - {//found the alignment associated to an Active Site - //add the active site as annotation element - /// AlignmentAnnotations[] annotations = root.getAlignmentAnnotations(); - //if (annotations == null) - // { - this.addActiveSite(root, sites.get(name)); - sites.remove(name); - // } - } - else - { - //look for PDB ID - //usely active sites are associated with PDB chain. - //check any seq has a PDB ID with an active site. - Sequence seqRef = (Sequence)seq.getRefid(); - if( !this.logger.isProduction())this.logger.sessionDebug(" sites "+sites); - // this.logger.sessionDebug(" sites "+sites.keys()); - if (seqRef != null) - { - boolean found = false; - int refNumber = seqRef.getDbRefCount() ; - while (!found && refNumber>0) - { - refNumber --; - DbRef ref = seqRef.getDbRef(refNumber); - if( ref == null ) continue; - String source = ref.getSource(); - this.logger.sessionDebug("DBRef "+ refNumber+ " "+source); - if (source != null && "PDB".equalsIgnoreCase(source)) - { - String accID = ref.getAccessionId(); - if( accID == null || accID.length()<1) continue; - accID = accID.trim().toLowerCase().intern(); - this.logger.sessionDebug("ACCID "+accID); - if( accID != null) - { - for ( Enumeration keys = sites.keys(); keys.hasMoreElements();) - { - String sitePDBID = keys.nextElement(); - if( sitePDBID == null) continue; - - int underPos = sitePDBID.indexOf("_"); - - this.logger.sessionDebug("position underscore "+underPos +" "+sitePDBID.substring(underPos+1, name.length())); - if( underPos>0 && (sitePDBID.substring(underPos+1, sitePDBID.length()).length()==1 || sitePDBID.substring(underPos+1, sitePDBID.length()).length()==0)) - {//remove chain name and leave the PDB ID - sitePDBID = sitePDBID.substring(0, underPos); - } - sitePDBID = sitePDBID.trim().toLowerCase().intern(); - if( sitePDBID.equalsIgnoreCase(accID)) - { - root = this.addActiveSite(root, sites.get(accID)); - } - } - //sites.remove(accID); - } - } - } - } - } - } - if( hasAnnotationToUpdate) - { - this.logger.sessionDebug("Testing "+name+ " for residue annotation."); - if(residueAnnotations.containsKey(name)) - {//found the alignment associated to an Active Site - //add the active site as annotation element - this.logger.sessionDebug("The sequence "+name+" has a residue annotation."); - //AlignmentAnnotations[] annotations = root.getAlignmentAnnotations(); - //if (annotations == null) - // { - this.addResidueAnnotation(root, residueAnnotations.remove(name)); - // } - } - else - { - //look for PDB ID - //usely active sites are associated with PDB chain. - //check any seq has a PDB ID with an active site. - Sequence seqRef = (Sequence)seq.getRefid(); - if (!this.logger.isProduction()) this.logger.sessionDebug(" residueAnnotations "+residueAnnotations); - - if (seqRef != null) - { - boolean found = false; - int refNumber = seqRef.getDbRefCount() ; - while (!found && refNumber>0) - { - refNumber --; - DbRef ref = seqRef.getDbRef(refNumber); - if( ref == null ) continue; - String source = ref.getSource(); - this.logger.sessionDebug("DBRef "+ refNumber+ " "+source); - if (source != null && "PDB".equalsIgnoreCase(source)) - { - String accID = ref.getAccessionId(); - if( accID == null || accID.length()<1) continue; - accID = accID.trim().toLowerCase().intern(); - this.logger.sessionDebug("ACCID "+accID); - if( accID != null && residueAnnotations.containsKey(accID)) - { - root = this.addResidueAnnotation(root, residueAnnotations.get(accID)); - } - } - } - - } - } - - } - } - - } - else - { - this.logger.sessionInfo("Update Alignment: no Residue alignment provided."); - } - }catch (Exception e) - { - this.logger.sessionError("Error during Alignment update ",e); - } - - } - - /** - * add an active site to the document - * @param sites - */ - private Alignment addActiveSite(Alignment align, ArrayList sites ) - { - this.logger.sessionDebug("adding active site"); - if(align == null ) - { - this.logger.sessionWarn("AddActiveSite: no Aligmnemt XML Entity."); - return align; - } - if( sites == null || sites.size()<1) - { - this.logger.sessionDebug("addActiveSite: No site to add."); - return align; - } - Hashtable > orderedSites = new Hashtable >(); - //order site per position - this.logger.sessionDebug(" Ordering sites: "+sites.size()); - for (int siteNumber = sites.size() -1; siteNumber>=0; siteNumber--) - { - AVActiveSite site = sites.get(siteNumber); - if (site == null) continue; - - //we suppose we can have several sites at the same position - //orderedSites.put(Integer.valueOf(siteNumber), site); - Integer position = Integer.valueOf(site.getPosition()); - this.logger.sessionDebug("position: "+position.toString()); - ArrayList s = orderedSites.get(position.toString().intern()); - if(s == null ) - { - s = new ArrayList(); - } - if (!s.contains(site)) s.add(site); - orderedSites.put(position.toString().intern(), s); - //orderedSites. - //site.getPosition(); - }//check if active site are already contained in the Annotation - for (int alignNumber = align.getAlignmentAnnotationsCount() - 1 ; alignNumber>=0; alignNumber--) - { - AlignmentAnnotations annotation= align.getAlignmentAnnotations(alignNumber); - if( annotation == null) continue; - this.logger.sessionDebug("annotation number : "+alignNumber); - this.logger.sessionDebug("Element count "+annotation.getAnnotationElementCount()); - for ( int elementNumber = annotation.getAnnotationElementCount() - 1;elementNumber>=0; elementNumber-- ) - { - AnnotationElement element = annotation.getAnnotationElement(elementNumber); - this.logger.sessionDebug("element "+elementNumber); - if( element == null) continue; - // if(this.activeSiteDescription.equalsIgnoreCase(element.getDescription())&& - // - Integer pos = Integer.valueOf(element.getPosition()); - String desc = element.getDescription(); - this.logger.sessionDebug("element position "+ pos+","); - this.logger.sessionDebug("positions "+orderedSites.keys()); - if(desc != null && desc.startsWith(this.activeSiteDescription) && orderedSites.containsKey(pos.toString().intern())) - { - this.logger.sessionInfo("AddActiveSite: The active site already exists at position: "+element.getPosition()); - ArrayList s = orderedSites.remove(pos.toString().intern()); - - //continue; - } - pos = null; - } - } - //the remaining sites must be added. - if(orderedSites !=null && orderedSites.size()>0 ) - { - AlignmentAnnotations annotation = new AlignmentAnnotations(); - - Collection> s = orderedSites.values(); - if( s != null && s.size()>0) - { - for ( Iterator > iter = s.iterator(); iter.hasNext();) - { - ArrayList list = iter.next(); - if (list == null || list.size()<1) continue; - for (int arrayNumber = list.size()-1; arrayNumber>=0; arrayNumber--) - { - AVActiveSite site = list.get(arrayNumber); - AnnotationElement element = new AnnotationElement(); - if (site == null ) continue; - this.logger.sessionDebug("site : "+site.getSequenceName() + " "+site.getPosition() ); - element.setDescription(this.activeSiteDescription +" "+site.getLigandName()); - element.setPosition(site.getPosition()); - //element.setValue(); - annotation.addAnnotationElement(element); - } - } - } - /*for (Enumeration siteEnum = ; siteEnum.hasMoreElements();) - { - AVActiveSite site = (AVActiveSite)siteEnum.nextElement(); - if (site == null) continue; - logger.Applidebug("site : "+site.getSequenceName()); - element.setDescription(this.activeSiteDescription +" "+site.getLigandName()); - element.setPosition(site.getPosition()); - //element.setValue(); - annotation.addAnnotationElement(element); - }*/ - //adding provenance entry to the annotation - Provenance provenance = annotation.getProvenance(); - Entry provenanceEntry = this.createProvenanceEntry(this.client, "Update - added ActiveSite"); - if(provenanceEntry != null )//otherwise something is wrong - { - if( provenance == null) provenance = new Provenance(); - provenance.addEntry(provenanceEntry); - } - align.addAlignmentAnnotations(annotation); - } - return align; - } - - /** - * add an active site to the document - * @param sites - */ - private Alignment addResidueAnnotation(Alignment align, ArrayList annotations ) - { - this.logger.sessionDebug("adding active site"); - if(align == null ) - { - this.logger.sessionWarn("AddResidueAnnotation: no Aligmnemt XML Entity."); - return align; - } - if( annotations == null || annotations.size()<1) - { - this.logger.sessionDebug("addResidueAnnotation: No annotation to add."); - return align; - } - Hashtable > orderedAnnotation = new Hashtable >(); - //order site per position - this.logger.sessionDebug(" Ordering sites: "+annotations.size()); - for (int siteNumber = annotations.size() -1; siteNumber>=0; siteNumber--) - { - ResidueAnnotation annotation = annotations.get(siteNumber); - if (annotation == null) continue; - - //we suppose we can have several sites at the same position - //orderedSites.put(Integer.valueOf(siteNumber), site); - Integer position = Integer.valueOf(annotation.getResidueNumber()); - this.logger.sessionDebug("position: "+position.toString()); - ArrayList s = orderedAnnotation.get(position.toString().intern()); - if(s == null ) - { - s = new ArrayList(); - } - if (!s.contains(annotation)) s.add(annotation); - orderedAnnotation.put(position.toString().intern(), s); - //orderedSites. - //site.getPosition(); - }//check if active site are already contained in the Annotation - for (int alignNumber = align.getAlignmentAnnotationsCount() - 1 ; alignNumber>=0; alignNumber--) - { - AlignmentAnnotations annotation= align.getAlignmentAnnotations(alignNumber); - if( annotation == null) continue; - this.logger.sessionDebug("annotation number : "+alignNumber); - this.logger.sessionDebug("Element count "+annotation.getAnnotationElementCount()); - for ( int elementNumber = annotation.getAnnotationElementCount() - 1;elementNumber>=0; elementNumber-- ) - { - AnnotationElement element = annotation.getAnnotationElement(elementNumber); - this.logger.sessionDebug("element "+elementNumber); - if( element == null) continue; - // if(this.activeSiteDescription.equalsIgnoreCase(element.getDescription())&& - // - Integer pos = Integer.valueOf(element.getPosition()); - String desc = element.getDescription(); - this.logger.sessionDebug("element position "+ pos+","); - if( !this.logger.isProduction()) this.logger.sessionDebug("positions "+orderedAnnotation.keys()); - if(desc != null && desc.startsWith(this.activeSiteDescription) && orderedAnnotation.containsKey(pos.toString().intern())) - { - this.logger.sessionInfo("AddActiveSite: The active site already exists at position: "+element.getPosition()); - ArrayList s = orderedAnnotation.remove(pos.toString().intern()); - - //continue; - } - pos = null; - } - } - //the remaining sites must be added. - if(orderedAnnotation !=null && orderedAnnotation.size()>0 ) - { - AlignmentAnnotations annots = new AlignmentAnnotations(); - - Collection> s = orderedAnnotation.values(); - if( s != null && s.size()>0) - { - for ( Iterator > iter = s.iterator(); iter.hasNext();) - { - ArrayList list = iter.next(); - if (list == null || list.size()<1) continue; - for (int arrayNumber = list.size()-1; arrayNumber>=0; arrayNumber--) - { - ResidueAnnotation annotation = list.get(arrayNumber); - AnnotationElement element = new AnnotationElement(); - if (annotation == null ) continue; - this.logger.sessionDebug("annotation : "+annotation.getSequenceName() + " "+annotation.getResidueNumber() ); - element.setDescription(annotation.getDescription()); - element.setPosition(annotation.getResidueNumber()); - if (annotation.getDisplayCharacter()!= null && annotation.getDisplayCharacter().length()>0) - element.setDisplayCharacter(annotation.getDisplayCharacter()); - else - element.setDisplayCharacter("?"); - if( annotation.getSecondaryStructure() != null && annotation.getSecondaryStructure().length()>0 ) - { - element.setSecondaryStructure(annotation.getSecondaryStructure()); - } - else - element.setSecondaryStructure("?"); - element.setValue(Float.parseFloat(annotation.getValue())); - //element.setValue(); - annots.addAnnotationElement(element); - } - } - } - /*for (Enumeration siteEnum = ; siteEnum.hasMoreElements();) - { - AVActiveSite site = (AVActiveSite)siteEnum.nextElement(); - if (site == null) continue; - logger.Applidebug("site : "+site.getSequenceName()); - element.setDescription(this.activeSiteDescription +" "+site.getLigandName()); - element.setPosition(site.getPosition()); - //element.setValue(); - annotation.addAnnotationElement(element); - }*/ - //adding provenance entry to the annotation - Provenance provenance = annots.getProvenance(); - Entry provenanceEntry = this.createProvenanceEntry(this.client, "Update - added Residue Annotation"); - if(provenanceEntry != null )//otherwise something is wrong - { - if( provenance == null) provenance = new Provenance(); - provenance.addEntry(provenanceEntry); - } - align.addAlignmentAnnotations(annots); - } - return align; - } - - private Hashtable addParameters(Hashtable newParameters, Hashtable parameters) - { - if (parameters == null) parameters = new Hashtable(); - if (newParameters != null && newParameters.size()>0) - { - boolean found = false; - /*for (Enumeration keys = newParameters.keys(); keys.hasMoreElements();) - { - String key = (String) keys.nextElement(); - if( key == null) continue; - Object value = newParameters.get(key); - if (value == null) continue; - - String newKey = null; - if("molecule".equals(key) ) - { - if( parameters.containsValue(value)) continue; - newKey = "molecule"+this.moleculeNumber; - } - else - if("name".equals(key) ) - { - if( parameters.containsValue(value)) continue; - newKey = "name"+this.moleculeNumber; - } - else newKey = key; - parameters.put(newKey, value); - logger.Applidebug("Adding new parameter "+newKey); - newParameters.remove(key); - key = null; - found = true; - } - found = false; - this.moleculeNumber++;*/ - boolean moreMolecules = true; - int molNumber = -1; - int highlightN= -1; - boolean moreHighlight = true; - if (!this.logger.isProduction() ) - { - for (Enumeration keys = newParameters.keys(); keys.hasMoreElements();) - { - this.logger.sessionDebug("new parameter "+keys.nextElement()); - } - for (Enumeration keys = parameters.keys(); keys.hasMoreElements();) - { - this.logger.sessionDebug("current stored parameter "+keys.nextElement()); - } - } - while (newParameters != null && !newParameters.isEmpty() && (moreMolecules || moreHighlight)) - { - highlightN++; - String currentParameterName = "highlightT"+highlightN; - Object hig = newParameters.remove(currentParameterName); - currentParameterName = null; - if(hig != null) - { - if (!parameters.containsValue(hig)) - { - this.logger.sessionDebug("Highlight found in the document"); - //newParameters.remove("highlight"+highlightNumber); - int currentNumber = this.highlightNumber++; - String newKey = "highlight"+currentNumber; - this.logger.sessionDebug("Adding new parameter "+newKey); - parameters.put(newKey, hig); - } - else - { - this.logger.sessionDebug("the highlight is already contained in the parameter list."); - } - } - else - { - moreHighlight = false; - //continue; - this.logger.sessionDebug("no more highlight"); - } - - molNumber++; - Object mol = newParameters.get("moleculeG"+molNumber); - if (mol == null) - { - moreMolecules = false; - continue; - } - newParameters.remove("moleculeG"+molNumber); - Object name = newParameters.get("nameG"+molNumber); - if (name == null) - { - //moreMolecules = false; - continue; - } - newParameters.remove("nameG"+molNumber); - if( parameters.containsValue(mol)) continue; - int currentNumber = this.moleculeNumber++; - String newKey = "molecule"+currentNumber; - this.logger.sessionDebug("Adding new parameter "+newKey); - parameters.put(newKey, mol); - if( parameters.containsValue(name)) continue; - newKey = "name"+currentNumber; - this.logger.sessionDebug("Adding new parameter "+newKey); - parameters.put(newKey, name); - } - if (newParameters!