/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
-import java.io.*;
-import java.util.*;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.IdentityHashMap;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Vector;
-import MCview.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
+import jalview.analysis.AlignSeq;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.Console;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.OrderCommand;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ContiguousI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
+import jalview.gui.IProgressIndicator;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.structure.StructureImportSettings.TFType;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.sifts.SiftsClient;
+import jalview.ws.sifts.SiftsException;
+import jalview.ws.sifts.SiftsSettings;
+import mc_view.Atom;
+import mc_view.PDBChain;
+import mc_view.PDBfile;
public class StructureSelectionManager
{
- static StructureSelectionManager instance;
- StructureMapping[] mappings;
- Hashtable mappingData = new Hashtable();
+ public final static String NEWLINE = System.lineSeparator();
- public static StructureSelectionManager getStructureSelectionManager()
+ static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
+
+ private List<StructureMapping> mappings = new ArrayList<>();
+
+ private boolean processSecondaryStructure = false;
+
+ private boolean secStructServices = false;
+
+ private boolean addTempFacAnnot = false;
+
+ /*
+ * Set of any registered mappings between (dataset) sequences.
+ */
+ private List<AlignedCodonFrame> seqmappings = new ArrayList<>();
+
+ private List<CommandListener> commandListeners = new ArrayList<>();
+
+ private List<SelectionListener> sel_listeners = new ArrayList<>();
+
+ /**
+ * @return true if will try to use external services for processing secondary
+ * structure
+ */
+ public boolean isSecStructServices()
{
- if (instance == null)
+ return secStructServices;
+ }
+
+ /**
+ * control use of external services for processing secondary structure
+ *
+ * @param secStructServices
+ */
+ public void setSecStructServices(boolean secStructServices)
+ {
+ this.secStructServices = secStructServices;
+ }
+
+ /**
+ * flag controlling addition of any kind of structural annotation
+ *
+ * @return true if temperature factor annotation will be added
+ */
+ public boolean isAddTempFacAnnot()
+ {
+ return addTempFacAnnot;
+ }
+
+ /**
+ * set flag controlling addition of structural annotation
+ *
+ * @param addTempFacAnnot
+ */
+ public void setAddTempFacAnnot(boolean addTempFacAnnot)
+ {
+ this.addTempFacAnnot = addTempFacAnnot;
+ }
+
+ /**
+ *
+ * @return if true, the structure manager will attempt to add secondary
+ * structure lines for unannotated sequences
+ */
+
+ public boolean isProcessSecondaryStructure()
+ {
+ return processSecondaryStructure;
+ }
+
+ /**
+ * Control whether structure manager will try to annotate mapped sequences
+ * with secondary structure from PDB data.
+ *
+ * @param enable
+ */
+ public void setProcessSecondaryStructure(boolean enable)
+ {
+ processSecondaryStructure = enable;
+ }
+
+ /**
+ * debug function - write all mappings to stdout
+ */
+ public void reportMapping()
+ {
+ if (mappings.isEmpty())
+ {
+ jalview.bin.Console.errPrintln("reportMapping: No PDB/Sequence mappings.");
+ }
+ else
{
- instance = new StructureSelectionManager();
+ jalview.bin.Console.errPrintln(
+ "reportMapping: There are " + mappings.size() + " mappings.");
+ int i = 0;
+ for (StructureMapping sm : mappings)
+ {
+ jalview.bin.Console.errPrintln("mapping " + i++ + " : " + sm.pdbfile);
+ }
}
+ }
+
+ /**
+ * map between the PDB IDs (or structure identifiers) used by Jalview and the
+ * absolute filenames for PDB data that corresponds to it
+ */
+ Map<String, String> pdbIdFileName = new HashMap<>();
+
+ Map<String, String> pdbFileNameId = new HashMap<>();
+ public void registerPDBFile(String idForFile, String absoluteFile)
+ {
+ pdbIdFileName.put(idForFile, absoluteFile);
+ pdbFileNameId.put(absoluteFile, idForFile);
+ }
+
+ public String findIdForPDBFile(String idOrFile)
+ {
+ String id = pdbFileNameId.get(idOrFile);
+ return id;
+ }
+
+ public String findFileForPDBId(String idOrFile)
+ {
+ String id = pdbIdFileName.get(idOrFile);
+ return id;
+ }
+
+ public boolean isPDBFileRegistered(String idOrFile)
+ {
+ return pdbFileNameId.containsKey(idOrFile)
+ || pdbIdFileName.containsKey(idOrFile);
+ }
+
+ private static StructureSelectionManager nullProvider = null;
+
+ public static StructureSelectionManager getStructureSelectionManager(
+ StructureSelectionManagerProvider context)
+ {
+ if (context == null)
+ {
+ if (nullProvider == null)
+ {
+ if (instances != null)
+ {
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_structure_selection_manager_null"),
+ new NullPointerException(MessageManager
+ .getString("exception.ssm_context_is_null")));
+ }
+ else
+ {
+ nullProvider = new StructureSelectionManager();
+ }
+ return nullProvider;
+ }
+ }
+ if (instances == null)
+ {
+ instances = new java.util.IdentityHashMap<>();
+ }
+ StructureSelectionManager instance = instances.get(context);
+ if (instance == null)
+ {
+ if (nullProvider != null)
+ {
+ instance = nullProvider;
+ }
+ else
+ {
+ instance = new StructureSelectionManager();
+ }
+ instances.put(context, instance);
+ }
return instance;
}
+ /**
+ * flag controlling whether SeqMappings are relayed from received sequence
+ * mouse over events to other sequences
+ */
+ boolean relaySeqMappings = true;
+
+ /**
+ * Enable or disable relay of seqMapping events to other sequences. You might
+ * want to do this if there are many sequence mappings and the host computer
+ * is slow
+ *
+ * @param relay
+ */
+ public void setRelaySeqMappings(boolean relay)
+ {
+ relaySeqMappings = relay;
+ }
+
+ /**
+ * get the state of the relay seqMappings flag.
