/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
-import java.io.*;
-import java.util.*;
-
-import MCview.*;
-import jalview.analysis.*;
-import jalview.api.AlignmentViewPanel;
+import jalview.analysis.AlignSeq;
import jalview.api.StructureSelectionManagerProvider;
-import jalview.datamodel.*;
+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.PDBEntry;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
+import jalview.gui.IProgressIndicator;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.StructureFile;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+import jalview.ws.sifts.SiftsClient;
+import jalview.ws.sifts.SiftsException;
+import jalview.ws.sifts.SiftsSettings;
+
+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.Map;
+import java.util.Vector;
+
+import MCview.Atom;
+import MCview.PDBChain;
+import MCview.PDBfile;
public class StructureSelectionManager
{
+ public final static String NEWLINE = System.lineSeparator();
+
static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
- StructureMapping[] mappings;
+ private List<StructureMapping> mappings = new ArrayList<StructureMapping>();
+
+ private boolean processSecondaryStructure = false;
+
+ private boolean secStructServices = false;
+
+ private boolean addTempFacAnnot = false;
+
+ private IProgressIndicator progressIndicator;
+
+ private SiftsClient siftsClient = null;
+
+ private long progressSessionId;
+
+ /*
+ * Set of any registered mappings between (dataset) sequences.
+ */
+ private List<AlignedCodonFrame> seqmappings = new ArrayList<AlignedCodonFrame>();
+
+ private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
+
+ private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
+
+ /**
+ * @return true if will try to use external services for processing secondary
+ * structure
+ */
+ public boolean isSecStructServices()
+ {
+ 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 == null)
+ if (mappings.isEmpty())
{
System.err.println("reportMapping: No PDB/Sequence mappings.");
}
else
{
- System.err.println("reportMapping: There are " + mappings.length
+ System.err.println("reportMapping: There are " + mappings.size()
+ " mappings.");
- for (int m = 0; m < mappings.length; m++)
+ int i = 0;
+ for (StructureMapping sm : mappings)
{
- System.err.println("mapping " + m + " : " + mappings[m].pdbfile);
+ System.err.println("mapping " + i++ + " : " + sm.pdbfile);
}
}
}
- Hashtable mappingData = new Hashtable();
+ /**
+ * 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<String, String>();
+
+ Map<String, String> pdbFileNameId = new HashMap<String, String>();
+
+ 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<StructureSelectionManagerProvider, StructureSelectionManager>();
StructureSelectionManager instance = instances.get(context);
if (instance == null)
{
- instances.put(context, instance = new StructureSelectionManager());
+ if (nullProvider != null)
+ {
+ instance = nullProvider;
+ }
+ else
+ {
+ instance = new StructureSelectionManager();
+ }
+ instances.put(context, instance);
}
return instance;
}
}
}
+ /**
+ * Returns the file name for a mapped PDB id (or null if 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().equals(pdbid))
{
- if (mappings[i].getPdbId().equals(pdbid))
- {
- return mappings[i].pdbfile;
- }
+ return sm.pdbfile;
}
}
return null;
}
/**
- * create sequence structure mappings between each sequence and the given
- * pdbFile (retrieved via the given protocol).
+ * 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
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
- synchronized public MCview.PDBfile setMapping(SequenceI[] sequence,
+ synchronized public StructureFile setMapping(SequenceI[] sequence,
String[] targetChains, String pdbFile, String protocol)
{
+ return setMapping(true, sequence, targetChains, pdbFile, protocol);
+ }
+
+ /**
+ * create sequence structure mappings between each sequence and the given
+ * pdbFile (retrieved via the given protocol).