= null && !newParameters.isEmpty())parameters.putAll(newParameters); - } - if (newParameters != null) - { - newParameters.clear(); - newParameters = null; - } - return parameters; - } - - /** @poseidon-generated */ - public SequenceGrouping getSequenceGrouping() { - return this.groupingManager; - } - /** @poseidon-generated */ - public void setSequenceGrouping(SequenceGrouping sequenceGrouping) { - this.groupingManager = sequenceGrouping; - } - - - private Entry createProvenanceEntry(IClient client, String action) - { - if (client == null) - { - this.logger.sessionError("No vamsas client provided to create provenance entry. The entry object will not be added."); - return null; - } - return this.createProvenanceEntry(client.getUserHandle().getFullName(), action); - } - - private Entry createProvenanceEntry(String user, String action) - { - if( user == null || user.length()<1) - { - this.logger.sessionError("No User name provided to create provenance entry. The entry object will not be added."); - return null; - } - if( action == null || action.length()<1) - { - this.logger.sessionError("No action provided to create provenance entry. The entry object will not be added."); - return null; - } - Entry provenanceEntry = new Entry(); - provenanceEntry.setUser(user); - provenanceEntry.setAction(action); - - /* - ** on some JDK, the default TimeZone is wrong - ** we must set the TimeZone manually!!! - ** Calendar cal = Calendar.getInstance(TimeZone.getTimeZone("EST")); - */ - Calendar cal = Calendar.getInstance(TimeZone.getDefault()); - org.exolab.castor.types.Date date = new org.exolab.castor.types.Date (cal.getTime()); - provenanceEntry.setDate(date); - cal = null; - return provenanceEntry; - } - - public ArrayList getGroupingModes() - { - ArrayList modes = new ArrayList(); - modes.add("structure"); - modes.add("Protein domain"); - return modes; - } - - /** - * Create a document following provided parameters - * - * @param parameters list of parameters, containing objects to map to the document objects/tree - * @return the IClient with the associated newly created document - * @throws IOException if an error occurs during VAMsas document file access - */ - public IClient createDocument(Hashtable parameters) throws IOException - { - if(parameters == null || parameters.size()<1) - { - this.logger.sessionError("No parameter provided to create the VAMSAS document. Abort."); - } - IClientDocument _doc = null; - - VamsasDocument doc = new VamsasDocument(); - VAMSAS root = new VAMSAS(); - doc.addVAMSAS(root); - - - Tree aTree = this.createTree(parameters); - if( aTree != null) root.addTree(aTree); - - DataSet set = this.createDataSet(parameters); - if (set != null) - root.addDataSet(set); - - IdFactory vorba = null; - // TODO: reduce size of vorba ids generated from these parameters to IdFactory (mainly sessionHandle rationalization ?) - try { - vorba= new IdFactory(this.client.getSessionHandle(), - this.client.getClientHandle(), ((VAMAVClient)this.client).getUserHandle());//makeVorbaIdFactory(); - // if session currently holds data - read it in - or get a dummy - this.logger.sessionDebug("Accessing document"); - } - catch (Exception e) { - File sessionDir = ((VAMAVClient)this.client).getVAMAVSession().getSessionDirectory(); - this.logger.sessionError("Failed to get session document for session directory '"+sessionDir.getAbsolutePath()+"'", e); - throw new IOException("Failed to get session document for session directory '"+sessionDir.getAbsolutePath()+"'"); - } - // Construct the IClientDocument instance - ApplicationData appliData = new ApplicationData(); - User user = new User(); - user.setFullname(this.client.getUserHandle().getFullName()); - user.setOrganization(this.client.getUserHandle().getOrganization()); - - appliData.addUser(user); - doc.addApplicationData(appliData); - _doc = new ClientDocument(doc, (VamsasArchive)null, vorba, this.client); - - //_doc = new ClientDocument(doc, new VAMSAS[]{root}, null,this.client); - this.client.updateDocument(_doc); - return this.client; - } - - /** Create Vamsas Tree object - * Currently do nothing - * @return the created tree - * @param parameters a list of parameters from an AstexViewer@MSD-EBI client - */ - private Tree createTree(Hashtable parameters) - { - return null; - } - - - private DataSet createDataSet(Hashtable parameters) - { - if (parameters == null || parameters.size()<1) - { - this.logger.sessionDebug("No parameter provided to create DataSet"); - return null; - } - this.logger.sessionDebug("Create DataSet "); - DataSet set = new DataSet(); - Alignment align = this.createAlignment(parameters); - if (align != null) set.addAlignment(align); - - set = this.createSequences(parameters,set); - - this.logger.sessionDebug("end CreateDataSet "); - return set; - } - - /** - * creates a Alignment entity following the given parameters - * @param parameters list of objects used to create the Alignment tree - */ - private Alignment createAlignment(Hashtable parameters) - { - this.logger.sessionDebug("Create Alignment"); - if( parameters == null || parameters.size()<1) - { - this.logger.sessionWarn("createAlignment: no object provided: Can not create."); - return null; - } - Alignment align = null; - //new Alignment(); - if (!this.logger.isProduction()) this.logger.sessionDebug("list of parameters: "+parameters); - return align; - } - - /** - * creates a Alignment entity following the given parameters - * @param parameters list of objects used to create the Alignment tree - */ - private DataSet createSequences(Hashtable parameters, DataSet set) - { - this.logger.sessionDebug("Create Sequences"); - if( parameters == null || parameters.size()<1) - { - this.logger.sessionWarn("createSequence: no object provided: Can not create."); - return null; - } - ArrayList sequences = (ArrayList) parameters.get("MSD.vamav.common.AVSequence"); - if( sequences != null && sequences.size()>0) - { - Alignment align = new Alignment(); - - for (int sequenceNumber = sequences.size() -1; sequenceNumber >=0; sequenceNumber-- ) - { - AVSequence sequence = sequences.get(sequenceNumber); - - //create sequence object - Sequence seq = new Sequence(); - seq.setName(sequence.getName()); - String sequenceWithoutGap = sequence.getSequence(); - if( sequenceWithoutGap != null && sequenceWithoutGap.length()>0) - { - sequenceWithoutGap = sequenceWithoutGap.replaceAll("-", ""); - } - seq.setSequence(sequenceWithoutGap); - set.addSequence(seq); - - //create Alignment object relative to thie Sequence object - - AlignmentSequence alignmSeq = new AlignmentSequence(); - alignmSeq.setName(sequence.getName()); - alignmSeq.setSequence(sequence.getSequence()); - alignmSeq.setRefid(seq); - align.addAlignmentSequence(alignmSeq); - } - set.addAlignment(align); - } - - if (!this.logger.isProduction()) this.logger.sessionDebug("list of parameters: "+parameters); - return set; - } - - - } diff --git a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/exceptions/IncorrectDocumentException.java b/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/exceptions/IncorrectDocumentException.java deleted file mode 100755 index 3b81398..0000000 --- a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/exceptions/IncorrectDocumentException.java +++ /dev/null @@ -1,61 +0,0 @@ -/* Created on 14 nov. 2005 - * * EMBL-EBI - * MSD Group - * VAMSAS Project - * VAMAV - * @author Pierre MARGUERITE - * @version 1 - * @since 14 nov. 2005 - */ -package uk.ac.ebi.msd.vamsas.vamav.documentmanagement.exceptions; - -/** - * Exception raises if the a Vamsas document is considered as incorrect - * @author Pierre MARGUERITE - * @version 1 - * @since 14 nov. 2005 - * - */ -public class IncorrectDocumentException extends Exception - { - - /** - * Constructor - * - */ - public IncorrectDocumentException() - { - super(); - } - - /** - * Constructor - * - * @param arg0 - */ - public IncorrectDocumentException(String arg0) - { - super(arg0); - } - - /** - * Constructor - * - * @param arg0 - * @param arg1 - */ - public IncorrectDocumentException(String arg0, Throwable arg1) - { - } - - /** - * Constructor - * - * @param arg0 - */ - public IncorrectDocumentException(Throwable arg0) - { - super(arg0); - } - - } diff --git a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/exceptions/UnableToProcessException.java b/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/exceptions/UnableToProcessException.java deleted file mode 100755 index 0454e0f..0000000 --- a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/exceptions/UnableToProcessException.java +++ /dev/null @@ -1,63 +0,0 @@ -/* Created on 12 janv. 2006 - * * EMBL-EBI - * MSD Group - * VAMSAS Project - * VAMAV - * @author Pierre MARGUERITE - * @version 1 - * @since 12 janv. 2006 - */ -package uk.ac.ebi.msd.vamsas.vamav.documentmanagement.exceptions; - -/** - * Exception raised when the application is unable to process a document - * or a session - * @author Pierre MARGUERITE - * @version 1 - * @since 12 janv. 2006 - * - */ -public class UnableToProcessException extends Exception - { - - /** - * Constructor - * - */ - public UnableToProcessException() - { - super(); - } - - /** - * Constructor - * - * @param arg0 - */ - public UnableToProcessException(String arg0) - { - super(arg0); - } - - /** - * Constructor - * - * @param arg0 - * @param arg1 - */ - public UnableToProcessException(String arg0, Throwable arg1) - { - super(arg0, arg1); - } - - /** - * Constructor - * - * @param arg0 - */ - public UnableToProcessException(Throwable arg0) - { - super(arg0); - } - - } diff --git a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/SequenceGrouping.java b/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/SequenceGrouping.java deleted file mode 100755 index 43f5184..0000000 --- a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/SequenceGrouping.java +++ /dev/null @@ -1,1169 +0,0 @@ -/* * EMBL-EBI -* MSD Group -* VAMSAS Project -* VAMAV -* * @author Pierre MARGUERITE - * @version 1 -*/ -package uk.ac.ebi.msd.vamsas.vamav.documentmanagement.grouping; - -import uk.ac.ebi.msd.vamsas.vamav.documentmanagement.grouping.exceptions.UnableToGroupSequencesException; -import uk.ac.ebi.msd.vamsas.vamav.exceptions.IncorrectVamavModuleInitialisation; -import uk.ac.ebi.msd.vamsas.vamav.util.data.DataBuffer; -import uk.ac.ebi.msd.vamsas.vamav.util.logger.VAMAVLogger; -import uk.ac.ebi.msd.vamsas.vamav.util.logger.VAMAVLoggerImpl; -import uk.ac.ebi.msd.vamsas.vamav.util.mapping.MappingManager; -import uk.ac.ebi.msd.vamsas.vamav.util.mapping.exceptions.MappingException; -import uk.ac.ebi.msd.vamsas.vamav.util.mapping.matrixrotation.RotationTranslationMatrix; -import uk.ac.ebi.msd.vamsas.vamav.util.multiplealignment.AlignmentManager; -import uk.ac.ebi.msd.vamsas.vamav.util.multiplealignment.ClustalW_EBIWSClient; -import uk.ac.ebi.msd.vamsas.vamav.util.multiplealignment.MultipleAlignmentIntf; -import uk.ac.ebi.msd.vamsas.vamav.util.multiplealignment.exceptions.AlignmentException; -import uk.ac.ebi.msd.vamsas.vamav.util.pool.DataBufferPool; -import uk.ac.ebi.msd.vamsas.vamav.util.pool.StringBufferPool; -import uk.ac.ebi.msd.vamsas.vamav.util.properties.PropertyManager; -import org.vamsas.objects.core.AnnotationElement; -import org.vamsas.objects.core.SequenceType; - -import java.io.BufferedWriter; -import java.io.File; -import java.io.FileOutputStream; -import java.io.FileWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.PrintWriter; -import java.io.Writer; -import java.math.BigDecimal; -import java.util.ArrayList; -import java.util.Collection; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.Properties; - -/** -* Abstract class for defining Structure grouping methods. -* -* Grouping mode should implement these methods -* -* Providing method definitions and code for atribute file generation - * @author Pierre MARGUERITE - * @version 1 -*/ - -public abstract class SequenceGrouping implements uk.ac.ebi.msd.vamsas.vamav.VamaVModule{ - - protected final String pdbidsproperty = "pdbids"; - - protected String modulePrefix = "sequence"; - protected final VAMAVLogger logger = new VAMAVLoggerImpl(this.getClass()); - - protected Hashtable > groups = null; - - /** - * List of PDB structures per group - * to allow rotation translation matrix mapping - */ - protected Hashtable > structuresPerGroup = null; - - protected char gapChar = 'X'; - protected Hashtable maxSeqLengthsPerGroup = null; - protected Hashtable fakeSequencePerLength = null; - - protected ArrayList sequenceFile = null; - protected final String atrFilePrefix = "atr"; - protected final String alignmentFilePrefix = ".aln"; - protected String workingDirectory = "atributeFile"; - //protected String atributeFile = this.workingDirectory+File.separator+"vamsas"+"."+this.atrFilePrefix; - protected static String enc = null; - protected static final boolean erase = true; - protected static final boolean append = false; - protected Hashtable> sequenceBreakPoints = null; - protected final boolean deleteOnExit = false; - /** - * Mapping manager to retrieve a mapping between ID for example - * - */ - protected MappingManager mapping = null; - - protected AlignmentManager alignManager = null; - - - /** - *