+ *
+ * @return true if sequence mouse overs are being relayed to other mapped
+ * sequences
+ */
+ public boolean isRelaySeqMappingsEnabled()
+ {
+ return relaySeqMappings;
+ }
+
Vector listeners = new Vector();
+
+ /**
+ * register a listener for alignment sequence mouseover events
+ *
+ * @param svl
+ */
public void addStructureViewerListener(Object svl)
{
if (!listeners.contains(svl))
}
}
+ /**
+ * Returns the filename the PDB id is already mapped to if known, or null if
+ * it is not mapped
+ *
+ * @param pdbid
+ * @return
+ */
public String alreadyMappedToFile(String pdbid)
{
- if (mappings != null)
+ for (StructureMapping sm : mappings)
{
- for (int i = 0; i < mappings.length; i++)
+ if (sm.getPdbId().equalsIgnoreCase(pdbid))
{
- if (mappings[i].getPdbId().equals(pdbid))
- {
- return mappings[i].pdbfile;
- }
+ return sm.pdbfile;
}
}
return null;
}
- /*
- There will be better ways of doing this in the future, for now we'll use
- the tried and tested MCview pdb mapping
+ /**
+ * Import structure data and register a structure mapping for broadcasting
+ * colouring, mouseovers and selection events (convenience wrapper).
+ *
+ * @param sequence
+ * - one or more sequences to be mapped to pdbFile
+ * @param targetChains
+ * - optional chain specification for mapping each sequence to pdb
+ * (may be nill, individual elements may be nill)
+ * @param pdbFile
+ * - structure data resource
+ * @param protocol
+ * - how to resolve data from resource
+ * @return null or the structure data parsed as a pdb file
+ */
+ synchronized public StructureFile setMapping(SequenceI[] sequence,
+ String[] targetChains, String pdbFile, DataSourceType protocol,
+ IProgressIndicator progress)
+ {
+ return computeMapping(true, sequence, targetChains, pdbFile, protocol,
+ progress, null, null, true);
+ }
+
+ /**
+ * Import a single structure file and register sequence structure mappings for
+ * broadcasting colouring, mouseovers and selection events (convenience
+ * wrapper).
+ *
+ * @param forStructureView
+ * when true, record the mapping for use in mouseOvers
+ * @param sequence
+ * - one or more sequences to be mapped to pdbFile
+ * @param targetChains
+ * - optional chain specification for mapping each sequence to pdb
+ * (may be nill, individual elements may be nill)
+ * @param pdbFile
+ * - structure data resource
+ * @param protocol
+ * - how to resolve data from resource
+ * @return null or the structure data parsed as a pdb file
*/
- public MCview.PDBfile setMapping(SequenceI[] sequence,
- String pdbFile,
- String protocol)
+ synchronized public StructureFile setMapping(boolean forStructureView,
+ SequenceI[] sequenceArray, String[] targetChainIds,
+ String pdbFile, DataSourceType sourceType, TFType tft,
+ String paeFilename)
{
- MCview.PDBfile pdb = null;
+ return setMapping(forStructureView, sequenceArray, targetChainIds,
+ pdbFile, sourceType, tft, paeFilename, true);
+ }
+
+
+ /**
+ * create sequence structure mappings between each sequence and the given
+ * pdbFile (retrieved via the given protocol). Either constructs a mapping
+ * using NW alignment or derives one from any available SIFTS mapping data.
+ *
+ * @param forStructureView
+ * when true, record the mapping for use in mouseOvers
+ *
+ * @param sequenceArray
+ * - one or more sequences to be mapped to pdbFile
+ * @param targetChainIds
+ * - optional chain specification for mapping each sequence to pdb
+ * (may be nill, individual elements may be nill) - JBPNote: JAL-2693
+ * - this should be List<List<String>>, empty lists indicate no
+ * predefined mappings
+ * @param pdbFile
+ * - structure data resource
+ * @param sourceType
+ * - how to resolve data from resource
+ * @param tft - specify how to interpret the temperature factor column in the atom data
+ * @param paeFilename - when not null, specifies a filename containing a matrix formatted in JSON using one of the known PAE formats
+ * @param doXferSettings - when true, transfer annotation to mapped sequences in sequenceArray
+ * @return null or the structure data parsed as a pdb file
+ */
+ synchronized public StructureFile setMapping(boolean forStructureView,
+ SequenceI[] sequenceArray, String[] targetChainIds,
+ String pdbFile, DataSourceType sourceType, TFType tft,
+ String paeFilename, boolean doXferSettings)
+ {
+ return computeMapping(forStructureView, sequenceArray, targetChainIds,
+ pdbFile, sourceType, null, tft, paeFilename, doXferSettings);
+ }
+
+ /**
+ * create sequence structure mappings between each sequence and the given
+ * pdbFile (retrieved via the given protocol). Either constructs a mapping
+ * using NW alignment or derives one from any available SIFTS mapping data.
+ *
+ * @param forStructureView
+ * when true, record the mapping for use in mouseOvers
+ *
+ * @param sequenceArray
+ * - one or more sequences to be mapped to pdbFile
+ * @param targetChainIds
+ * - optional chain specification for mapping each sequence to pdb
+ * (may be nill, individual elements may be nill) - JBPNote: JAL-2693
+ * - this should be List<List<String>>, empty lists indicate no
+ * predefined mappings
+ * @param pdbFile
+ * - structure data resource
+ * @param sourceType
+ * - how to resolve data from resource
+ * @param IProgressIndicator
+ * reference to UI component that maintains a progress bar for the
+ * mapping operation
+ * @param tft - specify how to interpret the temperature factor column in the atom data
+ * @param paeFilename - when not null, specifies a filename containing a matrix formatted in JSON using one of the known PAE formats
+ * @param doXferSettings - when true, transfer annotation to mapped sequences in sequenceArray
+ * @return null or the structure data parsed as a pdb file
+ */
+ synchronized public StructureFile computeMapping(boolean forStructureView,
+ SequenceI[] sequenceArray, String[] targetChainIds,
+ String pdbFile, DataSourceType sourceType,
+ IProgressIndicator progress, TFType tft, String paeFilename,
+ boolean doXferSettings)
+ {
+ long progressSessionId = System.currentTimeMillis() * 3;
+
+ /**
+ * do we extract and transfer annotation from 3D data ?