+ *
+ * @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)
+ * @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(boolean forStructureView,
+ SequenceI[] sequenceArray, String[] targetChainIds,
+ String pdbFile, String protocol)
+ {
/*
* There will be better ways of doing this in the future, for now we'll use
* the tried and tested MCview pdb mapping
*/
- MCview.PDBfile pdb = null;
+ boolean parseSecStr = processSecondaryStructure;
+ if (isPDBFileRegistered(pdbFile))
+ {
+ for (SequenceI sq : sequenceArray)
+ {
+ SequenceI ds = sq;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ ;
+ if (ds.getAnnotation() != null)
+ {
+ 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)))
+ {
+ parseSecStr = false;
+ }
+ }
+ }
+ }
+ }
+ StructureFile pdb = null;
+ boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
- pdb = new MCview.PDBfile(pdbFile, protocol);
+ pdb = new JmolParser(pdbFile, protocol);
+
+ if (pdb.getId() != null && pdb.getId().trim().length() > 0
+ && AppletFormatAdapter.FILE.equals(protocol))
+ {
+ registerPDBFile(pdb.getId().trim(), pdbFile);
+ }
+ // if PDBId is unavailable then skip SIFTS mapping execution path
+ isMapUsingSIFTs = pdb.isPPDBIdAvailable();
+
} catch (Exception ex)
{
ex.printStackTrace();
return null;
}
- String targetChain;
- for (int s = 0; s < sequence.length; s++)
+ try
+ {
+ if (isMapUsingSIFTs)
+ {
+ siftsClient = new SiftsClient(pdb);
+ }
+ } catch (SiftsException e)
+ {
+ isMapUsingSIFTs = false;
+ e.printStackTrace();
+ }
+
+ String targetChainId;
+ for (int s = 0; s < sequenceArray.length; s++)
{
boolean infChain = true;
- if (targetChains != null && targetChains[s] != null)
+ final SequenceI seq = sequenceArray[s];
+ SequenceI ds = seq;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+
+ if (targetChainIds != null && targetChainIds[s] != null)
{
infChain = false;
- targetChain = targetChains[s];
+ targetChainId = targetChainIds[s];
}
- else if (sequence[s].getName().indexOf("|") > -1)
+ else if (seq.getName().indexOf("|") > -1)
{
- targetChain = sequence[s].getName().substring(
- sequence[s].getName().lastIndexOf("|") + 1);
- if (targetChain.length() > 1)
+ targetChainId = seq.getName().substring(
+ seq.getName().lastIndexOf("|") + 1);
+ if (targetChainId.length() > 1)
{
- if (targetChain.trim().length() == 0)
+ if (targetChainId.trim().length() == 0)
{
- targetChain = " ";
+ targetChainId = " ";
}
else
{
// not a valid chain identifier
- targetChain = "";
+ targetChainId = "";
}
}
}
else
- targetChain = "";
+ {
+ targetChainId = "";
+ }
+ /*
+ * Attempt pairwise alignment of the sequence with each chain in the PDB,
+ * and remember the highest scoring chain
+ */
int max = -10;
AlignSeq maxAlignseq = null;
String maxChainId = " ";
PDBChain maxChain = null;
boolean first = true;
- for (int i = 0; i < pdb.chains.size(); i++)
+ for (PDBChain chain : pdb.getChains())
{
- PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
- if (targetChain.length() > 0 && !targetChain.equals(chain.id)
+ 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
- AlignSeq as = new AlignSeq(sequence[s],
- ((PDBChain) pdb.chains.elementAt(i)).sequence,
- ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
- : AlignSeq.PEP);
- as.calcScoreMatrix();
- as.traceAlignment();
+ 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 (first || as.maxscore > max
- || (as.maxscore == max && chain.id.equals(targetChain)))
+ || (as.maxscore == max && chain.id.equals(targetChainId)))
{
first = false;
maxChain = chain;
{
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 (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
{
- public void print(String x)
+ pdbFile = "INLINE" + pdb.getId();
+ }
+
+ ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+ if (isMapUsingSIFTs && seq.isProtein())
+ {
+ setProgressBar(null);
+ setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_sifts"));
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .getMappingFromS1(false);
+ if (targetChainId != null && !targetChainId.trim().isEmpty())
{
- mappingDetails.append(x);
+ StructureMapping siftsMapping;
+ try
+ {
+ siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
+ pdb, maxChain, sqmpping, maxAlignseq);
+ seqToStrucMapping.add(siftsMapping);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
+ // "IEA:SIFTS" ?
+ maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+
+ } catch (SiftsException e)
+ {
+ // fall back to NW alignment
+ System.err.println(e.getMessage());
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ targetChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+ // "IEA:Jalview" ?
+ maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+ }
}
-
- public void println()
+ else
{
- mappingDetails.append("\n");
+ ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+ for (PDBChain chain : pdb.getChains())
+ {
+ try
+ {
+ StructureMapping siftsMapping = getStructureMapping(seq,
+ pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
+ foundSiftsMappings.add(siftsMapping);
+ } catch (SiftsException e)
+ {
+ System.err.println(e.getMessage());
+ }
+ }
+ if (!foundSiftsMappings.isEmpty())
+ {
+ seqToStrucMapping.addAll(foundSiftsMappings);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
+ // "IEA:SIFTS" ?
+ maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
+ sqmpping);
+ ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
+ }
+ else
+ {
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ maxChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
+ maxChain.transferRESNUMFeatures(seq, null); // 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));
+ }
+ else
+ {
+ setProgressBar(null);
+ setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_nw_alignment"));
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ maxChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
- maxChain.makeExactMapping(maxAlignseq, sequence[s]);
+ }
- maxChain.transferRESNUMFeatures(sequence[s], null);
+ if (forStructureView)
+ {
+ mappings.addAll(seqToStrucMapping);
+ }
+ }
+ return pdb;
+ }
- // allocate enough slots to store the mapping from positions in
- // sequence[s] to the associated chain
- int[][] mapping = new int[sequence[s].findPosition(sequence[s]
- .getLength()) + 2][2];
- int resNum = -10000;
- int index = 0;
+ private boolean isCIFFile(String filename)
+ {
+ String fileExt = filename.substring(filename.lastIndexOf(".") + 1,
+ filename.length());
+ return "cif".equalsIgnoreCase(fileExt);
+ }
- do
+ /**
+ * 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
+ * @return
+ * @throws SiftsException
+ */
+ private StructureMapping getStructureMapping(SequenceI seq,
+ String pdbFile, String targetChainId, StructureFile pdb,
+ PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
+ AlignSeq maxAlignseq) throws SiftsException
+ {
+ StructureMapping curChainMapping = siftsClient
+ .getSiftsStructureMapping(seq, pdbFile, targetChainId);
+ try
+ {
+ PDBChain chain = pdb.findChain(targetChainId);
+ if (chain != null)
{
- Atom tmp = (Atom) maxChain.atoms.elementAt(index);
- if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
- {
- resNum = tmp.resNumber;
- mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
- mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
- }
+ chain.transferResidueAnnotation(curChainMapping, sqmpping);
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ return curChainMapping;
+ }
- index++;
- } while (index < maxChain.atoms.size());
+ 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)
+ {
+ mappingDetails.append(x);
+ }
- if (mappings == null)
+ @Override
+ public void println()
{
- mappings = new StructureMapping[1];
+ mappingDetails.append(NEWLINE);
}
- else
+ };
+
+ maxAlignseq.printAlignment(ps);
+
+ 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);
+
+ HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
+ 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)
{
- StructureMapping[] tmp = new StructureMapping[mappings.length + 1];
- System.arraycopy(mappings, 0, tmp, 0, mappings.length);
- mappings = tmp;
+ resNum = tmp.resNumber;
+ insCode = tmp.insCode;
+ if (tmp.alignmentMapping >= -1)
+ {
+ mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber,
+ tmp.atomIndex });
+ }
}
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
- pdbFile = "INLINE" + pdb.id;
+ index++;
+ } while (index < maxChain.atoms.size());
- mappings[mappings.length - 1] = new StructureMapping(sequence[s],
- pdbFile, pdb.id, maxChainId, mapping,
- mappingDetails.toString());
- maxChain.transferResidueAnnotation(mappings[mappings.length - 1]);
- }
- // ///////
-
- return pdb;
+ StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
+ pdb.getId(), maxChainId, mapping, mappingDetails.toString());
+ maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+ return nwMapping;
}
public void removeStructureViewerListener(Object svl, String[] pdbfiles)
{
return;
}
- boolean removeMapping = true;
- String[] handlepdbs;
- Vector pdbs = new Vector();
- for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++]))
- ;
+
+ /*
+ * Remove mappings to the closed listener's PDB files, but first check if
+ * another listener is still interested
+ */
+ List<String> pdbs = new ArrayList<String>(Arrays.asList(pdbfiles));
+
StructureListener sl;
for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof StructureListener)
{
sl = (StructureListener) listeners.elementAt(i);
- handlepdbs = sl.getPdbFile();
- for (int j = 0; j < handlepdbs.length; j++)
+ for (String pdbfile : sl.getPdbFile())
{
- if (pdbs.contains(handlepdbs[j]))
- {
- pdbs.removeElement(handlepdbs[j]);
- }
+ pdbs.remove(pdbfile);
}
-
}
}
- if (pdbs.size() > 0 && 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<StructureMapping>();
+ for (StructureMapping sm : mappings)
{
- if (!pdbs.contains(mappings[i].pdbfile))
+ if (!pdbs.contains(sm.pdbfile))
{
- tmp.addElement(mappings[i]);
+ tmp.add(sm);
}
}
- mappings = new StructureMapping[tmp.size()];
- tmp.copyInto(mappings);
+ mappings = tmp;
}
}
+ /**
+ * Propagate mouseover of a single position in a structure
+ *
