/*
- * 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 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * 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 jalview.analysis.AlignSeq;
+import jalview.api.StructureSelectionManagerProvider;
+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.io.AppletFormatAdapter;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
-import MCview.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
+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.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+
+import MCview.Atom;
+import MCview.PDBChain;
+import MCview.PDBfile;
public class StructureSelectionManager
{
- static StructureSelectionManager instance;
- StructureMapping[] mappings;
- Hashtable mappingData = new Hashtable();
+ public final static String NEWLINE = System.lineSeparator();
+
+ static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
+
+ private List<StructureMapping> mappings = new ArrayList<StructureMapping>();
+
+ private boolean processSecondaryStructure = false;
+
+ private boolean secStructServices = false;
+
+ private boolean addTempFacAnnot = false;
+
+ /*
+ * Set of any registered mappings between (dataset) sequences.
+ */
+ public Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
+
+ private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
+
+ private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
- public static StructureSelectionManager getStructureSelectionManager()
+ /**
+ * @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())
{
- instance = new StructureSelectionManager();
+ System.err.println("reportMapping: No PDB/Sequence mappings.");
}
+ else
+ {
+ System.err.println("reportMapping: There are " + mappings.size()
+ + " mappings.");
+ int i = 0;
+ for (StructureMapping sm : mappings)
+ {
+ System.err.println("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<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)
+ {
+ 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 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;
}
- /*
- 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 MCview.PDBfile setMapping(SequenceI[] sequence,
- String pdbFile,
- String protocol)
+ synchronized public PDBfile setMapping(SequenceI[] sequence,
+ String[] targetChains, String pdbFile, String protocol)
{
- MCview.PDBfile pdb = null;
- try
+ 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 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 PDBfile setMapping(boolean forStructureView,
+ SequenceI[] sequence, String[] targetChains, 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
+ */
+ boolean parseSecStr = processSecondaryStructure;
+ if (isPDBFileRegistered(pdbFile))
{
- pdb = new MCview.PDBfile(pdbFile, protocol);
+ for (SequenceI sq : sequence)
+ {
+ 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;
+ }
+ }
+ }
+ }
}
- catch (Exception ex)
+ PDBfile pdb = null;
+ try
+ {
+ pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
+ pdbFile, protocol);
+ if (pdb.id != null && pdb.id.trim().length() > 0
+ && AppletFormatAdapter.FILE.equals(protocol))
+ {
+ registerPDBFile(pdb.id.trim(), pdbFile);
+ }
+ } catch (Exception ex)
{
ex.printStackTrace();
return null;
}
+ String targetChain;
for (int s = 0; s < sequence.length; s++)
{
- String targetChain = "";
-
- if (sequence[s].getName().indexOf("|") > -1)
+ boolean infChain = true;
+ final SequenceI seq = sequence[s];
+ if (targetChains != null && targetChains[s] != null)
{
- targetChain = sequence[s].getName().substring(
- sequence[s].getName().lastIndexOf("|") + 1);
+ infChain = false;
+ targetChain = targetChains[s];
+ }
+ else if (seq.getName().indexOf("|") > -1)
+ {
+ targetChain = seq.getName().substring(
+ seq.getName().lastIndexOf("|") + 1);
+ if (targetChain.length() > 1)
+ {
+ if (targetChain.trim().length() == 0)
+ {
+ targetChain = " ";
+ }
+ else
+ {
+ // not a valid chain identifier
+ targetChain = "";
+ }
+ }
+ }
+ else
+ {
+ targetChain = "";
}
+ /*
+ * 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;
-
- for (int i = 0; i < pdb.chains.size(); i++)
+ boolean first = true;
+ for (PDBChain chain : pdb.chains)
{
- 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 (targetChain.length() > 0 && !targetChain.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(targetChain)))