+ */
+ // FIXME: possibly should just delete
+
+ boolean parseSecStr = processSecondaryStructure
+ && !isStructureFileProcessed(pdbFile, sequenceArray);
+
+ StructureFile pdb = null;
+ boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
- pdb = new MCview.PDBfile(pdbFile, protocol);
- }
- catch (Exception ex)
+ // FIXME if sourceType is not null, we've lost data here
+ sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
+ pdb = new JmolParser(false, pdbFile, sourceType);
+ if (paeFilename != null)
+ {
+ pdb.setPAEMatrix(paeFilename);
+ }
+ pdb.setTemperatureFactorType(tft);
+ pdb.addSettings(parseSecStr && processSecondaryStructure,
+ parseSecStr && addTempFacAnnot,
+ parseSecStr && secStructServices);
+ // save doXferSettings and reset after doParse()
+ boolean temp = pdb.getDoXferSettings();
+ pdb.setDoXferSettings(doXferSettings);
+ pdb.doParse();
+ pdb.setDoXferSettings(temp);
+ if (pdb.getId() != null && pdb.getId().trim().length() > 0
+ && DataSourceType.FILE == sourceType)
+ {
+ registerPDBFile(pdb.getId().trim(), pdbFile);
+ }
+ // if PDBId is unavailable then skip SIFTS mapping execution path
+ // TODO: JAL-3868 need to know if structure is actually from
+ // PDB (has valid PDB ID and has provenance suggesting it
+ // actually came from PDB)
+ boolean isProtein = false;
+ for (SequenceI s : sequenceArray)
+ {
+ if (s.isProtein())
+ {
+ isProtein = true;
+ break;
+ }
+ }
+ isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable()
+ && !pdb.getId().startsWith("AF-") && isProtein;
+
+ } catch (Exception ex)
{
ex.printStackTrace();
return null;
}
+ /*
+ * sifts client - non null if SIFTS mappings are to be used
+ */
+ SiftsClient siftsClient = null;
+ try
+ {
+ if (isMapUsingSIFTs)
+ {
+ siftsClient = new SiftsClient(pdb);
+ }
+ } catch (SiftsException e)
+ {
+ isMapUsingSIFTs = false;
+ Console.error("SIFTS mapping failed", e);
+ Console.error("Falling back on Needleman & Wunsch alignment");
+ siftsClient = null;
+ }
- for (int s = 0; s < sequence.length; s++)
+ String targetChainId;
+ for (int s = 0; s < sequenceArray.length; s++)
{
- String targetChain = "";
+ boolean infChain = true;
+ final SequenceI seq = sequenceArray[s];
+ SequenceI ds = seq;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
- if (sequence[s].getName().indexOf("|") > -1)
+ if (targetChainIds != null && targetChainIds[s] != null)
+ {
+ infChain = false;
+ targetChainId = targetChainIds[s];
+ }
+ else if (seq.getName().indexOf("|") > -1)
{
- targetChain = sequence[s].getName().substring(
- sequence[s].getName().lastIndexOf("|") + 1);
+ targetChainId = seq.getName()
+ .substring(seq.getName().lastIndexOf("|") + 1);
+ if (targetChainId.length() > 1)
+ {
+ if (targetChainId.trim().length() == 0)
+ {
+ targetChainId = " ";
+ }
+ else
+ {
+ // not a valid chain identifier
+ targetChainId = "";
+ }
+ }
+ }
+ else
+ {
+ targetChainId = "";
}
- int max = -10;
+ /*
+ * Attempt pairwise alignment of the sequence with each chain in the PDB,
+ * and remember the highest scoring chain
+ */
+ float max = -10;
AlignSeq maxAlignseq = null;
String maxChainId = " ";
PDBChain maxChain = null;
-
- for (int i = 0; i < pdb.chains.size(); i++)
+ boolean first = true;
+ for (PDBChain chain : pdb.getChains())
{
- AlignSeq as = new AlignSeq(sequence[s],
- ( (PDBChain) pdb.chains.elementAt(i)).
- sequence,
- AlignSeq.PEP);
- as.calcScoreMatrix();
- as.traceAlignment();
- PDBChain chain = ( (PDBChain) pdb.chains.elementAt(i));
+ if (targetChainId.length() > 0 && !targetChainId.equals(chain.id)
+ && !infChain)
+ {
+ continue; // don't try to map chains don't match.
+ }
+ // TODO: correctly determine sequence type for mixed na/peptide
+ // structures
+ final String type = chain.isNa ? AlignSeq.DNA : AlignSeq.PEP;
+ AlignSeq as = AlignSeq.doGlobalNWAlignment(seq, chain.sequence,
+ type);
+ // equivalent to:
+ // AlignSeq as = new AlignSeq(sequence[s], chain.sequence, type);
+ // as.calcScoreMatrix();
+ // as.traceAlignment();
- if (as.maxscore > max
- || (as.maxscore == max && chain.id.equals(targetChain)))
+ if (first || as.maxscore > max
+ || (as.maxscore == max && chain.id.equals(targetChainId)))
{
+ first = false;
maxChain = chain;
max = as.maxscore;
maxAlignseq = as;
maxChainId = chain.id;
}
}
+ if (maxChain == null)
+ {
+ continue;
+ }
- final StringBuffer mappingDetails = new StringBuffer();
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = " +
- maxChain.sequence.getSequenceAsString());
- mappingDetails.append("\nNo of residues = " +
- maxChain.residues.
- size() +
- "\n\n");
- PrintStream ps = new PrintStream(System.out)
+ if (sourceType == DataSourceType.PASTE)
{
- public void print(String x)
+ pdbFile = "INLINE" + pdb.getId();
+ }
+
+ List<StructureMapping> seqToStrucMapping = new ArrayList<>();
+ if (isMapUsingSIFTs && seq.isProtein())
+ {
+ if (progress != null)
{
- mappingDetails.append(x);
+ progress.setProgressBar(
+ MessageManager
+ .getString("status.obtaining_mapping_with_sifts"),
+ progressSessionId);
}
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .getMappingFromS1(false);
+ if (targetChainId != null && !targetChainId.trim().isEmpty())
+ {
+ StructureMapping siftsMapping;
+ try
+ {
+ siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
+ pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
+ seqToStrucMapping.add(siftsMapping);
+ maxChain.makeExactMapping(siftsMapping, seq);
+ maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS",
+ pdb.getId().toLowerCase(Locale.ROOT));
+ maxChain.transferResidueAnnotation(siftsMapping, null);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
- public void println()
+ } catch (SiftsException e)
+ {
+ // fall back to NW alignment
+ Console.error(e.getMessage());
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ targetChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",
+ pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
+ // this
+ // "IEA:Jalview" ?
+ maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+ }
+ }
+ else
{
- mappingDetails.append("\n");
+ List<StructureMapping> foundSiftsMappings = new ArrayList<>();
+ for (PDBChain chain : pdb.getChains())
+ {
+ StructureMapping siftsMapping = null;
+ try
+ {
+ siftsMapping = getStructureMapping(seq, pdbFile, chain.id,
+ pdb, chain, sqmpping, maxAlignseq, siftsClient);
+ foundSiftsMappings.add(siftsMapping);
+ chain.makeExactMapping(siftsMapping, seq);
+ chain.transferRESNUMFeatures(seq, "IEA: SIFTS",
+ pdb.getId().toLowerCase(Locale.ROOT));// FIXME: is this
+ // "IEA:SIFTS" ?
+ chain.transferResidueAnnotation(siftsMapping, null);
+ } catch (SiftsException e)
+ {
+ jalview.bin.Console.errPrintln(e.getMessage());
+ } catch (Exception e)
+ {
+ jalview.bin.Console.errPrintln(
+ "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
+ jalview.bin.Console.errPrintln(e.getMessage());
+ }
+ }
+ if (!foundSiftsMappings.isEmpty())
+ {
+ seqToStrucMapping.addAll(foundSiftsMappings);
+ ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
+ }
+ else
+ {
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ maxChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
+ maxChain.transferRESNUMFeatures(seq, null,
+ pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is this
+ // "IEA:Jalview" ?
+ maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+ }
}
- };
-
- maxAlignseq.printAlignment(ps);
-
- mappingDetails.append("\nPDB start/end " + maxAlignseq.seq2start + " " +
- maxAlignseq.seq2end);
- mappingDetails.append("\nSEQ start/end "
- + (maxAlignseq.seq1start + sequence[s].getStart() - 1) +
- " "
- + (maxAlignseq.seq1end + sequence[s].getEnd() - 1));
-
- maxChain.makeExactMapping(maxAlignseq, sequence[s]);
-
- maxChain.transferRESNUMFeatures(sequence[s], null);
-
- int[][] mapping = new int[sequence[s].getEnd() + 2][2];
- int resNum = -10000;
- int index = 0;
-
+ }
+ else
+ {
+ if (progress != null)
+ {
+ progress.setProgressBar(
+ MessageManager.getString(
+ "status.obtaining_mapping_with_nw_alignment"),
+ progressSessionId);
+ }
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId,
+ maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+ }
+ if (forStructureView)
+ {
+ for (StructureMapping sm : seqToStrucMapping)
+ {
+ addStructureMapping(sm); // not addAll!
+ }
+ }
+ if (progress != null)
+ {
+ progress.setProgressBar(null, progressSessionId);
+ }
+ }
+ return pdb;
+ }
- do
+ /**
+ * check if we need to extract secondary structure from given pdbFile and
+ * transfer to sequences
+ *
+ * @param pdbFile
+ * @param sequenceArray
+ * @return
+ */
+ private boolean isStructureFileProcessed(String pdbFile,
+ SequenceI[] sequenceArray)
+ {
+ boolean processed = false;
+ if (isPDBFileRegistered(pdbFile))
+ {
+ for (SequenceI sq : sequenceArray)
{
- Atom tmp = (Atom) maxChain.atoms.elementAt(index);
- if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
+ SequenceI ds = sq;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ ;
+ if (ds.getAnnotation() != null)
{
- resNum = tmp.resNumber;
- mapping[tmp.alignmentMapping+1][0] = tmp.resNumber;
- mapping[tmp.alignmentMapping+1][1] = tmp.atomIndex;
+ for (AlignmentAnnotation ala : ds.getAnnotation())
+ {
+ // false if any annotation present from this structure
+ // JBPNote this fails for jmol/chimera view because the *file* is
+ // passed, not the structure data ID -
+ if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
+ {
+ processed = true;
+ }
+ }
}
+ }
+ }
+ return processed;
+ }
- index++;
+ public void addStructureMapping(StructureMapping sm)
+ {
+ if (!mappings.contains(sm))
+ {
+ mappings.add(sm);
+ }
+ }
+
+ /**
+ * retrieve a mapping for seq from SIFTs using associated DBRefEntry for
+ * uniprot or PDB
+ *
+ * @param seq
+ * @param pdbFile
+ * @param targetChainId
+ * @param pdb
+ * @param maxChain
+ * @param sqmpping
+ * @param maxAlignseq
+ * @param siftsClient
+ * client for retrieval of SIFTS mappings for this structure
+ * @return
+ * @throws SiftsException
+ */
+ private StructureMapping getStructureMapping(SequenceI seq,
+ String pdbFile, String targetChainId, StructureFile pdb,
+ PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
+ AlignSeq maxAlignseq, SiftsClient siftsClient)
+ throws SiftsException
+ {
+ StructureMapping curChainMapping = siftsClient
+ .getSiftsStructureMapping(seq, pdbFile, targetChainId);
+ try
+ {
+ PDBChain chain = pdb.findChain(targetChainId);
+ if (chain != null)
+ {
+ chain.transferResidueAnnotation(curChainMapping, null);
}
- while(index < maxChain.atoms.size());
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ return curChainMapping;
+ }
- if (mappings == null)
+ private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
+ String maxChainId, PDBChain maxChain, StructureFile pdb,
+ AlignSeq maxAlignseq)
+ {
+ final StringBuilder mappingDetails = new StringBuilder(128);
+ mappingDetails.append(NEWLINE)
+ .append("Sequence \u27f7 Structure mapping details");
+ mappingDetails.append(NEWLINE);
+ mappingDetails
+ .append("Method: inferred with Needleman & Wunsch alignment");
+ mappingDetails.append(NEWLINE).append("PDB Sequence is :")
+ .append(NEWLINE).append("Sequence = ")
+ .append(maxChain.sequence.getSequenceAsString());
+ mappingDetails.append(NEWLINE).append("No of residues = ")
+ .append(maxChain.residues.size()).append(NEWLINE)
+ .append(NEWLINE);
+ PrintStream ps = new PrintStream(System.out)
+ {
+ @Override
+ public void print(String x)
{
- mappings = new StructureMapping[1];
+ mappingDetails.append(x);
}
- else
+
+ @Override
+ public void println()
{
- StructureMapping[] tmp = new StructureMapping[mappings.length + 1];
- System.arraycopy(mappings, 0, tmp, 0, mappings.length);
- mappings = tmp;
+ mappingDetails.append(NEWLINE);
}
+ };
- if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
- pdbFile = "INLINE"+pdb.id;
+ maxAlignseq.printAlignment(ps);
- mappings[mappings.length - 1]
- = new StructureMapping(sequence[s], pdbFile, pdb.id, maxChainId,
- mapping, mappingDetails.toString());
- }
- /////////
+ mappingDetails.append(NEWLINE).append("PDB start/end ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq2start))
+ .append(" ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
+ mappingDetails.append(NEWLINE).append("SEQ start/end ");
+ mappingDetails
+ .append(String
+ .valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
+ .append(" ");
+ mappingDetails.append(
+ String.valueOf(maxAlignseq.seq1end + (seq.getStart() - 1)));
+ mappingDetails.append(NEWLINE);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .getMappingFromS1(false);
+ maxChain.transferRESNUMFeatures(seq, null,
+ pdb.getId().toLowerCase(Locale.ROOT));
- return pdb;
+ HashMap<Integer, int[]> mapping = new HashMap<>();
+ int resNum = -10000;
+ int index = 0;
+ char insCode = ' ';
+
+ do
+ {
+ Atom tmp = maxChain.atoms.elementAt(index);
+ if ((resNum != tmp.resNumber || insCode != tmp.insCode)
+ && tmp.alignmentMapping != -1)
+ {
+ resNum = tmp.resNumber;
+ insCode = tmp.insCode;
+ if (tmp.alignmentMapping >= -1)
+ {
+ mapping.put(tmp.alignmentMapping + 1,
+ new int[]
+ { tmp.resNumber, tmp.atomIndex });
+ }
+ }
+
+ index++;
+ } while (index < maxChain.atoms.size());
+
+ StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
+ pdb.getId(), maxChainId, mapping, mappingDetails.toString());
+ maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+ return nwMapping;
}
- public void removeStructureViewerListener(Object svl, String pdbfile)
+ public void removeStructureViewerListener(Object svl, String[] pdbfiles)
{
listeners.removeElement(svl);
+ if (svl instanceof SequenceListener)
+ {
+ for (int i = 0; i < listeners.size(); i++)
+ {
+ if (listeners.elementAt(i) instanceof StructureListener)
+ {
+ ((StructureListener) listeners.elementAt(i))
+ .releaseReferences(svl);
+ }
+ }
+ }
+
+ if (pdbfiles == null)
+ {
+ return;
+ }
- boolean removeMapping = true;
+ /*
+ * Remove mappings to the closed listener's PDB files, but first check if
+ * another listener is still interested
+ */
+ List<String> pdbs = new ArrayList<>(Arrays.asList(pdbfiles));
StructureListener sl;
for (int i = 0; i < listeners.size(); i++)
if (listeners.elementAt(i) instanceof StructureListener)
{
sl = (StructureListener) listeners.elementAt(i);
- if (sl.getPdbFile().equals(pdbfile))
+ for (String pdbfile : sl.getStructureFiles())
{
- removeMapping = false;
- break;
+ pdbs.remove(pdbfile);
}
}
}
- if (removeMapping && mappings!=null)
+ /*
+ * Rebuild the mappings set, retaining only those which are for 'other' PDB
+ * files
+ */
+ if (pdbs.size() > 0)
{
- Vector tmp = new Vector();
- for (int i = 0; i < mappings.length; i++)
+ List<StructureMapping> tmp = new ArrayList<>();
+ for (StructureMapping sm : mappings)
{
- if (!mappings[i].pdbfile.equals(pdbfile))
+ if (!pdbs.contains(sm.pdbfile))
{
- tmp.addElement(mappings[i]);
+ tmp.add(sm);
}
}
- mappings = new StructureMapping[tmp.size()];
- tmp.copyInto(mappings);
+ mappings = tmp;
}
}
- public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
+ /**
+ * hack to highlight a range of positions at once on any structure views
+ *
+ * @param sequenceRef
+ * @param is
+ * - series of int start-end ranges as positions on sequenceRef
+ * @param i
+ * @param object
+ */
+ public void highlightPositionsOn(SequenceI sequenceRef, int[][] is,
+ Object source)
{
- SequenceListener sl;
+ boolean hasSequenceListeners = handlingVamsasMo
+ || !seqmappings.isEmpty();
+ SearchResultsI results = null;
+ ArrayList<Integer> listOfPositions = new ArrayList<Integer>();
+ for (int[] s_e : is)
+ {
+ for (int p = s_e[0]; p <= s_e[1]; listOfPositions.add(p++))
+ ;
+ }
+ int seqpos[] = new int[listOfPositions.size()];
+ int i = 0;
+ for (Integer p : listOfPositions)
+ {
+ seqpos[i++] = p;
+ }
+
+ for (i = 0; i < listeners.size(); i++)
+ {
+ Object listener = listeners.elementAt(i);
+ if (listener == source)
+ {
+ // TODO listener (e.g. SeqPanel) is never == source (AlignViewport)
+ // Temporary fudge with SequenceListener.getVamsasSource()
+ continue;
+ }
+ if (listener instanceof StructureListener)
+ {
+ highlightStructure((StructureListener) listener, sequenceRef,
+ seqpos);
+ }
+
+ }
+ }
+
+ /**
+ * Propagate mouseover of a single position in a structure
+ *
+ * @param pdbResNum
+ * @param chain
+ * @param pdbfile
+ * @return
+ */
+ public String mouseOverStructure(int pdbResNum, String chain,
+ String pdbfile)
+ {
+ AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
+ List<AtomSpec> atoms = Collections.singletonList(atomSpec);
+ return mouseOverStructure(atoms);
+ }
+
+ /**
+ * Propagate mouseover or selection of multiple positions in a structure
+ *
+ * @param atoms
+ */
+ public String mouseOverStructure(List<AtomSpec> atoms)
+ {
+ if (listeners == null)
+ {
+ // old or prematurely sent event
+ return null;
+ }
+ boolean hasSequenceListener = false;
for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof SequenceListener)
{
- sl = (SequenceListener) listeners.elementAt(i);
+ hasSequenceListener = true;
+ }
+ }
+ if (!hasSequenceListener)
+ {
+ return null;
+ }
- for (int j = 0; j < mappings.length; j++)
+ SearchResultsI results = findAlignmentPositionsForStructurePositions(
+ atoms);
+ String result = null;
+ for (Object li : listeners)
+ {
+ if (li instanceof SequenceListener)
+ {
+ String s = ((SequenceListener) li).highlightSequence(results);
+ if (s != null)
{
- if (mappings[j].pdbfile.equals(pdbfile) &&
- mappings[j].pdbchain.equals(chain))
+ result = s;
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Constructs a SearchResults object holding regions (if any) in the Jalview
+ * alignment which have a mapping to the structure viewer positions in the
+ * supplied list
+ *
+ * @param atoms
+ * @return
+ */
+ public SearchResultsI findAlignmentPositionsForStructurePositions(
+ List<AtomSpec> atoms)
+ {
+ SearchResultsI results = new SearchResults();
+ for (AtomSpec atom : atoms)
+ {
+ SequenceI lastseq = null;
+ int lastipos = -1;
+ for (StructureMapping sm : mappings)
+ {
+ if (sm.pdbfile.equals(atom.getPdbFile())
+ && sm.pdbchain.equals(atom.getChain()))
+ {
+ int indexpos = sm.getSeqPos(atom.getPdbResNum());
+ if (lastipos != indexpos || lastseq != sm.sequence)
{
- sl.highlightSequence(mappings[j].sequence,
- mappings[j].getSeqPos(pdbResNum));
+ results.appendResult(sm.sequence, indexpos, indexpos);
+ lastipos = indexpos;
+ lastseq = sm.sequence;
+ // construct highlighted sequence list
+ for (AlignedCodonFrame acf : seqmappings)
+ {
+ acf.markMappedRegion(sm.sequence, indexpos, results);
+ }
}
}
-
- sl.highlightSequence(null, pdbResNum);
}
}
+ return results;
}
- public void mouseOverSequence(SequenceI seq, int index)
+ /**
+ * highlight regions associated with a position (indexpos) in seq
+ *
+ * @param seq
+ * the sequence that the mouse over occurred on
+ * @param indexpos
+ * the absolute position being mouseovered in seq (0 to seq.length())
+ * @param seqPos
+ * the sequence position (if -1, seq.findPosition is called to
+ * resolve the residue number)
+ */
+ public void mouseOverSequence(SequenceI seq, int indexpos, int seqPos,
+ VamsasSource source)
{
- StructureListener sl;
- int atomNo = 0;
+ boolean hasSequenceListeners = handlingVamsasMo
+ || !seqmappings.isEmpty();
+ SearchResultsI results = null;
+ if (seqPos == -1)
+ {
+ seqPos = seq.findPosition(indexpos);
+ }
for (int i = 0; i < listeners.size(); i++)
{
- if (listeners.elementAt(i) instanceof StructureListener)
+ Object listener = listeners.elementAt(i);
+ if (listener == source)
{
- sl = (StructureListener) listeners.elementAt(i);
+ // TODO listener (e.g. SeqPanel) is never == source (AlignViewport)
+ // Temporary fudge with SequenceListener.getVamsasSource()
+ continue;
+ }
+ if (listener instanceof StructureListener)
+ {
+ highlightStructure((StructureListener) listener, seq, seqPos);
+ }
+ else
+ {
+ if (listener instanceof SequenceListener)
+ {
+ final SequenceListener seqListener = (SequenceListener) listener;
+ if (hasSequenceListeners
+ && seqListener.getVamsasSource() != source)
+ {
+ if (relaySeqMappings)
+ {
+ if (results == null)
+ {
+ results = MappingUtils.buildSearchResults(seq, seqPos,
+ seqmappings);
+ }
+ if (handlingVamsasMo)
+ {
+ results.addResult(seq, seqPos, seqPos);
- for (int j = 0; j < mappings.length; j++)
+ }
+ if (!results.isEmpty())
+ {
+ seqListener.highlightSequence(results);
+ }
+ }
+ }
+ }
+ else if (listener instanceof VamsasListener && !handlingVamsasMo)
+ {
+ ((VamsasListener) listener).mouseOverSequence(seq, indexpos,
+ source);
+ }
+ else if (listener instanceof SecondaryStructureListener)
+ {
+ ((SecondaryStructureListener) listener).mouseOverSequence(seq,
+ indexpos, seqPos);
+ }
+ }
+ }
+ }
+
+ /**
+ * Send suitable messages to a StructureListener to highlight atoms
+ * corresponding to the given sequence position(s)
+ *
+ * @param sl
+ * @param seq
+ * @param positions
+ */
+ public void highlightStructure(StructureListener sl, SequenceI seq,
+ int... positions)
+ {
+ if (!sl.isListeningFor(seq))
+ {
+ return;
+ }
+ int atomNo;
+ List<AtomSpec> atoms = new ArrayList<>();
+ for (StructureMapping sm : mappings)
+ {
+ if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()
+ || (sm.sequence.getDatasetSequence() != null && sm.sequence
+ .getDatasetSequence() == seq.getDatasetSequence()))
+ {
+ for (int index : positions)
{
- if (mappings[j].sequence == seq)
+ atomNo = sm.getAtomNum(index);
+
+ if (atomNo > 0)
{
- atomNo = mappings[j].getAtomNum(index);
+ atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain,
+ sm.getPDBResNum(index), atomNo));
+ }
+ }
+ }
+ }
+ sl.highlightAtoms(atoms);
+ }
- if (atomNo > 0)
+ public void highlightStructureRegionsFor(StructureListener sl,
+ SequenceI[] seqs, int... columns)
+ {
+ List<SequenceI> to_highlight = new ArrayList<SequenceI>();
+ for (SequenceI seq : seqs)
+ {