- * - */ - // private MultipleAlignmentIntf multipleAlignment; - - - /** - * List of breakpoints for the current alignmentSet - */ - protected ArrayList breakpoints = null; - /** - * Saves adding order of sequences - */ - protected ArrayList groupOrder = null; - - /** - * - * Constructor of the SequenceGrouping class, given a mapping manager - * - * @param _mappingManager the mapping manager to use for mapping - */ - public SequenceGrouping( MappingManager _mappingManager) - { - this.mapping = _mappingManager; - - } - - /** - * Inits the Sequence Grouping sub module, with a list of configuration properties. - */ - public void init (Properties moduleProperties) throws IncorrectVamavModuleInitialisation - { - PropertyManager propManager = new PropertyManager(); - this.alignManager = new AlignmentManager(); - try - { - Properties props = propManager.getModuleProperties(moduleProperties, this.alignManager.getModulePrefix()); - this.alignManager.init(props); - props = null; - } - catch (IncorrectVamavModuleInitialisation ivmie) - { - logger.appliError("Unable to init Alignment Manager."); - throw new IncorrectVamavModuleInitialisation(ivmie); - } - propManager = null; - if (moduleProperties == null || moduleProperties.size()<1) - { - this.logger.appliInfo("SequenceGrouping - No properties provided. Uses default."); - return; - } - String gap = moduleProperties.getProperty("gapcharacter", String.valueOf(this.gapChar)); - if( gap !=null && gap.length()<1) - this.gapChar = gap.charAt(0); - - } - - - - - - - /** - * Retrieves the mapping attribut - * - * @return Returns the mapping. - */ - protected MappingManager getMapping() - { - return this.mapping; - } - - /** - * retrieves the MultipleAlignmentIntf associated to the current object, - * to execute multiple alignment - * @return the MultipleAlignmentIntf object associated to the current object. - */ - /* private MultipleAlignmentIntf getMultipleAlignment() { - return this.multipleAlignment; - }*/ - - /** - * Set the MultipleAlignmentIntf for the current object - * @param multipleAlignmentIntf the MultipleAlignmentIntf object ot associated to the object. - */ - /* private void setMultipleAlignment(MultipleAlignmentIntf _multipleAlignment) - { - this.multipleAlignment = _multipleAlignment; - }*/ - - /** - * Add a sequence for grouping. - * - * @param sequence chain sequence to add - * @param name name of the sequence to add - * @return a list of parameters to call the AstexViewer - * @throws UnableToGroupSequencesException if an error occurs during the adding. - */ - public abstract Hashtable addSequence(String sequence, String name) throws UnableToGroupSequencesException; - - /** - * Add a sequence for grouping, with an associated accessionID and its source. - * - * @param sequence chain sequence to add for grouping - * @param name name of the sequence to add - * @param accessionID accessionId associated to the sequence - * @param source source of the accessionID - * @return list of parameters to call the AstexViewer, if needed. Null, otherwise. - * @throws UnableToGroupSequencesException if an error occurs during the adding. - */ - public abstract Hashtable addSequence(String sequence, String name, String accessionID, String source) throws UnableToGroupSequencesException; - - /** - * Registers a PDB ID as belonging to a group - * @param groupName name of the group to add the structure in it. - * @param pdbID Id of the PDB structure to add - */ - protected void addStructureToGroup(String groupName, String pdbID) - { - if (this.structuresPerGroup == null) - { - this.structuresPerGroup = new Hashtable>(); - } - ArrayList structs= this.structuresPerGroup.get(groupName); - if (structs == null) - {//create new list of the group - structs = new ArrayList (); - } - //add structure - if (!structs.contains(pdbID)) - { - structs.add(pdbID); - logger.sessionDebug("Adding structure"+pdbID+" to group "+groupName); - // readd list to be sure to have the right list in the global list - this.structuresPerGroup.put(groupName, structs); - } - } - /** - * Add a sequence to a group - * @param groupName name of the group to add the sequence into - * @param sequence sequence to add - * @param sequenceName name of the sequence to add - */ - protected void addSequenceToGroup(String groupName, String sequence, String sequenceName) - { - if (groupName == null || groupName.length()<1) - { - this.logger.sessionError("There is no group name. Can not add the sequence to the group."); - return; - } - if (sequence == null || sequence.length()<1) - { - this.logger.sessionError("There is no sequence. Can not add the sequence to the group."); - return; - } - - this.logger.sessionInfo("Adding "+sequenceName+" sequence to "+groupName+" group."); - ArrayList elements = getGroups().get(groupName); - if (elements == null) - { - elements = new ArrayList(); - this.logger.sessionInfo("No previous list, create one"); - } - if (sequence ==null) - this.logger.sessionError("No sequence provided for "+sequenceName+"."); - else - { - if (sequence.length()>0) - { - Integer maxLength = getMaxSeqLengthsPerGroup().get(groupName); - if(maxLength!=null&& maxLength.intValue()>0 ) - { - int maxSeqLength = maxLength.intValue(); - int seqLen = sequence.length(); - if (maxSeqLength < seqLen) - { - maxSeqLength = seqLen; - maxLength = Integer.valueOf(maxSeqLength); - getMaxSeqLengthsPerGroup().put(groupName, maxLength); - } - } - else - { - int seqLen = sequence.length(); - maxLength = Integer.valueOf(seqLen); - getMaxSeqLengthsPerGroup().put(groupName, maxLength); - } - } - SequenceType seq = new SequenceType() ; - seq.setName(sequenceName); - seq.setSequence(sequence); - if( !elements.contains(seq)) - { - if (!this.logger.isProduction()) - { - this.logger.sessionDebug("sequences size before "); - this.logger.sessionDebug(""+elements.size()); - } - elements.add(seq); - } - //else - //seq = null; - if( !this.logger.isProduction()) - { - this.logger.sessionDebug("sequences size after "); - this.logger.sessionDebug("" +elements.size()); - this.logger.sessionDebug("groups size before "); - this.logger.sessionDebug(""+getGroups().size()); - } - getGroups().put(groupName, elements); - if( !this.logger.isProduction()) - { - this.logger.sessionDebug("groups size after "); - this.logger.sessionDebug(""+getGroups().size()); - } - addGroupToOrder(groupName); - } - } - - /** - * Retrieves the groups attribut - * - * @return Returns the groups. - */ - protected Hashtable> getGroups() - { - if (this.groups == null) - this.groups = new Hashtable> (); - return this.groups; - } - - /** - * Retrieves the fakeSequencePerLength attribut - * - * @return Returns the fakeSequencePerLength. - */ - public Hashtable getFakeSequencePerLength() - { - if (this.fakeSequencePerLength == null) - { - this.fakeSequencePerLength = new Hashtable(); - } - return this.fakeSequencePerLength; - } - - /** - * Retrieves the maxSeqLengthsPerGroup attribut - * - * @return Returns the maxSeqLengthsPerGroup. - */ - public Hashtable getMaxSeqLengthsPerGroup() - { - if( this.maxSeqLengthsPerGroup == null) - this.maxSeqLengthsPerGroup = new Hashtable(); - return this.maxSeqLengthsPerGroup; - } - - /** - * Retrieves the sequenceOrder attribut - * - * @return Returns the sequenceOrder. - */ - protected ArrayList getGroupOrder() { - if( this.groupOrder == null) - this.groupOrder = new ArrayList (); - return this.groupOrder; - } - - protected void addGroupToOrder(String groupName) - { - if (!(getGroupOrder().contains(groupName))) - getGroupOrder().add(groupName); - } - - /** - * Clear the sequence order List - */ - public void groupOrderClear() { - if( this.groupOrder != null) - this.groupOrder = null; - } - - /** - * Retrieves the modulePrefix attribut - * - * @return Returns the modulePrefix. - */ - public String getModulePrefix() - { - return this.modulePrefix; - } - - /** - * Add a breakpoint to the grouping - * @param element annotation element associated to a breakpoint. - */ - public void addBreakpoint(AnnotationElement element) - { - if (element == null) - { - this.logger.sessionError("Sequence Grouping addBreakPoint - There is no annotation element. Can not add the breakpoint to groups"); - return; - } - this.logger.sessionDebug("Adding breakpoint"); - getBreakpoints().add(element); - } - - /** - * Retrieves the breakpoints attribut - * - * @return Returns the breakpoints. - */ - protected ArrayList getBreakpoints() - { - if (this.breakpoints == null) - this.breakpoints= new ArrayList(); - return this.breakpoints; - } - - /** - * Create a fake sequence containing provided breakpoints. - * @param breaks list of breakpoints - * @param groupName name of the group the fake sequence will be associated. - * @return the created fake sequence corresponding to the list of breakpoint - */ - protected String createFakeSequence(String groupName, ArrayList breaks) - { - - if(breaks == null || breaks.size()<1) return null; - this.logger.sessionInfo("Creating BreakPoint sequence for "+groupName ); - this.logger.sessionDebug("break points: "+breaks.size()); - String fakeSequence = null; - Integer len = getMaxSeqLengthsPerGroup().get(groupName); - if (len != null) - { - //retrieves store fake sequence: - fakeSequence = getFakeSequencePerLength().get(len); - if( fakeSequence == null || fakeSequence.length()<1) - { - Hashtable positions = new Hashtable (breaks.size()); - StringBuffer sequence = StringBufferPool.getString(); - for (int breakNumber = breaks.size()-1; breakNumber >=0; breakNumber --) - { - AnnotationElement bp = breaks.get(breakNumber); - if (bp == null) continue; - int pos = bp.getPosition()-1;//position in the sequence start at 1 - if (pos >=0) - { - positions.put(new Integer(pos), bp); - //System.out.println("adding position "+pos); - } - } - - int maxSeqLength = len.intValue(); - int size = maxSeqLength -1; - for (int i = 0; i< maxSeqLength; i++ ) - { - int reversePos = i; - //System.out.println("reverse pos "+reversePos); - Integer p = new Integer(reversePos); - if (positions.containsKey(p)) - { - AnnotationElement bp = positions.get(p); - sequence.append(bp.getDisplayCharacter()); - } - else - { - sequence.append(this.gapChar); - //System.out.println("no breakpoint found at pos "+reversePos); - } - } - positions = null; - fakeSequence = sequence.toString(); - StringBufferPool.returnString(sequence); - getFakeSequencePerLength().put(len, fakeSequence); - } - } - else - { - this.logger.sessionDebug("no len"); - } - this.logger.sessionDebug("fake sequence "+fakeSequence); - return fakeSequence; - } - - - /** - * Writes created groups into an atribute file for tha AstexViewer - * - * @throws UnableToGroupSequencesException, if unable to group added sequences - * @return the atribute file corresponding to the grouping of added sequences - * - */ - public File storeGroups() throws UnableToGroupSequencesException - { - int size = this.getGroups().size(); - if (size<1) - { - this.logger.sessionWarn("Sequence Grouping - There is no computed group. Can not store groups."); - // return null; - throw new UnableToGroupSequencesException(); - } - - //test if there is at least a sequence in each group. - boolean correct = true; - for (Enumeration _groups = this.getGroups().keys(); _groups.hasMoreElements() && correct; ) - { - String groupName = _groups.nextElement(); - ArrayList sequences = this.getGroups().get(groupName); - this.logger.sessionDebug("Group "+groupName); - if (sequences == null || sequences.size()<1) - { - correct = false; - } - else - { - this.logger.sessionDebug("group size "+sequences.size()); - } - } - if (!correct) - { - this.logger.sessionWarn("Sequence Grouping - There is no computed group. Can not store groups."); - //return null; - throw new UnableToGroupSequencesException(); - } - if (this.sequenceFile == null) - this.sequenceFile = new ArrayList(); - else - this.sequenceFile.clear(); - File atrFile = null; - try - { - this.workingDirectory = this.getOutputDirectory(); - String atributeFile = this.workingDirectory+File.separator+"vamav-"+this.getSessionID()+"."+this.atrFilePrefix; - logger.sessionInfo("Creating atribute file: "+atributeFile); - //writing Atribute file - if( atributeFile == null) - { - throw new UnableToGroupSequencesException("No atribute file path provided."); - } - if (!atributeFile.endsWith(this.atrFilePrefix)) - { - atributeFile = atributeFile.concat("."+this.atrFilePrefix); - } - atrFile = new File (atributeFile); - //atrFile.mkdirs(); - this.logger.sessionInfo("SequenceGrouping - Writing Atribute File."); - PrintWriter out = openFile(atrFile); - if( out == null) - throw new UnableToGroupSequencesException("Unable to open file to write. "+atrFile.getAbsolutePath());; - //return null; - DataBuffer line = DataBufferPool.getString(); - - //write header - line.setString("Atribute file Version 1.0"); - writeLine(line, out); - line.setString(""); - writeLine(line, out); - /*int groupNumber = 0; - for (Enumeration keys = getGroups().keys(); keys.hasMoreElements();) - {*/ - - this.alignManager.setSession(this.getSessionID()); - for (int groupNumber = 0; groupNumber < getGroupOrder().size() ;groupNumber++ ) - { - - - String groupName = getGroupOrder().get(groupNumber); - getGroups(); - //exporting fasta file - ArrayList sequences = getGroups().get(groupName); - - //generate alignment file name - // MultipleAlignmentIntf - // AlignmentManager clustal = new AlignmentManager();//ClustalW_EBIWSClient(this.getSessionID()); - //clustal.setSession(this.getSessionID()); - String extension = ""; - String alignmentfileExtension = alignManager.getMultipleAligmnentFileExtension(); - if (alignmentfileExtension != null && alignmentfileExtension.length()>0) - if (alignmentfileExtension.startsWith(".")) - extension = alignmentfileExtension; - else - extension = ".".concat(alignmentfileExtension); - - String alignmentFileName = groupName + extension; - if( sequences != null && sequences.size()>0) - { - //(groupName, "atributeFile"); - this.logger.sessionDebug("Preparing multiple alignment "+groupName); - if(getBreakpoints()!=null && getBreakpoints().size()>0) - { - alignManager.HasBreakPoint(); - String sequence = createFakeSequence(groupName,getBreakpoints() ); - if (sequence !=null) - { - String sequenceName = groupName+"Breakpoints_"; - alignManager.addSequence(sequenceName, this.prepareAddSequence(sequence,sequenceName)); - } - } - else - { - alignManager.HasNoBreakPoint(); - } - for (int seqNumber = sequences.size() -1; seqNumber>=0; seqNumber--) - { - SequenceType seq = sequences.get(seqNumber); - if (seq == null) - { - this.logger.sessionWarn("No sequence to add"); - continue; - } - this.logger.sessionDebug("Add sequence for multiple alignment "+seq.getName() + " "+seq.getSequence()); - alignManager.addSequence(seq.getName(), this.prepareAddSequence(seq.getSequence(), seq.getName())); - } - String alignment = alignManager.execMultipleAlignment(); - if (alignment!= null) - { - File alignmentFile = this.unModifieSequences(alignment, groupName,this.workingDirectory + File.separator+alignmentFileName); - if (alignmentFile != null) - this.getSequenceFiles().add(alignmentFile); - } - else - { - logger.sessionDebug("No alignment retrieved."); - } - - // add group - ArrayList structs = null; - DataBuffer ids = DataBufferPool.getString(); - - if( this.structuresPerGroup != null && this.structuresPerGroup.size()>0) - { - structs = this.structuresPerGroup.get(groupName); - - if (structs == null || structs.size()<1) - { - ids.append("groupName"); - - logger.sessionInfo("no pdb structure for the group "+groupName+". No matrix added"); - line.setString(" Molecule "+groupName+" "+groupName+" {\n"); - // writeLine(line, out); - line.append(" }\n"); - //writeLine(line, out); - } - else - { - String primaryID = structs.remove(structs.size()-1); - line.setString(" Molecule "+primaryID+" {\n"); - // writeLine(line, out); - line.append(" }\n"); - //writeLine(line, out); - ids.append(primaryID); - for (int structNumber = structs.size()-1; structNumber>=0; structNumber--) - { - String id = structs.get(structNumber); - line.append(" Molecule "+id+" {\n"); - //writeLine(line, out); - ids.append(" ".concat(id)); - try - { - Collection matrixes = this.mapping.getRotationTranslationMatrix(primaryID, id); - if (matrixes != null) - { - for (RotationTranslationMatrix matrix : matrixes) - { - if( matrix != null) - { - boolean isChain = false; - String chainID = matrix.getPrimaryPDBIDChain(); - if(chainID!