{
+ first = false;
maxChain = chain;
max = as.maxscore;
maxAlignseq = as;
maxChainId = chain.id;
}
}
-
- 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");
+ if (maxChain == null)
+ {
+ continue;
+ }
+ final StringBuilder mappingDetails = new StringBuilder(128);
+ 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);
}
+ @Override
public void println()
{
- mappingDetails.append("\n");
+ mappingDetails.append(NEWLINE);
}
};
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));
+ mappingDetails.append(NEWLINE).append("PDB start/end ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq2start)).append(
+ " ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
- maxChain.makeExactMapping(maxAlignseq, sequence[s]);
+ mappingDetails.append(NEWLINE).append("SEQ start/end ");
+ mappingDetails.append(
+ String.valueOf(maxAlignseq.seq1start + seq.getStart() - 1))
+ .append(" ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq1end
+ + seq.getEnd() - 1));
- maxChain.transferRESNUMFeatures(sequence[s], null);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .getMappingFromS1(false);
+ jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping(
+ sqmpping.getMap().getInverse());
+ maxChain.transferRESNUMFeatures(seq, null);
- int[][] mapping = new int[sequence[s].getEnd() + 2][2];
+ // allocate enough slots to store the mapping from positions in
+ // sequence[s] to the associated chain
+ int[][] mapping = new int[seq.findPosition(seq.getLength()) + 2][2];
int resNum = -10000;
int index = 0;
-
do
{
- Atom tmp = (Atom) maxChain.atoms.elementAt(index);
+ Atom tmp = 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;
+ if (tmp.alignmentMapping >= -1)
+ {
+ // TODO (JAL-1836) address root cause: negative residue no in PDB
+ // file
+ mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
+ mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
+ }
}
index++;
- }
- while(index < maxChain.atoms.size());
+ } while (index < maxChain.atoms.size());
- if (mappings == null)
+ if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
{
- mappings = new StructureMapping[1];
+ pdbFile = "INLINE" + pdb.id;
}
- else
+ StructureMapping newMapping = new StructureMapping(seq, pdbFile,
+ pdb.id, maxChainId, mapping, mappingDetails.toString());
+ if (forStructureView)
{
- StructureMapping[] tmp = new StructureMapping[mappings.length + 1];
- System.arraycopy(mappings, 0, tmp, 0, mappings.length);
- mappings = tmp;
+ mappings.add(newMapping);
}
-
- if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
- pdbFile = "INLINE"+pdb.id;
-
- mappings[mappings.length - 1]
- = new StructureMapping(sequence[s], pdbFile, pdb.id, maxChainId,
- mapping, mappingDetails.toString());
- maxChain.transferResidueAnnotation(mappings[mappings.length-1]);
+ maxChain.transferResidueAnnotation(newMapping, sqmpping);
}
- /////////
+ // ///////
return pdb;
}
- 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);
+ }
+ }
+ }
- boolean removeMapping = true;
+ if (pdbfiles == null)
+ {
+ return;
+ }
+
+ /*
+ * 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);
- if (sl.getPdbFile().equals(pdbfile))
+ for (String pdbfile : sl.getPdbFile())
{
- 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<StructureMapping>();
+ 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;
}
}
+ /**
+ * Propagate mouseover of a single position in a structure
+ *
+ * @param pdbResNum
+ * @param chain
+ * @param pdbfile
+ */
public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
{
- SequenceListener sl;
+ 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 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;
+ }
- for (int j = 0; j < mappings.length; j++)
+ 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()))
{
- if (mappings[j].pdbfile.equals(pdbfile) &&
- mappings[j].pdbchain.equals(chain))
+ int indexpos = sm.getSeqPos(atom.getPdbResNum());
+ if (lastipos != indexpos && lastseq != sm.sequence)
{
- sl.highlightSequence(mappings[j].sequence,
- mappings[j].getSeqPos(pdbResNum));
+ results.addResult(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);
+ }
+ }
+ for (Object li : listeners)
+ {
+ if (li instanceof SequenceListener)
+ {
+ ((SequenceListener) li).highlightSequence(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 index
+ * the sequence position (if -1, seq.findPosition is called to
+ * resolve the residue number)
+ */
+ public void mouseOverSequence(SequenceI seq, int indexpos, int index,
+ VamsasSource source)
{
- StructureListener sl;
- int atomNo = 0;
+ boolean hasSequenceListeners = handlingVamsasMo
+ || !seqmappings.isEmpty();
+ SearchResults results = null;
+ if (index == -1)
+ {
+ index = 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);
-
- for (int j = 0; j < mappings.length; j++)
+ // TODO listener (e.g. SeqPanel) is never == source (AlignViewport)
+ // Temporary fudge with SequenceListener.getVamsasSource()
+ continue;
+ }
+ if (listener instanceof StructureListener)
+ {
+ highlightStructure((StructureListener) listener, seq, index);
+ }
+ else
+ {
+ if (listener instanceof SequenceListener)
{
- if (mappings[j].sequence == seq)
+ final SequenceListener seqListener = (SequenceListener) listener;
+ if (hasSequenceListeners
+ && seqListener.getVamsasSource() != source)
{
- atomNo = mappings[j].getAtomNum(index);
-
- if (atomNo > 0)
+ if (relaySeqMappings)
{
- sl.highlightAtom(atomNo,
- mappings[j].getPDBResNum(index),
- mappings[j].pdbchain,
- mappings[j].pdbfile);
+ if (results == null)
+ {
+ results = MappingUtils.buildSearchResults(seq, index,
+ seqmappings);
+ }
+ if (handlingVamsasMo)
+ {
+ results.addResult(seq, index, index);
+
+ }
+ 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, index);
+ }
}
}
}
- public Annotation[] colourSequenceFromStructure(SequenceI seq, String pdbid)
+ /**
+ * Send suitable messages to a StructureListener to highlight atoms
+ * corresponding to the given sequence position.
+ *
+ * @param sl
+ * @param seq
+ * @param index
+ */
+ protected void highlightStructure(StructureListener sl, SequenceI seq,
+ int index)
+ {
+ 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())
+ {
+ 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
+ */
+ 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)
+ {
+ handlingVamsasMo = true;
+ long msg = sequenceI.hashCode() * (1 + position);
+ if (lastmsg != msg)
+ {
+ 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())) {
+ * System.out.println(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()
{
- Annotation [] annotations = new Annotation[seq.getLength()];
+ }
+ public void sequenceSelectionChanged()
+ {
+ }
+
+ public void sequenceColoursChanged(Object source)
+ {
StructureListener sl;
- int atomNo = 0;
for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof StructureListener)
{
sl = (StructureListener) listeners.elementAt(i);
+ sl.updateColours(source);
+ }
+ }
+ }
- for (int j = 0; j < mappings.length; j++)
- {
+ public StructureMapping[] getMapping(String pdbfile)
+ {
+ List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+ for (StructureMapping sm : mappings)
+ {
+ if (sm.pdbfile.equals(pdbfile))
+ {
+ tmp.add(sm);
+ }
+ }
+ return tmp.toArray(new StructureMapping[tmp.size()]);
+ }
- if (mappings[j].sequence == seq
- && mappings[j].getPdbId().equals(pdbid)
- && mappings[j].pdbfile.equals(sl.getPdbFile()))
- {
- System.out.println(pdbid+" "+mappings[j].getPdbId()
- +" "+mappings[j].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)
+ {
+ if (pdbfile == null || seqs == null || seqs.isEmpty())
+ {
+ return "";
+ }
- java.awt.Color col;
- for(int index=0; index<seq.getLength(); index++)
- {
- if(jalview.util.Comparison.isGap(seq.getCharAt(index)))
- continue;
+ StringBuilder sb = new StringBuilder(64);
+ for (StructureMapping sm : mappings)
+ {
+ if (sm.pdbfile.equals(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);
- 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);
+ return sb.toString();
+ }
- // System.out.println(atomNo+" "+mappings[j].getPDBResNum(index)
- // +" "+index+" "+col);
- }
+ /**
+ * 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");
+ }
+ }
+ }
- annotations[index] = new Annotation("X",null,' ',0,col);
- }
- return annotations;
- }
- }
+ /**
+ * Add each of the given codonFrames to the stored set, if not aready present.
+ *
+ * @param set
+ */
+ public void registerMappings(Set<AlignedCodonFrame> set)
+ {
+ if (set != null)
+ {
+ for (AlignedCodonFrame acf : set)
+ {
+ registerMapping(acf);
}
}
+ }
- return annotations;
+ /**
+ * Add the given mapping to the stored set, unless already stored.
+ */
+ public void registerMapping(AlignedCodonFrame acf)
+ {
+ if (acf != null)
+ {
+ if (!seqmappings.contains(acf))
+ {
+ seqmappings.add(acf);
+ }
+ }
}
+ /**
+ * 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 structureSelectionChanged()
+ public void addSelectionListener(SelectionListener selecter)
{
- StructureListener svl;
- for (int i = 0; i < listeners.size(); i++)
+ if (!sel_listeners.contains(selecter))
{
- svl = (StructureListener) listeners.elementAt(i);
+ sel_listeners.add(selecter);
}
}
- public void sequenceSelectionChanged()
+ public void removeSelectionListener(SelectionListener toremove)
{
- StructureListener svl;
- for (int i = 0; i < listeners.size(); i++)
+ if (sel_listeners.contains(toremove))
{
- svl = (StructureListener) listeners.elementAt(i);
+ sel_listeners.remove(toremove);
}
}
- public void sequenceColoursChanged(Object source)
+ public synchronized void sendSelection(
+ jalview.datamodel.SequenceGroup selection,
+ jalview.datamodel.ColumnSelection colsel, SelectionSource source)
{
- StructureListener sl;
- for (int i = 0; i < listeners.size(); i++)
+ for (SelectionListener slis : sel_listeners)
{
- if (listeners.elementAt(i) instanceof StructureListener)
+ if (slis != source)
{
- sl = (StructureListener) listeners.elementAt(i);
- sl.updateColours(source);
+ slis.selection(selection, colsel, source);
}
}
}
- public StructureMapping[] getMapping(String pdbfile)
+ Vector<AlignmentViewPanelListener> view_listeners = new Vector<AlignmentViewPanelListener>();
+
+ public synchronized void sendViewPosition(
+ jalview.api.AlignmentViewPanel source, int startRes, int endRes,
+ int startSeq, int endSeq)
{
- Vector tmp = new Vector();
- for (int i = 0; i < mappings.length; i++)
+
+ if (view_listeners != null && view_listeners.size() > 0)
{
- if (mappings[i].pdbfile.equals(pdbfile))
+ Enumeration<AlignmentViewPanelListener> listeners = view_listeners
+ .elements();
+ while (listeners.hasMoreElements())
{
- tmp.addElement(mappings[i]);
+ AlignmentViewPanelListener slis = listeners.nextElement();
+ if (slis != source)
+ {
+ slis.viewPosition(startRes, endRes, startSeq, endSeq, source);
+ }
+ ;
}
}
+ }
- StructureMapping[] ret = new StructureMapping[tmp.size()];
- for (int i = 0; i < tmp.size(); i++)
+ /**
+ * release all references associated with this manager provider
+ *
+ * @param jalviewLite
+ */
+ public static void release(StructureSelectionManagerProvider jalviewLite)
+ {
+ // synchronized (instances)
{
- ret[i] = (StructureMapping) tmp.elementAt(i);
+ if (instances == null)
+ {
+ return;
+ }
+ StructureSelectionManager mnger = (instances.get(jalviewLite));
+ if (mnger != null)
+ {
+ instances.remove(jalviewLite);
+ try
+ {
+ mnger.finalize();
+ } catch (Throwable x)
+ {
+ }
+ }
}
+ }
- return ret;
+ public void registerPDBEntry(PDBEntry pdbentry)
+ {
+ if (pdbentry.getFile() != null
+ && pdbentry.getFile().trim().length() > 0)
+ {
+ registerPDBFile(pdbentry.getId(), pdbentry.getFile());
+ }
}
- public String printMapping(String pdbfile)
+ public void addCommandListener(CommandListener cl)
{
- StringBuffer sb = new StringBuffer();
- for (int i = 0; i < mappings.length; i++)
+ if (!commandListeners.contains(cl))
{
- if (mappings[i].pdbfile.equals(pdbfile))
- {
- sb.append(mappings[i].mappingDetails);
- }
+ commandListeners.add(cl);
}
+ }
- return sb.toString();
+ 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;
}
}
git://source.jalview.org / jalview.git / blobdiff