+ if (sl.isListeningFor(seq))
+ {
+ to_highlight.add(seq);
+ }
+ }
+ if (to_highlight.size() == 0)
+ {
+ return;
+ }
+ List<AtomSpec> atoms = new ArrayList<>();
+ for (SequenceI seq : to_highlight)
+ {
+ int atomNo;
+ for (StructureMapping sm : mappings)
+ {
+ if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()
+ || (sm.sequence.getDatasetSequence() != null && sm.sequence
+ .getDatasetSequence() == seq.getDatasetSequence()))
+ {
+
+ for (int i = 0; i < columns.length; i += 2)
+ {
+ ContiguousI positions = seq.findPositions(columns[i] + 1,
+ columns[i + 1] + 1);
+ if (positions == null)
{
- sl.highlightAtom(atomNo,
- mappings[j].getPDBResNum(index),
- mappings[j].pdbchain,
- mappings[j].pdbfile);
+ continue;
+ }
+ for (int index = positions.getBegin(); index <= positions
+ .getEnd(); index++)
+ {
+
+ atomNo = sm.getAtomNum(index);
+
+ if (atomNo > 0)
+ {
+ atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain,
+ sm.getPDBResNum(index), atomNo));
+ }
}
}
}
}
+ if (atoms.size() > 0)
+ {
+ sl.highlightAtoms(atoms);
+ }
}
}
- public void structureSelectionChanged()
+ /**
+ * true if a mouse over event from an external (ie Vamsas) source is being
+ * handled
+ */
+ boolean handlingVamsasMo = false;
+
+ long lastmsg = 0;
+
+ /**
+ * as mouseOverSequence but only route event to SequenceListeners
+ *
+ * @param sequenceI
+ * @param position
+ * in an alignment sequence
+ */
+ public void mouseOverVamsasSequence(SequenceI sequenceI, int position,
+ VamsasSource source)
{
- StructureListener svl;
- for (int i = 0; i < listeners.size(); i++)
+ handlingVamsasMo = true;
+ long msg = sequenceI.hashCode() * (1 + position);
+ if (lastmsg != msg)
{
- svl = (StructureListener) listeners.elementAt(i);
+ lastmsg = msg;
+ mouseOverSequence(sequenceI, position, -1, source);
}
+ handlingVamsasMo = false;
+ }
+
+ public Annotation[] colourSequenceFromStructure(SequenceI seq,
+ String pdbid)
+ {
+ return null;
+ // THIS WILL NOT BE AVAILABLE IN JALVIEW 2.3,
+ // UNTIL THE COLOUR BY ANNOTATION IS REWORKED
+ /*
+ * Annotation [] annotations = new Annotation[seq.getLength()];
+ *
+ * StructureListener sl; int atomNo = 0; for (int i = 0; i <
+ * listeners.size(); i++) { if (listeners.elementAt(i) instanceof
+ * StructureListener) { sl = (StructureListener) listeners.elementAt(i);
+ *
+ * for (int j = 0; j < mappings.length; j++) {
+ *
+ * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid)
+ * && mappings[j].pdbfile.equals(sl.getPdbFile())) {
+ * jalview.bin.Console.outPrintln(pdbid+" "+mappings[j].getPdbId() +"
+ * "+mappings[j].pdbfile);
+ *
+ * java.awt.Color col; for(int index=0; index<seq.getLength(); index++) {
+ * if(jalview.util.Comparison.isGap(seq.getCharAt(index))) continue;
+ *
+ * atomNo = mappings[j].getAtomNum(seq.findPosition(index)); col =
+ * java.awt.Color.white; if (atomNo > 0) { col = sl.getColour(atomNo,
+ * mappings[j].getPDBResNum(index), mappings[j].pdbchain,
+ * mappings[j].pdbfile); }
+ *
+ * annotations[index] = new Annotation("X",null,' ',0,col); } return
+ * annotations; } } } }
+ *
+ * return annotations;
+ */
+ }
+
+ public void structureSelectionChanged()
+ {
}
public void sequenceSelectionChanged()
{
- StructureListener svl;
- for (int i = 0; i < listeners.size(); i++)
- {
- svl = (StructureListener) listeners.elementAt(i);
- }
}
public void sequenceColoursChanged(Object source)
public StructureMapping[] getMapping(String pdbfile)
{
- Vector tmp = new Vector();
- for (int i = 0; i < mappings.length; i++)
+ List<StructureMapping> tmp = new ArrayList<>();
+ for (StructureMapping sm : mappings)
+ {
+ if (sm.pdbfile.equals(pdbfile))
+ {
+ tmp.add(sm);
+ }
+ }
+ return tmp.toArray(new StructureMapping[tmp.size()]);
+ }
+
+ /**
+ * Returns a readable description of all mappings for the given pdbfile to any
+ * of the given sequences
+ *
+ * @param pdbfile
+ * @param seqs
+ * @return
+ */
+ public String printMappings(String pdbfile, List<SequenceI> seqs)
+ {
+ if (pdbfile == null || seqs == null || seqs.isEmpty())
+ {
+ return "";
+ }
+
+ StringBuilder sb = new StringBuilder(64);
+ for (StructureMapping sm : mappings)
+ {
+ if (Platform.pathEquals(sm.pdbfile, pdbfile)
+ && seqs.contains(sm.sequence))
+ {
+ sb.append(sm.mappingDetails);
+ sb.append(NEWLINE);
+ // separator makes it easier to read multiple mappings
+ sb.append("=====================");
+ sb.append(NEWLINE);
+ }
+ }
+ sb.append(NEWLINE);
+
+ return sb.toString();
+ }
+
+ /**
+ * Remove the given mapping
+ *
+ * @param acf
+ */
+ public void deregisterMapping(AlignedCodonFrame acf)
+ {
+ if (acf != null)
+ {
+ boolean removed = seqmappings.remove(acf);
+ if (removed && seqmappings.isEmpty())
+ { // debug
+ jalview.bin.Console.outPrintln("All mappings removed");
+ }
+ }
+ }
+
+ /**
+ * Add each of the given codonFrames to the stored set, if not aready present.
+ *
+ * @param mappings
+ */
+ public void registerMappings(List<AlignedCodonFrame> mappings)
+ {
+ if (mappings != null)
{
- if (mappings[i].pdbfile.equals(pdbfile))
+ for (AlignedCodonFrame acf : mappings)
{
- tmp.addElement(mappings[i]);
+ registerMapping(acf);
}
}
+ }
- StructureMapping[] ret = new StructureMapping[tmp.size()];
- for (int i = 0; i < tmp.size(); i++)
+ /**
+ * Add the given mapping to the stored set, unless already stored.