= null &&chainID.length()>0 ) - { - isChain = true; - line.append(" Chain "+chainID+ " {\n"); - } - if( matrix != null) - { - line.append(" Matrix "); - line.append(BigDecimal.valueOf(matrix.get(0, 0).doubleValue())+ " "+BigDecimal.valueOf(matrix.get(0,1).doubleValue())+ " "+BigDecimal.valueOf(matrix.get(0,2).doubleValue())+ " "+ - BigDecimal.valueOf(matrix.get(1,0).doubleValue())+ " "+BigDecimal.valueOf(matrix.get(1, 1).doubleValue())+ " "+BigDecimal.valueOf(matrix.get(1, 2).doubleValue())+ " "+ - BigDecimal.valueOf(matrix.get(2,0).doubleValue())+ " "+BigDecimal.valueOf(matrix.get(2, 1).doubleValue())+ " "+BigDecimal.valueOf(matrix.get(2,2).doubleValue())+ " " - + BigDecimal.valueOf(matrix.get(0,3).doubleValue()) + " " + BigDecimal.valueOf(matrix.get(1, 3).doubleValue()) + " " + BigDecimal.valueOf(matrix.get(2, 3).doubleValue()) ); - //writeLine(line, out); - line.append("\n"); - } - if( isChain) - { - line.append("}\n"); - } - } - } - } - } - catch (MappingException mexcep) - { - logger.sessionError("Error during RTM mapping.",mexcep); - } - line.append(" }\n"); - //writeLine(line, out); - } - - } - - } - DataBuffer groupLine = DataBufferPool.getString(); - groupLine.setString("Group \""+groupName+"\" "+ids+" {"); - // groupLine.setString("Group \""+groupName+"\" {"); - writeLine(groupLine, out); - DataBufferPool.returnString(groupLine); - DataBufferPool.returnString(ids); - line.append(" Sequence \""+alignmentFileName+"\" \n");//\""+groupName+".aln"+"\" "); - //writeLine(line, out); - line.append(" Text \"This is a group "+groupName+"\"\n"); - //writeLine(line, out); - writeLine(line, out); - //Group "dfr" 7dfr 8dfr { - - line.setString("}\n"); - writeLine(line, out); - - - - } - else - this.logger.sessionWarn("No sequence to add to group "+ groupName); - } - line.setString("}\n"); - writeLine(line, out); - closeFile(out); - alignManager = null; - } - catch (AlignmentException ae ) - { - atrFile = null; - throw new UnableToGroupSequencesException(); - } - catch (IOException ioe) - { - this.logger.sessionError("Error during Atribute file writing "+atrFile+". ",ioe); - //ioe.printStackTrace(System.out); - atrFile = null; - } - return atrFile; - } - - /** - * Readds breakpoints after the multiple alignment ( as display character for breakpoint, are not supported by multiple alignment tools - * - * @param alignment alignment String - * @param alignmentName name of the alignment - * @return the file containing the alignment with breakpoints - */ - protected File unModifieSequences (String alignment, String alignmentName, String masterFileName) - { - if (alignment == null) - { - this.logger.sessionError("UnModifiedSequences - No aligment found. Can not unmodified sequences."); - return null; - } - // logger.Applidebug("Readded breakpoint to sequences "+alignment); - - - // String masterFileName = this.workingDirectory + File.separator+alignmentName+ alignmentfileExtension; - // WORK_ROOT + "/" +sessionId+ "/master_" + i + ".seq"; - //check workingDirectory exists, can be read and is a directory - File workingDir = new File (this.workingDirectory); - if(!(workingDir !=null && workingDir.exists())) - { - if (!workingDir.mkdir()) - { - this.logger.sessionError( "%%% WARNING: couldn't open master " - + "sequence file for writing. Working directory does not exist. Can not be created. "+this.workingDirectory ); - return null; - } - } - if(! (workingDir.isDirectory()&& workingDir.canRead())) - { - logger.sessionError( "%%% WARNING: couldn't open master " - + "sequence file for writing. Working directory does not exist. " ); - return null; - } - File masterFile = new File(masterFileName ); - try - { - Writer masterWriter = new FileWriter( masterFile ); - PrintWriter master = new PrintWriter( masterWriter ); - if(this.deleteOnExit) masterFile.deleteOnExit(); - - //write alignment - boolean endAlignment = false; - int len = 0; - DataBuffer brkSequence = DataBufferPool.getString(); - logger.sessionDebug("Retrieving alignment"); - String[] lines = alignment.split("\n"); - if (lines == null || lines.length<1) - { - logger.sessionError("No line retrieving - something wrong."); - return null; - } - logger.sessionDebug(lines.length+" lines found."); - for ( int lineNumber = 0; lineNumber bkpts = this.getSequenceBreakPoints().get(name); - if (bkpts == null)//no breakpoint associated - write line - { - logger.sessionDebug("No breakpoint export line "+line); - master.println(line); - /*System.out.println("no break point");*/ - } - else - {//modified at positions - //get sequence - /*System.out.println(line);*/ - logger.sessionDebug("No breakpoint found "); - String sequence = line.substring(pos+1,line.length()).trim(); - /*System.out.println("sequence: "+sequence);*/ - int seqPos = line.indexOf(sequence); - /*System.out.println("break point "+bkpts.size());*/ - - char[] chars = sequence.toCharArray(); - int currentResidentNumber = 0; - for (int charNumber = 0; charNumber< chars.length;charNumber++ ) - { - char currentChar = chars[charNumber]; - if (currentChar == '-') - { - //System.out.print(" gap "); - continue; - } - //check if breakpoint - /*System.out.print(" "+currentResidentNumber+" ");*/ - Integer resN = Integer.valueOf(currentResidentNumber++); - StringBuffer displayCharacter = bkpts.get(resN); - len++; - //System.out.print("|"+(currentResidentNumber-1)+"-"+len+"|"); - if (displayCharacter == null ||displayCharacter.length()<1 ) - { - continue; - } - //breakpoint found - chars[charNumber] = displayCharacter.charAt(0); - /*System.out.print(displayCharacter.charAt(0));*/ - bkpts.remove(resN);resN=null; - } - int resCount = currentResidentNumber; - sequence = String.valueOf(chars); - /*System.out.println("new seq: "+sequence);*/ - if (brkSequence.length()<=0) brkSequence.setString(sequence); - else brkSequence.append(sequence); - line = line.substring(0,seqPos).concat(sequence); - master.println(line); - Hashtable newBkpts = new Hashtable (bkpts.size()); - - for (Enumeration positions = bkpts.keys(); positions.hasMoreElements();) - { - Integer position = (Integer) positions.nextElement(); - if (position == null|| position.intValue()<0) continue; - StringBuffer character = bkpts.get(position); - if( character == null || character.length()!=1) - continue; - /*System.out.println("previous breakpoint position "+position.intValue());*/ - bkpts.remove(position); - //position = null; - position = Integer.valueOf(position.intValue() - (resCount)); - /*System.out.println("new breakpoint position "+position.intValue());*/ - //use temporary table to avoid deadlock - newBkpts.put(position, character); - } - /*for (Enumeration positions = bkpts.keys(); positions.hasMoreElements();) - { - Integer position = (Integer) positions.nextElement(); - if (position == null|| position.intValue()<0) continue; - StringBuffer character = bkpts.get(position); - if( character == null || character.length()!=1) - continue; - if( position.intValue()0) - this.getSequenceBreakPoints().put(name, newBkpts); - } - } - - //release unused object - this.clearSequenceBreakPoints(); - //StringBufferPool.returnString(this.sequences); - alignment = null; - master.close(); - master = null; - alignmentName = null; - // System.out.println("new bk seq "+brkSequence); - DataBufferPool.returnString(brkSequence); - } - catch( IOException ioe ) - { - logger.sessionError( "%%% WARNING: couldn't open master "+ "sequence file for writing: " + ioe ); - // ioe.printStackTrace(System.out); - masterFile = null; - } - return masterFile; - } - - /** - * As multiple alignment tools do not support breakpoint display characters, they are removed from the sequence, replaced by 'X' character - * and stored for readding after the multiple alignment (see unModifieSequences method) - * @param sequence sequence to prepare for alignment - * @param name name of the sequence to prepare - * @return the sequence without breakpoint display character - */ - - protected String prepareAddSequence(String sequence, String name) - { -// save position for breakpoint sequences - //modified non expected character ( A R D N B C E Z Q G H I L K M F P S T W Y V X) - //t o the same/unique one ->"|" - // - /*sequences.setLength(0); - sequences.trimToSize(); - sequences.append(sequence);*/ - //System.out.println("current seq "+sequences); - String temp = sequence.replaceAll("[^ARDNBCEZQGHILKMFPSTWYVX-]", "|"); - StringBuffer s = StringBufferPool.getString(); - s.setLength(0); - s.trimToSize(); - s.append(temp); - int pos = s.indexOf("|"); - //System.out.println("tem p seq "+temp); - Hashtable breakpointPositions = null; - while (pos>0) - { - logger.sessionInfo("new breakpoint "+pos); - if (breakpointPositions == null) breakpointPositions = new Hashtable(); - breakpointPositions.put(Integer.valueOf(pos), new StringBuffer(sequence.subSequence(pos, pos+1))); - s.setCharAt(pos, 'X'); - pos = s.indexOf("|"); - } - if(breakpointPositions!=null ) - {//a breakpoint has been found at least - this.getSequenceBreakPoints().put(name.trim().toLowerCase(), breakpointPositions); - } - String seq = s.toString(); - StringBufferPool.returnString(s); - return seq; - } - - /** - * Retrieves the sequenceFile attribut - * - * @return Returns the sequenceFile. - */ - public ArrayList getSequenceFiles() { - if( this.sequenceFile == null) - this.sequenceFile = new ArrayList (); - return this.sequenceFile; - } - - - /** - * Opens a file for writing - * - *@param file file to open. - *@return a printwriter to writer into it - * @exception IOException if an error occurs - */ - protected PrintWriter openFile(File file) throws IOException - { - PrintWriter out = null; - if (file == null) - { - //Application log(no such file) - throw new IOException("Unknown file"); - } - - // check if the current file exists - file = new File(file.getAbsolutePath()); - logger.sessionDebug("atribute file "+file.getAbsolutePath()); - if (!file.exists() ) - { - File directory = new File(file.getParent()); - logger.sessionDebug("parent directory "+ directory.getParent()); - // but first, see if it exists already. If so, we don't need - // to run the groups calculation again, so just return and - // we're done - if( directory.exists() ) { - // - } else { - if( ! directory.mkdirs() ) { - logger.sessionError( "%%% ERROR: Grouping; couldn't create " - + "directory for grouping /atribute file " ); - } - } - if (!file.createNewFile()) - { - throw new IOException("Can't create file: " - + file.getAbsolutePath()); - } - } - // the file will be overwritten, if the file already exists (but it should be indicated in the log) - - if (file.exists() && !erase) - { - throw new IOException("The file already exists: "+ file.getAbsolutePath()+ " Shall we overwrite?"); - } - - - if (!file.canWrite() ) - { - throw new IOException("Can not write in file: " - + file.getAbsolutePath()); - } - - // check possible problem with the reader - // The file is already opened. So, we close the file, before reopening it. - if (out != null) - { - closeFile(out); - logger.sessionWarn("The file "+ file.getName()+" has already been opened."); - } - - if (enc != null) - { - logger.sessionDebug("Opening File: "+file.getName()); - logger.sessionDebug("set output with encoding : "+enc+" "+file.getAbsolutePath()); - FileOutputStream fos = new FileOutputStream(file.getAbsolutePath(), append); - try - { - OutputStreamWriter ow = new OutputStreamWriter(fos, enc); - out = new PrintWriter(ow,true); - logger.sessionDebug("Encoding "+ow.getEncoding()+" support "+java.nio.charset.Charset.isSupported(enc)); - } - catch (java.io.UnsupportedEncodingException ue) - { - logger.sessionError("unsupported encoding ",ue); - } - } - else - { - - logger.sessionDebug("Opening File: "+file.getName()); - FileWriter fw = new FileWriter(file.getAbsolutePath(), append); - out = new PrintWriter(new BufferedWriter(fw),true); - } - return out; - } - - - /** - * Closes a data text file. - * @param out writer of the file to close. - * - */ - protected void closeFile(PrintWriter out) - { - if (out != null) - { - out.flush(); - out.close(); - out = null; - } - } - - - /** - *

- * Retrieves a line from a data file - * Only when termination requirements have been met, the method should return a - * String object. - *

- * @param line containing data items in one String - * @param out PrintWriter of the file to write line into. - */ - protected void writeLine(DataBuffer line, PrintWriter out ) - { - /*System.out.println("Writeline ");*/ - if (line != null) - { - if (line.length() == 0) - { - /*System.out.println("line empty");*/ - out.println(""); - } - else - { - out.println(line); - /* System.out.println("Writeline :" + line);*/ - } - } - } - - - /** - * Retrieves the sequenceBreakPoints attribut - * - * @return Returns the sequenceBreakPoints. - */ - protected Hashtable> getSequenceBreakPoints() - { - if(this.sequenceBreakPoints == null) - { - this.sequenceBreakPoints = new Hashtable>(); - } - - return this.sequenceBreakPoints; - } - - /** - * Clears breakpoint lisr - * - */ - protected void clearSequenceBreakPoints() - { - if(this.sequenceBreakPoints != null) - { - this.sequenceBreakPoints.clear(); - this.sequenceBreakPoints = null; - } - } - - /** - * Retrieves the pdbidsproperty attribut - * - * @return Returns the pdbidsproperty. - */ - public String getPdbidsproperty() - { - return this.pdbidsproperty; - } - - /** - * Retrieves the working directory for output file. - * @return the path to the output/working directory - */ - public abstract String getOutputDirectory(); - - /** - * retrieves current sessionID - * @return the ID of the current session for the document grouping. - */ - public abstract String getSessionID(); - } diff --git a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/SequenceGrouping_domain.java b/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/SequenceGrouping_domain.java deleted file mode 100755 index 9d95fa3..0000000 --- a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/SequenceGrouping_domain.java +++ /dev/null @@ -1,272 +0,0 @@ -/* Created on 3 janv. 2006 - * * EMBL-EBI - * MSD Group - * VAMSAS Project - * VAMAV - * @author Pierre MARGUERITE - * @version 1 - * @since 3 janv. 2006 - */ -package uk.ac.ebi.msd.vamsas.vamav.documentmanagement.grouping; - -import uk.ac.ebi.msd.vamsas.vamav.documentmanagement.PDBUtil; -import uk.ac.ebi.msd.vamsas.vamav.documentmanagement.grouping.exceptions.UnableToGroupSequencesException; -import uk.ac.ebi.msd.vamsas.vamav.exceptions.IncorrectVamavModuleInitialisation; -import uk.ac.ebi.msd.vamsas.vamav.session.VAMAVSession; -import uk.ac.ebi.msd.vamsas.vamav.util.data.PDBEntry; -import uk.ac.ebi.msd.vamsas.vamav.util.mapping.MappingManager; -import uk.ac.ebi.msd.vamsas.vamav.util.pool.StringBufferPool; - -import java.io.File; -import java.util.ArrayList; -import java.util.Hashtable; -import java.util.Properties; - -/** - * Groups sequence per PFAM domain. - * - * For each sequence provided, the UniProtID is retrieved (if not provided, as source) by MSD lite. - * Then, the UniProt ID is mapped to PFAM domains, using the sanger web server. - * - * @author Pierre MARGUERITE - * @version 1 - * @since 3 janv. 2006 - * - */ -public class SequenceGrouping_domain extends SequenceGrouping - { - - protected VAMAVSession vamavSession = null; - - - /** - * - * Constructor of the SequenceGrouping class, given a mapping manager - * - * @param _mappingManager the mapping manager to use for mapping - */ - public SequenceGrouping_domain( MappingManager _mappingManager) - { - super(_mappingManager); - } - - /** - * - * Constructor of the SequenceGrouping class, given a mapping manager - * - * @param _mappingManager the mapping manager to use for mapping - * @param sessionID current session for which will be used the current sequence grouping. - */ - public SequenceGrouping_domain(MappingManager _mappingManager, VAMAVSession session ) - { - super(_mappingManager); - this.logger.setSession(session.getSessionID()); - this.vamavSession = session; - } - - /** - * Inits the Sequence Grouping sub module, with a list of configuration properties. - */ - public void init (Properties moduleProperties) throws IncorrectVamavModuleInitialisation - { - super.init(moduleProperties); - } - - - /** - * Adds a sequence to group - * @see uk.ac.ebi.msd.vamsas.vamav.documentmanagement.grouping.SequenceGrouping#addSequence(java.lang.String, java.lang.String) - */ - @Override - public Hashtable addSequence(String sequence, - String name) throws UnableToGroupSequencesException - { - // TODO Auto-generated method stub - return null; - } - /** - * Add a sequence for grouping, with an associated accessionID and its source. - * - * @param sequence chain sequence to add for grouping - * @param name name of the sequence to add - * @param accessionID accessionId associated to the sequence - * @param source source of the accessionID - * @return list of parameters to call the AstexViewer, if needed. Null, otherwise. - * @throws UnableToGroupSequencesException if an error occurs during the adding. - * - * @see uk.ac.ebi.msd.vamsas.vamav.documentmanagement.grouping.SequenceGrouping#addSequence(java.lang.String, java.lang.String, java.lang.String, java.lang.String) - - */ - @Override - public Hashtable addSequence(String sequence, - String name, String accessionID, String source) - throws UnableToGroupSequencesException - { - - if( sequence == null || sequence.length()<1) - { - this.logger.sessionError("SequenceGrouping - addSequence: Can not add sequence / The sequence is unknown."); - return null; - } - if( name == null || name.length()<1) - { - this.logger.sessionError("SequenceGrouping - addSequence: Can not add sequence / The name is unknown."); - return null; - } - if( source == null || source.length()<1) - { - this.logger.sessionWarn("SequenceGrouping - addSequence: the accession ID source is not provided / try to determine PDBID from the sequence."); - return this.addSequence(sequence, name); - } - if( accessionID == null || accessionID.length()<1) - { - this.logger.sessionWarn("SequenceGrouping - addSequence: the accession ID is not provided / try to determine PDBID from the sequence."); - return this.addSequence(sequence, name); - } - Hashtable parameters = null; - try - { - ArrayList entries = null; - - if("PDB".equals(source)) - { - PDBEntry entry = this.getMapping().getPDBEntryFromPDBID(accessionID); - if( entry != null) - { - entries = new ArrayList(1); - entries.add(entry); - } - } - if ("UNIPROT".equalsIgnoreCase(source)) - { - entries = this.getMapping().retrievePDBIDFromUniprotAC(accessionID); - } - if( entries == null || entries.size()<1) - { - this.logger.sessionError("No associated PDB ID to the accessionAC "+ accessionID + " from "+source); - return this.addSequence(sequence, name); - } - -// retrieved associated domains - - - ArrayList domains = this.mapping.retrievePFAMDomain(accessionID); - if (domains == null || domains.isEmpty()) - { - logger.sessionWarn("No domain associated to "+accessionID); - logger.sessionWarn("The sequence can not be grouped."); - return null; - } - - //boolean notFound = false; - //hasAlignmentSequences = true; - parameters = new Hashtable(); - - int molNumber = 0; - StringBuffer pdbIDs = null; - if (entries != null || entries.size()<1) - { -// Retrieves PDB chains, before adding them to group - //add molecule to AV parameters - ArrayList associatedChains = new ArrayList(); - PDBUtil util = new PDBUtil(this.vamavSession); - for (int entryNumber = entries.size() -1; entryNumber >=0; entryNumber --) - { - PDBEntry entry = entries.get(entryNumber); - - parameters.put("moleculeG"+molNumber,entry); - parameters.put("nameG"+molNumber, entry.getPdbID()); - if( !logger.isProduction()) logger.sessionDebug("Adding PDB parameters "+parameters); - ArrayList chains = util.GetChain(entry); - - if( chains != null) - { - this.logger.sessionDebug(" chains found "); - associatedChains.addAll(chains); - } - else - this.logger.sessionDebug("no chains found "); - - - if( pdbIDs == null) pdbIDs = StringBufferPool.getString(); - if(pdbIDs.length()>0)pdbIDs.append(", "+entry.getPdbID()); - else pdbIDs.append(entry.getPdbID()); - //entries.remove(entry); - } - - //treating retrieved domains - for (int domainNumber = domains.size() - 1; domainNumber >=0; domainNumber --) - {//add sequence to the current domain - String domainID = domains.get(domainNumber); - if (domainID == null || domainID.length()<0) - { - logger.sessionDebug("No domain. something wrong, while adding sequence to domain group."); - continue; - } - this.addSequenceToGroup(domainID, sequence, name); - //adding PDB chains to the group - if( associatedChains!=null && !associatedChains.isEmpty()) - { - for (int chainNumber = associatedChains.size()-1; chainNumber>=0; chainNumber--) - { - PDBUtil.Chain chain = associatedChains.get(chainNumber); - if (chain == null) continue; - - this.addSequenceToGroup(domainID, chain.getSequence(), chain.getName()); - } - } - if( entries != null && !entries.isEmpty()) - { - for (int entryNumber = entries.size() -1; entryNumber >=0; entryNumber --) - { - PDBEntry entry = entries.get(entryNumber); - if( entry == null) continue; - - this.addStructureToGroup(domainID, entry.getPdbID()); - //entries.remove(entry); - } - } - } - //this.addSequenceToGroup(entry.getPdbID(), sequence, name); - util = null; - if(!"PDB".equals(source))parameters.put(this.pdbidsproperty,pdbIDs.toString()); - StringBufferPool.returnString(pdbIDs); - entries.clear(); - entries = null; - } - - //} - /*catch (IncorrectVamavModuleInitialisation inE) - { - logger.AppliError("Sequence Grouping addSequence - error during mapping execution. Can not proceed.", inE); - throw new UnableToGroupSequencesException(); - }*/ - } - catch (Exception inE) - { - this.logger.sessionError("Sequence Grouping addSequence - error during mapping execution. Can not proceed.", inE); - throw new UnableToGroupSequencesException(); - } - return parameters; - } - - /** Retrieves the directory to store files in. - * @return the output directory for created file by the sequence grouping processing. - */ - public String getOutputDirectory() - { - File sessionDir = this.vamavSession.getSessionDirectory(); - if( sessionDir != null) - return sessionDir.getAbsolutePath(); - return null; //should not happen, has directory file is attached during object creation. - } - /** - * @see uk.ac.ebi.msd.vamsas.vamav.documentmanagement.grouping.SequenceGrouping#getSessionID() - */ - @Override - public String getSessionID() - { - return this.vamavSession.getSessionID(); - } - - } diff --git a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/SequenceGrouping_structure.java b/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/SequenceGrouping_structure.java deleted file mode 100755 index c70ba70..0000000 --- a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/SequenceGrouping_structure.java +++ /dev/null @@ -1,298 +0,0 @@ -/* * EMBL-EBI -* MSD Group -* VAMSAS Project -* VAMAV -*/ -package uk.ac.ebi.msd.vamsas.vamav.documentmanagement.grouping; - -import uk.ac.ebi.msd.vamsas.vamav.documentmanagement.PDBUtil; -import uk.ac.ebi.msd.vamsas.vamav.documentmanagement.grouping.exceptions.UnableToGroupSequencesException; -import uk.ac.ebi.msd.vamsas.vamav.exceptions.IncorrectVamavModuleInitialisation; -import uk.ac.ebi.msd.vamsas.vamav.session.VAMAVSession; -import uk.ac.ebi.msd.vamsas.vamav.util.data.PDBEntry; -import uk.ac.ebi.msd.vamsas.vamav.util.mapping.MappingManager; -import uk.ac.ebi.msd.vamsas.vamav.util.pool.StringBufferPool; - - -import java.io.File; -import java.util.ArrayList; -import java.util.Hashtable; -import java.util.Properties; - -/** - *Group sequences per structure - * - * First, add sequences, with DB ref is provided ( addSequence methods) - * then, - *storeGroup Method (To create atribute file and alignment files) - * - *Each time a sequence is added, it is added to the determined grou. - * @version 1 - *@author Pierre MARGUERITE - */ -public class SequenceGrouping_structure extends SequenceGrouping //implements uk.ac.ebi.msd.vamsas.vamav.VamaVModule{ -{ - - - //private final VAMAVLogger logger = new VAMAVLoggerImpl(this.getClass()); - protected VAMAVSession vamavSession = null; - - - /** - * - * Constructor of the SequenceGrouping class, given a mapping manager - * - * @param _mappingManager the mapping manager to use for mapping - */ - public SequenceGrouping_structure( MappingManager _mappingManager) - { - super(_mappingManager); - } - - /** - * - * Constructor of the SequenceGrouping class, given a mapping manager - * - * @param _mappingManager the mapping manager to use for mapping - * @param sessionID current session for which will be used the current sequence grouping. - */ - public SequenceGrouping_structure(MappingManager _mappingManager, VAMAVSession session ) - { - super(_mappingManager); - this.logger.setSession(session.getSessionID()); - this.vamavSession = session; - } - - /** - * Inits the Sequence Grouping sub module, with a list of configuration properties. - */ - public void init (Properties moduleProperties) throws IncorrectVamavModuleInitialisation - { - super.init(moduleProperties); - } - - /** - * Add a sequence for grouping. - * - * @param sequence chain sequence to add - * @param name name of the sequence to add - * @return a list of parameters to call the AstexViewer - * @throws UnableToGroupSequencesException if an error occurs during the adding. - */ - public Hashtable addSequence(String sequence, String name) throws UnableToGroupSequencesException - { - if( sequence == null || sequence.length()<1) - { - this.logger.sessionWarn("SequenceGrouping addSequence - no Sequence Provided. Can not add."); - return null; - } - if( name == null || name.length()<1) - { - this.logger.sessionWarn("SequenceGrouping addSequence - no name Provided. Can not add."); - return null; - } - ArrayList entries = null; - try - { - entries = this.getMapping().retrievePDBIDFromSequence(sequence); - } - catch (IncorrectVamavModuleInitialisation inE) - { - this.logger.sessionError("Sequence Grouping addSequence - error during mapping execution. Can not proceed.", inE); - throw new UnableToGroupSequencesException(); - } - Hashtable parameters = null; - if (entries == null ) return null; - StringBuffer pdbIDs = StringBufferPool.getString(); - for (int entryNumber = entries.size() -1; entryNumber>=0; entryNumber--) - { - PDBEntry entry = entries.get(entryNumber); - if (entry == null) continue; - - parameters = new Hashtable(); - int molNumber = 0; - if( !parameters.containsValue(entry)) - { - parameters.put("moleculeG"+molNumber,entry); - parameters.put("nameG"+molNumber, entry.getPdbID()); - this.logger.sessionDebug("New molecule added "+entry); - - molNumber++; - } - PDBUtil util = new PDBUtil(this.vamavSession); - - ArrayList chains = util.GetChain(entry); - util = null; - if( chains != null) - { - /*System.out.println(" chains found ");*/ - for (int chainN = chains.size()-1; chainN>=0; chainN --) - { - PDBUtil.Chain chain =chains.get(chainN); - if (chain == null)continue; - /*System.out.println("chain "+chain.getName()+ " "+chain.getSequence());*/ - String groupName = chain.getName(); - int pos = groupName.indexOf("_"); - if( pos>0) groupName = groupName.substring(0,pos); - this.addSequenceToGroup(groupName,chain.getSequence(),chain.getName()); - this.addStructureToGroup(groupName, entry.getPdbID()); - } - } - else - this.logger.sessionWarn("no chains found "); - String id = entry.getPdbID(); - this.addSequenceToGroup(id, sequence, name); - if(pdbIDs.length()<1) pdbIDs.append(id); - else pdbIDs.append(", "+id); - } - parameters.put(this.pdbidsproperty,pdbIDs.toString()); - StringBufferPool.returnString(pdbIDs); - return parameters; - } - - /** - * Add a sequence for grouping, with an associated accessionID and its source. - * - * @param sequence chain sequence to add for grouping - * @param name name of the sequence to add - * @param accessionID accessionId associated to the sequence - * @param source source of the accessionID - * @return list of parameters to call the AstexViewer, if needed. Null, otherwise. - * @throws UnableToGroupSequencesException if an error occurs during the adding. - */ - public Hashtable addSequence(String sequence, String name, String accessionID, String source) throws UnableToGroupSequencesException - { - - if( sequence == null || sequence.length()<1) - { - this.logger.sessionError("SequenceGrouping - addSequence: Can not add sequence / The sequence is unknown."); - return null; - } - if( name == null || name.length()<1) - { - this.logger.sessionError("SequenceGrouping - addSequence: Can not add sequence / The name is unknown."); - return null; - } - if( source == null || source.length()<1) - { - this.logger.sessionWarn("SequenceGrouping - addSequence: the accession ID source is not provided / try to determine PDBID from the sequence."); - return this.addSequence(sequence, name); - } - if( accessionID == null || accessionID.length()<1) - { - this.logger.sessionWarn("SequenceGrouping - addSequence: the accession ID is not provided / try to determine PDBID from the sequence."); - return this.addSequence(sequence, name); - } - Hashtable parameters = null; - try - { - ArrayList entries = null; - - if("PDB".equals(source)) - { - PDBEntry entry = this.getMapping().getPDBEntryFromPDBID(accessionID); - if( entry != null) - { - entries = new ArrayList(1); - entries.add(entry); - } - } - if ("UNIPROT".equalsIgnoreCase(source)) - { - entries = this.getMapping().retrievePDBIDFromUniprotAC(accessionID); - } - if( entries == null || entries.size()<1) - { - this.logger.sessionError("No associated PDB ID to the accessionAC "+ accessionID + " from "+source); - return this.addSequence(sequence, name); - } - //boolean notFound = false; - //hasAlignmentSequences = true; - parameters = new Hashtable(); - - //currenty only use the first entry - //for ( int entryNumber = entries.size()-1; entryNumber>=0; entryNumber --) - //{ - int molNumber = 0; - StringBuffer pdbIDs = null; - if (entries != null || entries.size()<1) - { - PDBUtil util = new PDBUtil(this.vamavSession); - for (int entryNumber = entries.size() -1; entryNumber >=0; entryNumber --) - { - PDBEntry entry = entries.get(entryNumber); - parameters.put("moleculeG"+molNumber,entry); - parameters.put("nameG"+molNumber, entry.getPdbID()); - - ArrayList chains = util.GetChain(entry); - - if( chains != null) - { - this.logger.sessionDebug(" chains found "); - // StringBuffer buff = StringBufferPool.getString(); - for (int chainN = chains.size()-1; chainN>=0; chainN --) - { - PDBUtil.Chain chain = chains.get(chainN); - if (chain == null)continue; - String groupName = chain.getName(); - int pos = groupName.indexOf("_"); - if( pos>0) groupName = groupName.substring(0,pos); - this.addSequenceToGroup(groupName, chain.getSequence(),chain.getName()); - this.addStructureToGroup(groupName, entry.getPdbID()); - chain = null; - } - } - else - this.logger.sessionDebug("no chains found "); - - this.addSequenceToGroup(entry.getPdbID(), sequence, name); - if( pdbIDs == null) pdbIDs = StringBufferPool.getString(); - if(pdbIDs.length()>0)pdbIDs.append(", "+entry.getPdbID()); - else pdbIDs.append(entry.getPdbID()); - entries.remove(entry); - } - util = null; - if(!"PDB".equals(source))parameters.put(this.pdbidsproperty,pdbIDs.toString()); - StringBufferPool.returnString(pdbIDs); - } - - //} - /*catch (IncorrectVamavModuleInitialisation inE) - { - logger.AppliError("Sequence Grouping addSequence - error during mapping execution. Can not proceed.", inE); - throw new UnableToGroupSequencesException(); - }*/ - } - catch (Exception inE) - { - this.logger.sessionError("Sequence Grouping addSequence - error during mapping execution. Can not proceed.", inE); - throw new UnableToGroupSequencesException(); - } - return parameters; - } - - /** - * Retrieves the directory to store files in. - * @return the output directory for created file by the sequence grouping processing. - */ - public String getOutputDirectory() - { - File sessionDir = this.vamavSession.getSessionDirectory(); - if( sessionDir != null) - return sessionDir.getAbsolutePath(); - return null; //should not happen, has directory file is attached during object creation. - } - - /** - * Retrieves current sessionID - * @see uk.ac.ebi.msd.vamsas.vamav.documentmanagement.grouping.SequenceGrouping#getSessionID() - */ - @Override - public String getSessionID() - { - - return this.vamavSession.getSessionID(); - } - - - } diff --git a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/exceptions/UnableToGroupSequencesException.java b/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/exceptions/UnableToGroupSequencesException.java deleted file mode 100755 index de14afa..0000000 --- a/src/uk/ac/ebi/msd/vamsas/vamav/documentmanagement/grouping/exceptions/UnableToGroupSequencesException.java +++ /dev/null @@ -1,61 +0,0 @@ -/* Created on 22 nov. 2005 - * * EMBL-EBI - * MSD Group - * VAMSAS Project - * VAMAV - * @author Pierre MARGUERITE - * @version 1 - * @since 22 nov. 2005 - */ -package uk.ac.ebi.msd.vamsas.vamav.documentmanagement.grouping.exceptions; - -/** - * - * @author Pierre MARGUERITE - * @version 1 - * @since 22 nov. 2005 - * - */ -public class UnableToGroupSequencesException extends Exception - { - - /** - * Constructor - * - */ - public UnableToGroupSequencesException() - { - super(); - } - - /** - * Constructor - * - * @param arg0 - */ - public UnableToGroupSequencesException(String arg0) - { - } - - /** - * Constructor - * - * @param arg0 - * @param arg1 - */ - public UnableToGroupSequencesException(String arg0, Throwable arg1) - { - super(arg0, arg1); - } - - /** - * Constructor - * - * @param arg0 - */ - public UnableToGroupSequencesException(Throwable arg0) - { - super(arg0); - } - - } diff --git a/src/uk/ac/ebi/msd/vamsas/vamav/session/SessionManager.java b/src/uk/ac/ebi/msd/vamsas/vamav/session/SessionManager.java deleted file mode 100755 index 595c3e7..0000000 --- a/src/uk/ac/ebi/msd/vamsas/vamav/session/SessionManager.java +++ /dev/null @@ -1,983 +0,0 @@ -/* - * /* - * EMBL - European Bioinformatics institute - * MSD Group - * VAMSAS Project - * - *Created on 14 d�c. 2005 - * @author Pierre MARGUERITE - * @version 1 - * @since 14 d�c. 2005 - */ -package uk.ac.ebi.msd.vamsas.vamav.session; - -import uk.ac.ebi.msd.vamsas.vamav.VAMAVClient; -import uk.ac.ebi.msd.vamsas.vamav.VamaVModule; -import uk.ac.ebi.msd.vamsas.vamav.exceptions.IncorrectVamavModuleInitialisation; -import uk.ac.ebi.msd.vamsas.vamav.session.exceptions.UnableToOpenSession; -import uk.ac.ebi.msd.vamsas.vamav.util.file.FileCopy; -import uk.ac.ebi.msd.vamsas.vamav.util.file.description.FileFormatDescription; -import uk.ac.ebi.msd.vamsas.vamav.util.file.description.SimpleFileFormatDescription; -import uk.ac.ebi.msd.vamsas.vamav.util.logger.VAMAVLogger; -import uk.ac.ebi.msd.vamsas.vamav.util.logger.VAMAVLoggerImpl; -import uk.ac.ebi.msd.vamsas.vamav.util.properties.PropertyManager; -import uk.ac.ebi.msd.vamsas.vamav.util.properties.exceptions.UnableToStorePropertiesException; - -import org.vamsas.client.ClientHandle; -import org.vamsas.client.IClient; -import org.vamsas.client.IClientFactory; -import org.vamsas.client.InvalidSessionUrnException; -import org.vamsas.client.NoDefaultSessionException; -import org.vamsas.client.UserHandle; -import org.vamsas.client.simpleclient.ArchiveUrn; -import org.vamsas.client.simpleclient.SessionUrn; -import org.vamsas.client.simpleclient.VamsasArchiveReader; -import org.vamsas.client.simpleclient.VamsasSession; - -import java.io.File; -import java.io.IOException; -import java.lang.reflect.Array; -import java.net.MalformedURLException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.Properties; - -/** - * Manager for VAMSAS session. - * Creates Session to which is attached clients - * - * Avoid to reinit a session previously treated. - * - * @author Pierre MARGUERITE - * @version 1 - * @since 14 d�c. 2005 - * - */ -public class SessionManager implements VamaVModule, IClientFactory - { - -/** - * Definition string for the VAMAV client - */ - private final String clientName = "VAMSAS - AstexViewer@MSD-EBI"; - private final String clientVersion = "0.6"; - - /** - * List of session ID and the associated session - * - */ - private Hashtable sessions = null; - - /** - * Property names - */ - private final String modulePrefix = "sessionmanager"; - - private final String sessionarenaProperty = "sessionarena"; - - private final String sessiondirectoryProperty = "sessiondirectory"; - private final String sessionLogFileProperty = "sessionlogfile"; - private final String appletFileProperty = "appletfile"; - private final String sessionDocumentFileNameProperty = "sessiondocumentfilename"; - - /*private VAMAVClientFactory clientfactory = null;*/ - - /** - * Logger to report messages - */ - private final VAMAVLogger logger = new VAMAVLoggerImpl(this.getClass()); - - /** - * Tags to replace at run-time from rules - */ - private final String temporaryTag = "@temp@"; - private final String sessionIDTag = "@sessionid@"; - private final String sessionDirTag = "@sessiondir@"; - private final String logExtensionTag = "@logfileextension@"; - private final String documentExtensionTag = "@documentextension@"; - - /** - * Rules for runtime variables (directories, files, ..) - */ - - private String sessionArenaRule = this.temporaryTag; - private String sessionDirectoryRule = this.sessionIDTag; - - private String sessionLogFileRule = this.sessionDirTag+File.separator+this.sessionIDTag+"."+this.logExtensionTag; - private String sessionDocumentFileNameRule = this.sessionDirTag+File.separator+"vamsas"+"."+this.documentExtensionTag; - private String appletFile = "index.html"; - - /** - * Keep a track of opened session. - * Stores session - */ - private Properties sessionTrack = null; - private final String trackFileName = "sessions.properties"; - private final String trackDefaultDirectory = "sessions"; - - /** - * root directory of the application - * Can be different of the current directory, in servlet server for example. - */ - private static String baseDirectory = null; - - - private File sessionArena = null; - - /** - * default constructor - called by CreateClientFactory only. - * - */ - public SessionManager() { - sessionArena = null; - } - /** - * Create a SessionManager that works parent directory for all session directories - * @param path - */ - public SessionManager(String path) throws IOException - { - // Check path is valid and read/writeable. - File newarena = new File(path); - if (newarena.exists() && newarena.isDirectory() && newarena.canRead() && newarena.canWrite()) - { - sessionArena = newarena; - } - else - { - sessionArena = null; - throw(new IOException("Cannot read and write to a directory called "+path)); - } - } - - /** - * Retrieves the modulePrefix attribut to init the current VAMAVModule - * - * @return Returns the modulePrefix. - */ - public String getModulePrefix() - { - return this.modulePrefix; - } - - - - /** - * Inits the Session Manager module following given properties - * - * @see uk.ac.ebi.msd.vamsas.vamav.VamaVModule#init(java.util.Properties) - */ - public void init(Properties properties) throws IncorrectVamavModuleInitialisation - { - logger.appliInfo("Init Session Manager: "); - /*/ try - { - this.clientfactory = new VAMAVClientFactory("factory"); - } - catch (IOException e) - { - throw new IncorrectVamavModuleInitialisation("Unable to create client factory"); - }*/ - if (properties != null && properties.size()>0) - { - this.sessionDirectoryRule = properties.getProperty(this.sessiondirectoryProperty, this.sessionDirectoryRule); - - this.sessionLogFileRule = properties.getProperty(this.sessionLogFileProperty, this.sessionLogFileRule); - this.appletFile = properties.getProperty(this.appletFileProperty, this.appletFile); - this.sessionDocumentFileNameRule = properties.getProperty(this.sessionDocumentFileNameProperty, this.sessionDocumentFileNameRule); - this.sessionArenaRule = properties.getProperty(this.sessionarenaProperty, this.sessionArenaRule); - } - if( this.sessionArenaRule.contains(this.temporaryTag)) - { - logger.applidebug("temporary tag found"); - try - { - File tempDir = createTempDir("VAMAV"); - if( !logger.isProduction()) logger.applidebug("temporary directory "+tempDir.getAbsolutePath()); - String preparePath = tempDir.getAbsolutePath().replaceAll("\\\\", "\\\\\\\\"); - this.sessionArenaRule = this.sessionArenaRule.replaceAll(this.temporaryTag,preparePath); - logger.applidebug("session arena rule "+this.sessionArenaRule); - } - catch (IOException exception) - { - this.logger.appliError("Session Manager/init: Unable to create temp directory.", exception); - throw new IncorrectVamavModuleInitialisation(exception); - } - } - else - { logger.applidebug("No temporary tag"); - if (baseDirectory!= null) - this.sessionArenaRule = baseDirectory.concat(File.separator).concat(this.sessionArenaRule); - } - if(this.sessionLogFileRule!=null && this.sessionLogFileRule.length()>0 ) - { - this.sessionLogFileRule = this.sessionLogFileRule.replaceAll(this.logExtensionTag,logger.getLogExtension()); - } - - Hashtable variables = new Hashtable(); - variables.put(this.logExtensionTag, logger.getLogExtension()); - variables.put(this.sessionDirTag, this.sessionDirectoryRule); - variables.put(this.sessionDocumentFileNameRule, this.sessionDirectoryRule); - this.replaceVariable(this.sessionDocumentFileNameRule, variables); - - this.sessionTrack = new Properties(); - PropertyManager propManager = new PropertyManager(); - this.sessionTrack = propManager.loadProperties(this.trackFileName, this.trackDefaultDirectory); - } - - /** - * Variables which can be found in property values, by correct value - * (except sessionId, which is no global to the application.) - * @param rule - * @return - */ - private String replaceVariable(String rule, Hashtable variables) - { - if(rule == null ) - { - logger.appliError("No rule provided to replace variables"); - return null; - } - if( rule.length()<1) - { - return rule; - } - if( variables == null || variables.size()<1) - { - return rule; - } - /** - * Prepare rule, otherwise '\' character is removed by replaceAll - */ - String preparePath = rule.replaceAll("\\\\", "\\\\\\\\"); - for (Enumeration keys = variables.keys(); keys.hasMoreElements();) - { - String var = (String)keys.nextElement(); - rule = rule.replaceAll(var,variables.get(var).replaceAll("\\\\", "\\\\\\\\")); - } - return rule; - - } - - - /** - * Reopens a session following the session ID for the new user - * - * @param firstName firstname of the user to open the session - * @param lastName lastname of the user - * @param sessionID ID of the session to open - * @return the created IClient according to the parameters provided - * @throws UnableToOpenSession if an error occurs while trying to open a session. - */ - public VAMAVClient openSession(String firstName, String lastName, String sessionID) throws UnableToOpenSession - { - if(sessionID == null || sessionID.length()<1 ) - { - this.logger.sessionFatal("Open Session - No sessionID provided: can not open session."); - return null; - } - VAMAVSession session = this.getSessions().get(sessionID); - VAMAVClient vorbaclient = null; - if (session == null) - { - //this.logger.sessionFatal("Open Session - No previous session exists. Can not open session."); - //return null; - this.logger.appliInfo("Opening closed session"); - String sessionDir = this.sessionTrack.getProperty(sessionID); - if( sessionDir == null || sessionDir.length()<1 ) - { - this.logger.appliFatal("Open Session - No previous session exists. Can not open session."); - return null; - } - File dir = new File (sessionDir); - String appletFileName = this.appletFile.replaceAll(this.sessionIDTag, sessionID); - if (dir.exists() && dir.canRead() && dir.isDirectory() && Arrays.asList(dir.list()).contains(appletFileName)) - {//the directory contains some files -// creating VAMSAS CLient - try - { - session = new VAMAVSession(dir); - //session.setSessionDirectory(new File (sessionDir)); - String preparePath = sessionDir.replaceAll("\\\\", "\\\\\\\\"); - session.setSessionLogFile(new File (this.sessionLogFileRule.replaceAll(this.sessionIDTag, sessionID).replaceAll(this.sessionDirTag, preparePath))); - session.setAppletFileName(appletFileName); - session.setClosedSession(true);//.setSessionID( true); - this.getSessions().put(sessionID, session); - } - catch (IOException ioe) - { - this.logger.appliError("unable to access to the session directory.", ioe); - throw new UnableToOpenSession (ioe); - } - } - } - ClientHandle app = new ClientHandle(this.clientName,this.clientVersion); - - if( firstName != null) - { - UserHandle user = new UserHandle(firstName,lastName); - vorbaclient = (VAMAVClient)this.getIClient(app, user, sessionID); - } - else - { - /*try - {*/ - vorbaclient = (VAMAVClient)this.getIClient(app); - /* } - catch (NoDefaultSessionException ndse) - { - this.logger.sessionError("Can not create client: ",ndse); - this.logger.appliError("Can not create client: ",ndse); - throw new UnableToOpenSession(ndse); - }*/ - } - session.addAttachedClient(vorbaclient); - return vorbaclient; - } - - /** - * Opens a new VAMSAS session for the provided VAMSAS document - * - * - * @param firstName firstname of the user to open the session - * @param lastName lastname of the user - * @param sessionID ID of the session to open - * @return the created IClient according to the parameters provided - * @throws UnableToOpenSession if an error occurs while trying to open a session. - */ - public VAMAVClient openSession(String firstName, String lastName, File documentPath) throws UnableToOpenSession - { - /** - * check document path - */ - if(documentPath == null || !documentPath.exists()) - { - this.logger.sessionFatal("No Document path provided or path incorrect. Can not open session."); - return null; - } - - if (!documentPath.canRead() || !documentPath.isFile()) - { - this.logger.sessionFatal("No Document path provided or path incorrect. Can not open session. "+documentPath); - return null; - } - - if ( (firstName == null ||firstName.length()<1 ) - && lastName == null||lastName.length()<1) - { - logger.appliError("No user information provided. Can not open session"); - throw new UnableToOpenSession("No user information provided. Can not open session"); - } - logger.applidebug("Starting new session with data from "+documentPath+"."); - //ArchiveUrn vamdoc = new ArchiveUrn(documentPath); - VamsasArchiveReader archive = new VamsasArchiveReader(documentPath); - // TODO: a real validity test. The below just checks it can be read. - if (!archive.isValid()) - throw new UnableToOpenSession(documentPath+" is not a valid vamsasDocument archive."); - ArchiveUrn vamsasdocument = null; - try - { - vamsasdocument = new ArchiveUrn(documentPath); - } - catch (MalformedURLException mue) - { - throw new UnableToOpenSession(); - } - - - ClientHandle app = new ClientHandle(this.clientName,this.clientVersion); - UserHandle user = new UserHandle(firstName,lastName); - - try - { - this.logger.applidebug("Opening session for "+documentPath + " "+vamsasdocument.asFile() +" "+vamsasdocument.getSessionUrn()); - return (VAMAVClient) this.openSession(app, user, vamsasdocument); - } - catch (IOException ioe) - { - throw new UnableToOpenSession(ioe); - } - } - - - - public IClient openSession(ClientHandle applicationHandle, UserHandle userId, ArchiveUrn vamsasdocument) throws IOException - { - this.logger.applidebug("openSession "+vamsasdocument.asFile()); - if (vamsasdocument == null) - { - return null; - } - - // create new session directory - if (sessionArena==null) - throw new Error("Improperly initialised SimpleClientFactory object - null sessionArena."); - File sessdir = File.createTempFile("sess", ".simpleclient", sessionArena); - if (!(sessdir.delete() && sessdir.mkdir())) - throw new IOException("Could not make session directory "+sessdir); - -// create session - //generate document copy in the session directory - VAMAVSession session = null; - try - {this.logger.applidebug("Creating VAMAVSession for "+sessdir); - session = new VAMAVSession(sessdir); - this.sessionTrack.setProperty(session.getSessionID(), sessdir.getAbsolutePath()); - String preparePath = sessdir.getAbsolutePath().replaceAll("\\\\", "\\\\\\\\"); - - session.setSessionLogFile(new File (this.sessionLogFileRule.replaceAll(this.sessionIDTag, session.getSessionID()).replaceAll(this.sessionDirTag, preparePath))); - session.setAppletFileName(this.appletFile); - this.getSessions().put(session.getSessionID(), session); - // copy document into session directory - File doc = vamsasdocument.asFile(); - this.logger.applidebug("setting document "+doc.getPath()); - this.logger.applidebug("setting document "+doc.getAbsolutePath()); - session.setVamsasDocument(doc); - } - catch (IOException ioe) - { - throw ioe;//new UnableToOpenSession(ioe); - } - IClient vorbaclient = this.getIClient(applicationHandle, userId, session); - session.addAttachedClient((VAMAVClient)vorbaclient); - //process the Vamsas Document to launch AstexViewer with suitable parameters - return vorbaclient; - } - - /** - * make a new vamsas session from the data in the archive vamsasdocument - * @param applicationHandle - * @param userId - * @param vamsasdocument - * @return - */ - /* public IClient openSession(ClientHandle applicationHandle, UserHandle userId, ArchiveUrn vamsasdocument) throws IOException { - // verify applicationHandle and userId - // TODO: verify applicationHandle and userId - // verify vamsasdocument is a valid document. - File vamdoc = vamsasdocument.asFile(); - this.logger.applidebug("Starting new session with data from "+vamsasdocument.getSessionUrn()+"(File is : "+vamdoc+")"); - VamsasArchiveReader archive = new VamsasArchiveReader(vamdoc); - // TODO: a real validity test. The below just checks it can be read. - if (!archive.isValid()) - throw new IOException(vamsasdocument.getSessionUrn()+" is not a valid vamsasDocument archive."); - // create new session directory - if (sessionArena==null) - throw new Error("Improperly initialised SimpleClientFactory object - null sessionArena."); - File sessdir = File.createTempFile("sess", ".simpleclient", sessionArena); - if (!(sessdir.delete() && sessdir.mkdir())) - throw new IOException("Could not make session directory "+sessdir); - VAMAVSession sess = new VAMAVSession(sessdir); - // copy document into session directory - sess.setVamsasDocument(vamsasdocument.asFile()); - // create client instance and return. - VAMAVClient client = new VAMAVClient(userId, applicationHandle, sess); - - return client; - }*/ - - /** - * opens session according to a provided sessionID or reads a provided VAMSAS document - * - * if no sessionID provided, creates a new session and opens the provided document. - * if the session Id is unknown, creates a new session and opens the provided document. - * if the session exists, and the provided document is newer, the provide document will replaced - * the current document in use. - * if the session has ben closed, the document is opened in a new session. - * @param firstName user firstname - * @param lastName user lastname - * @param documentPath path to a VAMSAS document - * @param sessionID ID of the session to open - * @return a VAMAVClient correspoding to the given parameters - * @throws UnableToOpenSession raises if an error during access to the document file - */ - public VAMAVClient openSession(String firstName, String lastName, File documentPath, String sessionID) throws UnableToOpenSession - { - if(sessionID == null || sessionID.length()<1 ) - { - logger.sessionWarn("Open Session - No sessionID provided: can not open session."); - return this.openSession(firstName, lastName, documentPath); - } - VAMAVSession session = this.getSessions().get(sessionID); - if (session == null) - { - return this.openSession(firstName, lastName, documentPath); - } - - /* - VAMAVSession session = null; - try - { - session = new VAMAVSession(new File(sessionDir)); - } - catch (IOException ioe) - { - throw new UnableToOpenSession(ioe); - }*/ - - - VAMAVClient newClient = null; - if (session.isOpen() && !session.isClosed()) - { - FileFormatDescription description = new SimpleFileFormatDescription(documentPath); - Hashtable variables = new Hashtable(); - variables.put(this.documentExtensionTag, description.getFileExtension()); - // String sessionDocumentPath = this.replaceVariable(this.sessionDocumentFileNameRule, variables); - File sessionDoc = session.getVamsasDocumentFile(); - //File sessionDoc = new File (sessionDocumentPath); - if (documentPath != null && documentPath.canRead() && documentPath.isFile() && documentPath.lastModified()< sessionDoc.lastModified()) - {//the provided document is newer than the document in the session directory. - logger.sessionInfo("The provided document is newer than the previously treated document. Proceed new document."); - return this.openSession(firstName, lastName, documentPath); - } - newClient = (VAMAVClient)session.getAttachedClient(0).clone(); - if( firstName != null && firstName.length()<1 && lastName!=null && lastName.length()<1) - { - UserHandle user = new UserHandle(firstName,lastName); - newClient.setUser(user); - } - try - { - FileCopy copyManager = new FileCopy(session.getSessionID()); - File newDoc = sessionDoc; - copyManager.copy(documentPath, newDoc); - documentPath = newDoc; - copyManager = null; - session.setVamsasDocumentFile(newDoc); - } - catch (IOException ioe) - { - logger.appliError("Unable to copy VAMSAS Document.", ioe); - } - } - else - newClient = this.openSession(firstName, lastName, documentPath); - /*String sessionID = vorbaclient.getSessionUrn(); - // String sessionDir = this.sessionDirectoryRule.replaceAll(this.sessionIDTag, sessionID); - // String preparePath = sessionDir.replaceAll("\\\\", "\\\\\\\\"); - // logger.applidebug("session directory "+sessionDir); - String appletFileName = this.appletFile.replaceAll(this.sessionIDTag, sessionID); - - // this.sessionTrack.setProperty(sessionID, sessionDir); - // session.setSessionDirectory(new File (sessionDir)); - // session.setSessionLogFile(new File (this.sessionLogFileRule.replaceAll(this.sessionIDTag, sessionID).replaceAll(this.sessionDirTag, preparePath))); - // session.setSessionID(sessionID,false); - session.addAttachedClient(vorbaclient); - session.setAppletFileName(appletFileName); - this.getSessions().put(sessionID, session); - - //Copying vamsas document file to session directory - FileFormatDescription description = new SimpleFileFormatDescription(documentPath); - Hashtable variables = new Hashtable(); - variables.put(this.documentExtensionTag, description.getFileExtension()); - variables.put(this.sessionDirTag, session.getSessionDirectory().getAbsolutePath()); - String sessionDocumentPath = this.replaceVariable(this.sessionDocumentFileNameRule, variables); - logger.sessionDebug("Session document "+ sessionDocumentPath); - //String sessionDocumentPath = this.sessionDocumentFileNameRule.replaceAll(preparePath, appletFileName);//sessionDir+File.separator+"vamsas"+"."+description.getFileExtension(); - try - { - FileCopy copyManager = new FileCopy(sessionID); - File newDoc = new File(sessionDocumentPath); - copyManager.copy(documentPath, newDoc); - documentPath = newDoc; - copyManager = null; - session.setVamsasDocumentFile(newDoc); - } - catch (IOException ioe) - { - logger.appliError("Unable to copy VAMSAS Document.", ioe); - } - */ - session.addAttachedClient(newClient); - return newClient; - } - - - /** - * Creates a new session of a given user. - * - * @param firstName first name of the user to open the session for - * @param lastName lastname of the user - * @return the created IClient according to the parameters provided - * @throws UnableToOpenSession raises if an error occurs during the accessing to the VAMSAS document. - *///DONE 14/03/2006 - public VAMAVClient createSession(String firstName, String lastName) throws UnableToOpenSession - { - // create new session directory - if (sessionArena==null) - throw new Error("Improperly initialised SimpleClientFactory object - null sessionArena."); - File sessdir = null; - try - { - sessdir = File.createTempFile("sess", ".simpleclient", sessionArena); - if (!(sessdir.delete() && sessdir.mkdir())) - throw new UnableToOpenSession("Could not make session directory "+sessdir); - } - catch (IOException ioe) - { - throw new UnableToOpenSession("Could not make session directory."); - - } - -// create session - //generate document copy in the session directory - VAMAVSession session = null; - //VAMAVClient vorbaclient = null; - try - { - session = new VAMAVSession(sessdir); - this.sessionTrack.setProperty(session.getSessionID(), sessdir.getAbsolutePath()); - String preparePath = sessdir.getAbsolutePath().replaceAll("\\\\", "\\\\\\\\"); - - session.setSessionLogFile(new File (this.sessionLogFileRule.replaceAll(this.sessionIDTag, session.getSessionID()).replaceAll(this.sessionDirTag, preparePath))); - session.setAppletFileName(this.appletFile); - this.getSessions().put(session.getSessionID(), session); - } - catch (IOException ioe) - { - throw new UnableToOpenSession(ioe); - } - ClientHandle app = new ClientHandle(this.clientName,this.clientVersion); - UserHandle user = new UserHandle(firstName,lastName); - IClient vorbaclient = this.getIClient(app, user, session); - session.addAttachedClient((VAMAVClient)vorbaclient); - //process the Vamsas Document to launch AstexViewer with suitable parameters - return (VAMAVClient) vorbaclient; - - } - - - - /** - * Create a new VAMAVCLient for a given clientHandle - * - * @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle) - */ - public IClient getIClient(ClientHandle applicationHandle) //throws NoDefaultSessionException - { - try - { - return new VAMAVClient(applicationHandle); - } - catch (InvalidSessionUrnException isue) - { - this.logger.appliError("Unable to get client ",isue); - this.logger.sessionError("Unable to get client ",isue); - // throw new NoDefaultSessionException(isue); - } - return null; - } - - /** - * - * Retrieves a client of a given session URN. - * If does not exist, create a new one. - * - * @param applicationHandle client handle object - * @param sessionUrn URN of the session to attach the client - * @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle, java.lang.String) - */ - //done 14 03 06 - public IClient getIClient(ClientHandle applicationHandle, String sessionUrn) - { - // applicationHandle also contains sessionURN - // applicationHandle.getClientUrn() - - /*VAMAVClient client = null; /* this.getClient(sessionUrn); - if (client == null) - { - client = new VAMAVClient(applicationHandle); - }*/ - VAMAVClient client = null; - try - { - VAMAVSession session = this.getSessions().get(sessionUrn); - client = new VAMAVClient(applicationHandle); - session.addAttachedClient(client); - client.setVAMAVSession(session); - } - catch (InvalidSessionUrnException isUExc) - { - this.logger.sessionError("The provided Session URN is incorrect.", isUExc); - this.logger.appliError("The provided Session URN is incorrect.", isUExc); - client = null; - } - return client; - } - - /** - * DONE 14/03/2006 - * @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle, org.vamsas.client.UserHandle, java.lang.String) - */ - public IClient getIClient(ClientHandle applicationHandle, UserHandle userId, - String sessionUrn) - { - /* VAMAVClient client = this.getClient(sessionUrn); - if (client == null) - { - client = new VAMAVClient(applicationHandle); - client.setUser(userId); - } - if (userId == null) - { - logger.appliError("There is non userID provided."); - } - else - { - /*this.addUser(sessionUrn,userId);*/ - /*}*/ - VAMAVClient client = null; - try - { - VAMAVSession session = this.getSessions().get(sessionUrn); - client = new VAMAVClient(userId, applicationHandle, session); - session.addAttachedClient(client); - client.setVAMAVSession(session); - } - catch (InvalidSessionUrnException isUExc) - { - this.logger.sessionError("The provided Session URN is incorrect.", isUExc); - this.logger.appliError("The provided Session URN is incorrect.", isUExc); - client = null; - } - return client; - } - - /** - * DONE - * @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle, org.vamsas.client.UserHandle) - */ - public VAMAVClient getIClient(ClientHandle applicationHandle, UserHandle userId, VAMAVSession session) - { - if (userId == null) - { - logger.appliInfo("There is non userID provided."); - } - else - { - /* String clientUrn = applicationHandle.getClientUrn(); - if (clientUrn != null && clientUrn.length()>0) - this.addUser(clientUrn, userId);*/ - } - if (session == null) - { - this.logger.appliError("No session provided. Can not create client if not associated to a session."); - return null; - } - - VAMAVClient client = null; - try - { - // String sessionID = new SessionHandle().generateSessionID(); - client = new VAMAVClient(userId, applicationHandle, session); - client.setUser(userId); - } - catch (InvalidSessionUrnException isUExc) - { - this.logger.sessionError("Unable to create session due to incorrect session.", isUExc); - this.logger.appliError("Unable to create session due to incorrect session.", isUExc); - - client = null; - } - // this.addClient(client.getSessionUrn(), client ); - // applicationHandle.setClientUrn(sessionID); - logger.appliInfo("generated sessionID "+client.getSessionUrn()); - return client; - } - - /** - * Remove a client - * - * Do nothing WHY? - * at a later stage? - * @param client the client to remove - */ - public void RemoveClient(VAMAVClient client) - { - if (client == null) - { - this.logger.appliError("SessionManager - Can not remove client. Client is null"); - return; - } - - } - - /** - * - * Finalize the current manager - */ - @Override - protected void finalize()throws Throwable - { - try - { - this.kill(); - } finally { - super.finalize(); - } - } - - /** - * Kill the current manager - * - */ - private void kill() - { - this.close(); - } - - -/** - * Closes the current manager. - * registers required data - * - */ -public void close() - { - if( this.sessionTrack != null && !this.sessionTrack.isEmpty()) - { - PropertyManager propManager = new PropertyManager(); - try - { - propManager.storeProperties(trackFileName, sessionTrack, "", trackDefaultDirectory); - } - catch (UnableToStorePropertiesException utspe) - { - logger.appliWarn("Unable to store session track"); - } - this.sessionTrack.clear(); - } - this.sessionTrack = null; - if (this.sessions!= null) - { - this.sessions.clear(); - this.sessions = null; - } - } - - /** - * Retrieves the sessions attribut - * - * @return Returns the sessions. - */ - private Hashtable getSessions() - { - if( this.sessions == null) - this.sessions = new Hashtable(); - return this.sessions; - } - - /** - * Creates a temp directory in a given directory. - * - * @param prefix prefix of the directory to create - * @param directory - * @throws IOException if an error occurs during file creation - * @return the temporary directory - */ - public File createTempDir(String prefix, File directory) throws IOException - { - if( prefix == null) - { - logger.sessionError("Error: no prefix provided to create temp file."); - throw new IOException(); - } - File tempFile = null; - if( directory == null ) - tempFile = File.createTempFile(prefix, ""); - else - tempFile = File.createTempFile(prefix, "", directory); - if (!tempFile.delete()) - throw new IOException(); - if (!tempFile.mkdir()) - throw new IOException(); - return tempFile; - } - - /** - * Creates a temp directory in the System temp directory. - * @param prefix prefix of the temp directory name - * @return the create file - * @throws IOException if an error during file creation - * - */ - public File createTempDir(String prefix) throws IOException - { - return this.createTempDir(prefix, null); - } - - /** - * Close the current session manager - * - */ - public void closeManager() - { - if (this.sessions != null) - { - for ( Enumeration ids = this.sessions.keys() ; ids.hasMoreElements();) - { - String sessionID = (String)ids.nextElement(); - if( sessionID == null || sessionID.length()<1)continue; - VAMAVSession session = this.sessions.remove(sessionID); - if (session != null) - { - session.close(); - session = null; - } - } - this.sessions.clear(); - this.sessions = null; - } - - } - /**Sets baseDirectory attribut - * - * @param _baseDirectory The baseDirectory to set. - */ - public static void setBaseDirectory(String _baseDirectory) - { - baseDirectory = _baseDirectory; - if( baseDirectory != null && baseDirectory.length()>0 && !baseDirectory.endsWith(File.separator)) - { - baseDirectory = baseDirectory.concat(File.separator); - } - } - - /** - * Retrieves the list of available sessions for the current session manager - */ - public ArrayList getAvailableSessions() - { - ArrayList sessionList = null; - for (Enumeration sessionIDs = sessions.keys();sessionIDs.hasMoreElements();) - { - String sessionID = sessionIDs.nextElement(); - if (sessionID == null || sessionID.length()<1) - { - continue; - } - if (sessionList == null) sessionList = new ArrayList(); - sessionList.add(sessionID); - } - return sessionList; - } - /* (non-Javadoc) - * @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle, org.vamsas.client.UserHandle) - */ - public IClient getIClient( - ClientHandle applicationHandle, - UserHandle userId) { - // TODO Auto-generated method stub - return null; - } - - /* (non-Javadoc) - * @see org.vamsas.client.IClientFactory#getCurrentSessions() - */ - public String[] getCurrentSessions() { - // TODO look in the arena and enumerate session handles for return. - return new String[] {}; - } - } diff --git a/src/uk/ac/ebi/msd/vamsas/vamav/session/VAMAVSession.java b/src/uk/ac/ebi/msd/vamsas/vamav/session/VAMAVSession.java deleted file mode 100755 index edd4c33..0000000 --- a/src/uk/ac/ebi/msd/vamsas/vamav/session/VAMAVSession.java +++ /dev/null @@ -1,462 +0,0 @@ -/* - * - * * EMBL - European Bioinformatics institute - * MSD Group - * VAMSAS Project - * - * Created on Feb 22, 2006 - * - * @author Pierre MARGUERITE - * @version 2 - * @since 22 Feb. 2006 - */ -package uk.ac.ebi.msd.vamsas.vamav.session; - -import java.io.File; -import java.io.IOException; -import java.util.ArrayList; - -import org.vamsas.client.simpleclient.SessionUrn; -import org.vamsas.client.simpleclient.VamsasSession; - -import uk.ac.ebi.msd.vamsas.vamav.VAMAVClient; -import uk.ac.ebi.msd.vamsas.vamav.util.logger.VAMAVLogger; -import uk.ac.ebi.msd.vamsas.vamav.util.logger.VAMAVLoggerImpl; - -/** - * This class represents a VAMSAS session, - * with a session ID, which can be opened and closed. - * @author Pierre MARGUERITE - * @since 22 Feb. 2006 - * @version 2 - * - */ -public class VAMAVSession extends VamsasSession { - - /** - * ID of the current session - */ - //private String sessionID = null; - - /** - * if the session is opened - */ - private boolean open = false; - - /** - * if the current session has been initialised. - */ - private boolean init = false; - - /** - * log file containing session messages - * TODO merge with VAMSAS session log ? - */ - private File sessionLogFile = null; - - /** - * Path to the HTML page used to call the AstexViewer@MSD- - * EBI as applet - */ - private String appletFileName = null; - - /** - * Path to the Vamsas document file - */ - private File vamsasDocumentFile = null; - - /** - * Logger to report messages - */ - private VAMAVLogger logger = new VAMAVLoggerImpl(this.getClass()); - - /** - * Structure grouping mode in use - */ - private int groupingMode = -1; - - /** - * List of attached VAMAV Client - * - */ - private ArrayList attachedClients = null; - - private SessionUrn sessionURN = null; - - /** - * Constructor specifying the session Directory - * - * @param sessionDir session directory containing all information relatives to the session - * @throws IOException if an error occurs during accessing to the session directory - */ - public VAMAVSession(File sessionDir) throws IOException - { - super(sessionDir); - sessionURN = new SessionUrn(this); - this.logger.applidebug("setting logger seession"); - this.logger.setSession(this); - } - - - /** - * Retrieves the sessionID attribut - * - * ID of the current session - * - * @return Returns the sessionID. - */ - public String getSessionID() - { - String id = null; - if (this.sessionURN != null) - { - String urn = this.sessionURN.asFile().getAbsolutePath(); - //this.logger.applidebug("session urn "+urn); - - if ("\\".equals(File.separator)) - { - //remove last separator at last position if found - if (urn.charAt(urn.length() - 1) == '/')urn = urn.substring(0, urn.length() - 1); - urn = urn.replaceAll("/", "\\\\"); - //this.logger.applidebug("session urn "+urn); - } - int index = urn.lastIndexOf(File.separator); - - if (index >-1) - {//separator found, keep last part of the urn - filename - id = urn.substring(index+1, urn.length()); - } - else - id = urn; - //this.logger.applidebug("session ID "+urn); - } - return id; - } - - - /** - * Sets sessionID attribut, ID of the current sesssion - * - * @param sessionID The sessionID to set. - */ - /* public void setSessionID(String sessionID) - { - //this.sessionID = sessionID; - this.logger.applidebug("setting logger seession"); - this.logger.setSession(this); - } -*/ - - /** - *specifies if the session - *has been closed. - * - * @param sessionID The sessionID to set. - */ - public void setClosedSession( boolean closedSession) - { - //this.sessionID = sessionID; - this.logger.applidebug("setting logger session"); - this.logger.setSession(this, closedSession); - } - - - /** - * Retrieves the open attribut - *Indicates if the session has been opened. - * - * @return Returns the open. - */ - public boolean isOpen() - { - return this.open; - } - - - /** - *Sets open attribut - * - * @param open The open to set. - */ - public void sessionOpen() - { - this.open = true; - this.init = true; - } - - /** - *Sets open attribut - * - * @return true if the session has been opened then closed. false, otherwise. - */ - public boolean isClosed() - { - return !this.open; - } - - /** - * finalize the object - */ - protected void finalize() throws Throwable - { - try - { - this.kill(); - } finally { - super.finalize(); - } - } - - /** - * kills the current session - * Stores required information - * - */ - private void kill() - { - if (this.attachedClients!= null) - { - for (int clientNumber = this.attachedClients.size() -1;clientNumber>=0; clientNumber-- ) - { - VAMAVClient client = this.attachedClients.get(clientNumber) ; - client = null; - } - this.attachedClients.clear(); - this.attachedClients = null; - } - /*if( this.sessionID != null) - { - this.sessionID = this.sessionID.replaceAll(this.sessionID, ""); - this.sessionID = null; - }*/ - } - - /** - * Retrieves the attachedClients attribut, list of client - * associated to the current session - * - * @return Returns the attachedClients. - */ - private ArrayList getAttachedClients() - { - return this.attachedClients; - } - - /** - * Retrieves an attachedClient at a given index - * - * - * @param index index of the client to retrieved - * @return the attached client at the given index, if found. null otherwise. - */ - public VAMAVClient getAttachedClient(int index ) - { - if (this.getAttachedClients() == null || index<0 || index>this.getAttachedClients().size()) - return null; - return this.getAttachedClients().get(index); - } - - /** - * Attached the client to a VAMAV Session - * - * @param client client to add the current session. - */ - public void addAttachedClient(VAMAVClient client) - { - if( this.getAttachedClients() == null) - { - this.attachedClients = new ArrayList(); - } - this.getAttachedClients().add(client); - client.setVAMAVSession(this); - } - - /** - * removes a client from the current session - * - * @param client client to remove - */ - public void removeClient(VAMAVClient client) - { - if( this.getAttachedClients() == null ) - { - logger.appliError("Unable to remove client. There is no client attached."); - } - this.getAttachedClients().remove(client); - if ( this.getAttachedClients().size()<1) - { - this.close(); - } - } - - /** - * Retrieves the sessionDirectory attribut - * - * retrieves the session directory containing files relatives to the session - * - * @return Returns the sessionDirectory. - */ - public File getSessionDirectory() - { - return this.sessionDir; - } - - - /** - *Sets sessionDirectory attribut - * - *Sets the path to the session directory - * - * @param sessionDirectory The sessionDirectory to set. - */ - public void setSessionDirectory(File sessionDirectory) - { - if( sessionDirectory!= null) - { - if(!sessionDirectory.exists()) - if( !sessionDirectory.mkdirs()) - { - logger.sessionError("Unable to create session directory."); - } - this.sessionDir = sessionDirectory; - if (!this.logger.isProduction()) this.logger.applidebug("session directory "+sessionDirectory.getAbsolutePath()); - - } - } - - /** - * Retrieves the sessionLogFile attribut - * - *Path the session log file containing reported messages relatives - *to the session - * - * @return Returns the sessionLogFile. - */ - public File getSessionLogFile() - { - return this.sessionLogFile; - } - - - /** - *Sets sessionLogFile attribut - * - *Sets the file containing all reported session messages - * - * @param sessionLogFile The sessionLogFile to set. - */ - public void setSessionLogFile(File sessionLogFile) - { - this.sessionLogFile = sessionLogFile; - if (sessionLogFile != null && !this.logger.isProduction()) - { - this.logger.applidebug(sessionLogFile.getAbsolutePath()); - } - - } - - /** - * Closes the current session - *Clears client list //TODO close attached clients - * - */ - public void close () - { - logger.sessionInfo("Closing session "+this.getSessionID() ); - this.open = false; - if (this.getAttachedClients() != null) - { - this.getAttachedClients().clear(); - this.attachedClients = null; - } - } - - - /** - * Retrieves the appletFileName attribut - *name of the file containing html page to call the AstexViewer@MSD-EBI - * - * @return Returns the appletFileName. - */ - public String getAppletFileName() - { - return this.appletFileName; - } - - /** - * Retrieves the appletFile object - * - * @return Returns the appletFile object - */ - public File getAppletFile() - { - return new File (this.getSessionDirectory().getAbsolutePath()+File.separator+this.appletFileName); - } - - - /** - *Sets appletFileName attribut - * - * @param appletFileName The appletFileName to set. - */ - public void setAppletFileName(String appletFileName) - { - this.appletFileName = appletFileName; - } - - - /** - * Retrieves the vamsasDocument File - * - * @return Returns the vamsasDocumentFile. - */ - public File getVamsasDocumentFile() - { - return this.vamsasDocumentFile; - } - - - /** - *Sets vamsasDocumentFile associated to /treated in the session - * - * @param vamsasDocumentFile The vamsasDocumentFile to set. - */ - public void setVamsasDocumentFile(File vamsasDocumentFile) - { - this.vamsasDocumentFile = vamsasDocumentFile; - } - - - /** - * Retrieves the groupingMode currently used in the - * session for process data - * - * @return Returns the groupingMode. - */ - public int getGroupingMode() - { - return this.groupingMode; - } - - - /** - *Sets groupingMode attribut - * - * @param groupingMode The groupingMode to set. - */ - public void setGroupingMode(int groupingMode) - { - this.groupingMode = groupingMode; - } - - - /** - * Retrieves the init attribut - * Indicates if the current session has been initialised - * @return Returns the init. - */ - public boolean isInit() - { - return this.init; - } -} diff --git a/src/uk/ac/ebi/msd/vamsas/vamav/session/exceptions/UnableToOpenSession.java b/src/uk/ac/ebi/msd/vamsas/vamav/session/exceptions/UnableToOpenSession.java deleted file mode 100755 index 5156c5f..0000000 --- a/src/uk/ac/ebi/msd/vamsas/vamav/session/exceptions/UnableToOpenSession.java +++ /dev/null @@ -1,50 +0,0 @@ -/* - * Created on Mar 9, 2006 - * - * To change the template for this generated file go to - * Window>Preferences>Java>Code Generation>Code and Comments - */ -package uk.ac.ebi.msd.vamsas.vamav.session.exceptions; - -/** - * @author pierre - * - * To change the template for this generated type comment go to - * Window>Preferences>Java>Code Generation>Code and Comments - */ -public class UnableToOpenSession extends Exception { - - /** - * - */ - public UnableToOpenSession() { - super(); - // TODO Auto-generated constructor stub - } - - /** - * @param message - */ - public UnableToOpenSession(String message) { - super(message); - // TODO Auto-generated constructor stub - } - - /** - * @param message - * @param cause - */ - public UnableToOpenSession(String message, Throwable cause) { - super(message, cause); - // TODO Auto-generated constructor stub - } - - /** - * @param cause - */ - public UnableToOpenSession(Throwable cause) { - super(cause); - // TODO Auto-generated constructor stub - } - -} -- 1.7.10.2