+ * @param pdbResNum
+ * @param chain
+ * @param pdbfile
+ */
public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
{
+ AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
+ List<AtomSpec> atoms = Collections.singletonList(atomSpec);
+ mouseOverStructure(atoms);
+ }
+
+ /**
+ * Propagate mouseover or selection of multiple positions in a structure
+ *
+ * @param atoms
+ */
+ public void mouseOverStructure(List<AtomSpec> atoms)
+ {
if (listeners == null)
{
// old or prematurely sent event
return;
}
- boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
- SearchResults results = null;
- SequenceI lastseq = null;
- int lastipos = -1, indexpos;
+ boolean hasSequenceListener = false;
for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof SequenceListener)
{
- if (results == null)
- {
- results = new SearchResults();
- }
- if (mappings != null)
+ hasSequenceListener = true;
+ }
+ }
+ if (!hasSequenceListener)
+ {
+ return;
+ }
+
+ SearchResults 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()))
{
- for (int j = 0; j < mappings.length; j++)
+ int indexpos = sm.getSeqPos(atom.getPdbResNum());
+ if (lastipos != indexpos && lastseq != sm.sequence)
{
- if (mappings[j].pdbfile.equals(pdbfile)
- && mappings[j].pdbchain.equals(chain))
+ results.addResult(sm.sequence, indexpos, indexpos);
+ lastipos = indexpos;
+ lastseq = sm.sequence;
+ // construct highlighted sequence list
+ for (AlignedCodonFrame acf : seqmappings)
{
- indexpos = mappings[j].getSeqPos(pdbResNum);
- if (lastipos != indexpos && lastseq != mappings[j].sequence)
- {
- results.addResult(mappings[j].sequence, indexpos, indexpos);
- lastipos = indexpos;
- lastseq = mappings[j].sequence;
- // construct highlighted sequence list
- if (seqmappings != null)
- {
-
- Enumeration e = seqmappings.elements();
- while (e.hasMoreElements())
-
- {
- ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
- mappings[j].sequence, indexpos, results);
- }
- }
- }
-
+ acf.markMappedRegion(sm.sequence, indexpos, results);
}
}
}
}
}
- if (results != null)
+ for (Object li : listeners)
{
- for (int i = 0; i < listeners.size(); i++)
+ if (li instanceof SequenceListener)
{
- Object li = listeners.elementAt(i);
- if (li instanceof SequenceListener)
- ((SequenceListener) li).highlightSequence(results);
+ ((SequenceListener) li).highlightSequence(results);
}
}
}
- Vector seqmappings = null; // should be a simpler list of mapped seuqence
-
/**
* highlight regions associated with a position (indexpos) in seq
*
* @param seq
- * the sequeence that the mouse over occured on
+ * the sequence that the mouse over occurred on
* @param indexpos
* the absolute position being mouseovered in seq (0 to seq.length())
- * @param index
+ * @param seqPos
* the sequence position (if -1, seq.findPosition is called to
* resolve the residue number)
*/
- public void mouseOverSequence(SequenceI seq, int indexpos, int index,
+ public void mouseOverSequence(SequenceI seq, int indexpos, int seqPos,
VamsasSource source)
{
- boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
+ boolean hasSequenceListeners = handlingVamsasMo
+ || !seqmappings.isEmpty();
SearchResults results = null;
- if (index == -1)
- index = seq.findPosition(indexpos);
- StructureListener sl;
- int atomNo = 0;
+ if (seqPos == -1)
+ {
+ seqPos = seq.findPosition(indexpos);
+ }
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)
{
- sl = (StructureListener) listener;
- if (mappings == null)
- {
- continue;
- }
- for (int j = 0; j < mappings.length; j++)
- {
- if (mappings[j].sequence == seq
- || mappings[j].sequence == seq.getDatasetSequence())
- {
- atomNo = mappings[j].getAtomNum(index);
-
- if (atomNo > 0)
- {
- sl.highlightAtom(atomNo, mappings[j].getPDBResNum(index),
- mappings[j].pdbchain, mappings[j].pdbfile);
- }
- }
- }
+ highlightStructure((StructureListener) listener, seq, seqPos);
}
else
{
- if (relaySeqMappings && hasSequenceListeners
- && listener instanceof SequenceListener)
+ if (listener instanceof SequenceListener)
{
- // DEBUG
- // System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
- // index);
-
- if (results == null)
+ final SequenceListener seqListener = (SequenceListener) listener;
+ if (hasSequenceListeners
+ && seqListener.getVamsasSource() != source)
{
- results = new SearchResults();
- if (index >= seq.getStart() && index <= seq.getEnd())
+ if (relaySeqMappings)
{
- // construct highlighted sequence list
-
- if (seqmappings != null)
+ if (results == null)
{
- Enumeration e = seqmappings.elements();
- while (e.hasMoreElements())
-
- {
- ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
- seq, index, results);
- }
+ results = MappingUtils.buildSearchResults(seq, seqPos,
+ seqmappings);
}
- // hasSequenceListeners = results.getSize() > 0;
if (handlingVamsasMo)
{
- // maybe have to resolve seq to a dataset seqeunce...