+ */
+ public void registerMapping(AlignedCodonFrame acf)
+ {
+ if (acf != null)
{
- ret[i] = (StructureMapping) tmp.elementAt(i);
+ if (!seqmappings.contains(acf))
+ {
+ seqmappings.add(acf);
+ }
}
+ }
- return ret;
+ /**
+ * Resets this object to its initial state by removing all registered
+ * listeners, codon mappings, PDB file mappings
+ */
+ public void resetAll()
+ {
+ if (mappings != null)
+ {
+ mappings.clear();
+ }
+ if (seqmappings != null)
+ {
+ seqmappings.clear();
+ }
+ if (sel_listeners != null)
+ {
+ sel_listeners.clear();
+ }
+ if (listeners != null)
+ {
+ listeners.clear();
+ }
+ if (commandListeners != null)
+ {
+ commandListeners.clear();
+ }
+ if (view_listeners != null)
+ {
+ view_listeners.clear();
+ }
+ if (pdbFileNameId != null)
+ {
+ pdbFileNameId.clear();
+ }
+ if (pdbIdFileName != null)
+ {
+ pdbIdFileName.clear();
+ }
+ }
+
+ public void addSelectionListener(SelectionListener selecter)
+ {
+ if (!sel_listeners.contains(selecter))
+ {
+ sel_listeners.add(selecter);
+ }
+ }
+
+ public void removeSelectionListener(SelectionListener toremove)
+ {
+ if (sel_listeners.contains(toremove))
+ {
+ sel_listeners.remove(toremove);
+ }
}
- public String printMapping(String pdbfile)
+ public synchronized void sendSelection(
+ jalview.datamodel.SequenceGroup selection,
+ jalview.datamodel.ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source)
{
- StringBuffer sb = new StringBuffer();
- for (int i = 0; i < mappings.length; i++)
+ for (SelectionListener slis : sel_listeners)
{
- if (mappings[i].pdbfile.equals(pdbfile))
+ if (slis != source)
{
- sb.append(mappings[i].mappingDetails);
+ slis.selection(selection, colsel, hidden, source);
}
}
+ }
- return sb.toString();
+ Vector<AlignmentViewPanelListener> view_listeners = new Vector<>();
+
+ public synchronized void sendViewPosition(
+ jalview.api.AlignmentViewPanel source, int startRes, int endRes,
+ int startSeq, int endSeq)
+ {
+
+ if (view_listeners != null && view_listeners.size() > 0)
+ {
+ Enumeration<AlignmentViewPanelListener> listeners = view_listeners
+ .elements();
+ while (listeners.hasMoreElements())
+ {
+ AlignmentViewPanelListener slis = listeners.nextElement();
+ if (slis != source)
+ {
+ slis.viewPosition(startRes, endRes, startSeq, endSeq, source);
+ }
+ ;
+ }
+ }
+ }
+
+ /**
+ * release all references associated with this manager provider
+ *
+ * @param jalviewLite
+ */
+ public static void release(StructureSelectionManagerProvider jalviewLite)
+ {
+ // synchronized (instances)
+ {
+ if (instances == null)
+ {
+ return;
+ }
+ StructureSelectionManager mnger = (instances.get(jalviewLite));
+ if (mnger != null)
+ {
+ instances.remove(jalviewLite);
+ try
+ {
+ /* bsoares 2019-03-20 finalize deprecated, no apparent external
+ * resources to close
+ */
+ // mnger.finalize();
+ } catch (Throwable x)
+ {
+ }
+ }
+ }
+ }
+
+ public void registerPDBEntry(PDBEntry pdbentry)
+ {
+ if (pdbentry.getFile() != null
+ && pdbentry.getFile().trim().length() > 0)
+ {
+ registerPDBFile(pdbentry.getId(), pdbentry.getFile());
+ }
+ }
+
+ public void addCommandListener(CommandListener cl)
+ {
+ if (!commandListeners.contains(cl))
+ {
+ commandListeners.add(cl);
+ }
+ }
+
+ public boolean hasCommandListener(CommandListener cl)
+ {
+ return this.commandListeners.contains(cl);
+ }
+
+ public boolean removeCommandListener(CommandListener l)
+ {
+ return commandListeners.remove(l);
+ }
+
+ /**
+ * Forward a command to any command listeners (except for the command's
+ * source).
+ *
+ * @param command
+ * the command to be broadcast (in its form after being performed)
+ * @param undo
+ * if true, the command was being 'undone'
+ * @param source
+ */
+ public void commandPerformed(CommandI command, boolean undo,
+ VamsasSource source)
+ {
+ for (CommandListener listener : commandListeners)
+ {
+ listener.mirrorCommand(command, undo, this, source);
+ }
}
+
+ /**
+ * Returns a new CommandI representing the given command as mapped to the
+ * given sequences. If no mapping could be made, or the command is not of a
+ * mappable kind, returns null.
+ *
+ * @param command
+ * @param undo
+ * @param mapTo
+ * @param gapChar
+ * @return
+ */
+ public CommandI mapCommand(CommandI command, boolean undo,
+ final AlignmentI mapTo, char gapChar)
+ {
+ if (command instanceof EditCommand)
+ {
+ return MappingUtils.mapEditCommand((EditCommand) command, undo, mapTo,
+ gapChar, seqmappings);
+ }
+ else if (command instanceof OrderCommand)
+ {
+ return MappingUtils.mapOrderCommand((OrderCommand) command, undo,
+ mapTo, seqmappings);
+ }
+ return null;
+ }
+
+ public List<AlignedCodonFrame> getSequenceMappings()
+ {
+ return seqmappings;
+ }
+
+ /**
+ * quick and dirty route to just highlight all structure positions for a range
+ * of columns
+ *
+ * @param sequencesArray
+ * @param is
+ * start-end columns on sequencesArray
+ * @param source
+ * origin parent AlignmentPanel
+ */
+ public void highlightPositionsOnMany(SequenceI[] sequencesArray, int[] is,
+ Object source)
+ {
+ for (int i = 0; i < listeners.size(); i++)
+ {
+ Object listener = listeners.elementAt(i);
+ if (listener == source)
+ {
+ // TODO listener (e.g. SeqPanel) is never == source (AlignViewport)
+ // Temporary fudge with SequenceListener.getVamsasSource()
+ continue;
+ }
+ if (listener instanceof StructureListener)
+ {
+ highlightStructureRegionsFor((StructureListener) listener,
+ sequencesArray, is);
+ }
+ }
+ }
+
+ public Map<String, String> getPdbFileNameIdMap()
+ {
+ return pdbFileNameId;
+ }
+
+ public Map<String, String> getPdbIdFileNameMap()
+ {
+ return pdbIdFileName;
+ }
+
}