- // add in additional direct sequence and/or dataset sequence
- // highlighting
- results.addResult(seq, index, index);
+ results.addResult(seq, seqPos, seqPos);
+
+ }
+ if (!results.isEmpty())
+ {
+ seqListener.highlightSequence(results);
}
}
}
- if (hasSequenceListeners)
- {
- ((SequenceListener) listener).highlightSequence(results);
- }
}
else if (listener instanceof VamsasListener && !handlingVamsasMo)
{
- // DEBUG
- // System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + "
- // " +
- // index);
- // pass the mouse over and absolute position onto the
- // VamsasListener(s)
- ((VamsasListener) listener).mouseOver(seq, indexpos, source);
+ ((VamsasListener) listener).mouseOverSequence(seq, indexpos,
+ source);
}
else if (listener instanceof SecondaryStructureListener)
{
((SecondaryStructureListener) listener).mouseOverSequence(seq,
- indexpos);
+ 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<AtomSpec>();
+ 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)
+ {
+ atomNo = sm.getAtomNum(index);
+
+ if (atomNo > 0)
+ {
+ atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
+ .getPDBResNum(index), atomNo));
+ }
+ }
+ }
+ }
+ sl.highlightAtoms(atoms);
+ }
+
+ /**
* true if a mouse over event from an external (ie Vamsas) source is being
* handled
*/
public StructureMapping[] getMapping(String pdbfile)
{
- Vector tmp = new Vector();
- if (mappings != null)
+ List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+ for (StructureMapping sm : mappings)
{
- for (int i = 0; i < mappings.length; i++)
+ if (sm.pdbfile.equals(pdbfile))
{
- if (mappings[i].pdbfile.equals(pdbfile))
- {
- tmp.addElement(mappings[i]);
- }
+ tmp.add(sm);
}
}
- StructureMapping[] ret = new StructureMapping[tmp.size()];
- for (int i = 0; i < tmp.size(); i++)
- {
- ret[i] = (StructureMapping) tmp.elementAt(i);
- }
-
- return ret;
+ return tmp.toArray(new StructureMapping[tmp.size()]);
}
- public String printMapping(String pdbfile)
+ /**
+ * 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)
{
- StringBuffer sb = new StringBuffer();
- for (int i = 0; i < mappings.length; i++)
+ if (pdbfile == null || seqs == null || seqs.isEmpty())
+ {
+ return "";
+ }
+
+ StringBuilder sb = new StringBuilder(64);
+ for (StructureMapping sm : mappings)
{
- if (mappings[i].pdbfile.equals(pdbfile))
+ if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence))
{
- sb.append(mappings[i].mappingDetails);
+ 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();
}
- private int[] seqmappingrefs = null; // refcount for seqmappings elements
+ /**
+ * Remove the given mapping
+ *
+ * @param acf
+ */
+ public void deregisterMapping(AlignedCodonFrame acf)
+ {
+ if (acf != null)
+ {
+ boolean removed = seqmappings.remove(acf);
+ if (removed && seqmappings.isEmpty())
+ { // debug
+ System.out.println("All mappings removed");
+ }
+ }
+ }
- private synchronized void modifySeqMappingList(boolean add,
- AlignedCodonFrame[] codonFrames)
+ /**
+ * Add each of the given codonFrames to the stored set, if not aready present.
+ *
+ * @param mappings
+ */
+ public void registerMappings(List<AlignedCodonFrame> mappings)
{
- if (!add && (seqmappings == null || seqmappings.size() == 0))
- return;
- if (seqmappings == null)
- seqmappings = new Vector();
- if (codonFrames != null && codonFrames.length > 0)
+ if (mappings != null)
{
- for (int cf = 0; cf < codonFrames.length; cf++)
+ for (AlignedCodonFrame acf : mappings)
{
- if (seqmappings.contains(codonFrames[cf]))
- {
- if (add)
- {
- seqmappingrefs[seqmappings.indexOf(codonFrames[cf])]++;
- }
- else
- {
- if (--seqmappingrefs[seqmappings.indexOf(codonFrames[cf])] <= 0)
- {
- int pos = seqmappings.indexOf(codonFrames[cf]);
- int[] nr = new int[seqmappingrefs.length - 1];
- if (pos > 0)
- {
- System.arraycopy(seqmappingrefs, 0, nr, 0, pos);
- }
- if (pos < seqmappingrefs.length - 1)
- {
- System.arraycopy(seqmappingrefs, pos + 1, nr, 0,
- seqmappingrefs.length - pos - 2);
- }
- }
- }
- }
- else
- {
- if (add)
- {
- seqmappings.addElement(codonFrames[cf]);
-
- int[] nsr = new int[(seqmappingrefs == null) ? 1
- : seqmappingrefs.length + 1];
- if (seqmappingrefs != null && seqmappingrefs.length > 0)
- System.arraycopy(seqmappingrefs, 0, nsr, 0,
- seqmappingrefs.length);
- nsr[(seqmappingrefs == null) ? 0 : seqmappingrefs.length] = 1;
- seqmappingrefs = nsr;
- }
- }
+ registerMapping(acf);
}
}
}
- public void removeMappings(AlignedCodonFrame[] codonFrames)
+ /**
+ * Add the given mapping to the stored set, unless already stored.
+ */
+ public void registerMapping(AlignedCodonFrame acf)
{
- modifySeqMappingList(false, codonFrames);
+ if (acf != null)
+ {
+ if (!seqmappings.contains(acf))
+ {
+ seqmappings.add(acf);
+ }
+ }
}
- public void addMappings(AlignedCodonFrame[] codonFrames)
+ /**
+ * Resets this object to its initial state by removing all registered
+ * listeners, codon mappings, PDB file mappings
+ */
+ public void resetAll()
{
- modifySeqMappingList(true, codonFrames);
+ 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();
+ }
}
- Vector<SelectionListener> sel_listeners = new Vector<SelectionListener>();
-
public void addSelectionListener(SelectionListener selecter)
{
if (!sel_listeners.contains(selecter))
{
- sel_listeners.addElement(selecter);
+ sel_listeners.add(selecter);
}
}
{
if (sel_listeners.contains(toremove))
{
- sel_listeners.removeElement(toremove);
+ sel_listeners.remove(toremove);
}
}
jalview.datamodel.SequenceGroup selection,
jalview.datamodel.ColumnSelection colsel, SelectionSource source)
{
- if (sel_listeners != null && sel_listeners.size() > 0)
+ for (SelectionListener slis : sel_listeners)
{
- Enumeration listeners = sel_listeners.elements();
- while (listeners.hasMoreElements())
+ if (slis != source)
{
- SelectionListener slis = ((SelectionListener) listeners
- .nextElement());
- if (slis != source)
- {
- slis.selection(selection, colsel, source);
- }
- ;
+ slis.selection(selection, colsel, source);
}
}
}
}
}
- public void finalize() throws Throwable
- {
- if (listeners != null)
- {
- listeners.clear();
- listeners = null;
- }
- if (mappingData != null)
- {
- mappingData.clear();
- mappingData = null;
- }
- if (sel_listeners != null)
- {
- sel_listeners.clear();
- sel_listeners = null;
- }
- if (view_listeners != null)
- {
- view_listeners.clear();
- view_listeners = null;
- }
- mappings = null;
- seqmappingrefs = null;
- }
-
/**
* release all references associated with this manager provider
*
} 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 IProgressIndicator getProgressIndicator()
+ {
+ return progressIndicator;
+ }
+
+ public void setProgressIndicator(IProgressIndicator progressIndicator)
+ {
+ this.progressIndicator = progressIndicator;
+ }
+
+ public long getProgressSessionId()
+ {
+ return progressSessionId;
+ }
+
+ public void setProgressSessionId(long progressSessionId)
+ {
+ this.progressSessionId = progressSessionId;
+ }
+
+ public void setProgressBar(String message)
+ {
+ if (progressIndicator == null)
+ {
+ return;
+ }
+ progressIndicator.setProgressBar(message, progressSessionId);
+ }
+
+ public List<AlignedCodonFrame> getSequenceMappings()
+ {
+ return seqmappings;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff