X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=156fc35c4c58fd19e12d6ded90acaf0824caf474;hb=fe72160257543fca39f7959fc1347665e95764a2;hp=175a249844c3d86b09460e7a6ed27bd5de581c0e;hpb=773945da6f64b05af53873bfd80c12189f141179;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 175a249..156fc35 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,48 +20,142 @@ */ package jalview.structure; +import java.io.PrintStream; +import java.util.ArrayList; +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 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 java.io.PrintStream; -import java.util.Enumeration; -import java.util.HashMap; -import java.util.IdentityHashMap; -import java.util.Vector; - -import MCview.Atom; -import MCview.PDBChain; - public class StructureSelectionManager { static IdentityHashMap instances; - StructureMapping[] mappings; + private List mappings = new ArrayList(); + + private boolean processSecondaryStructure = false; + + private boolean secStructServices = false; + + private boolean addTempFacAnnot = false; + + /* + * Set of any registered mappings between (dataset) sequences. + */ + Set seqmappings = new LinkedHashSet(); + + /* + * Reference counters for the above mappings. Remove mappings when ref count + * goes to zero. + */ + Map seqMappingRefCounts = new HashMap(); + + private List commandListeners = new ArrayList(); + + private List sel_listeners = new ArrayList(); + + /** + * @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); } } } @@ -182,16 +276,19 @@ public class StructureSelectionManager } } + /** + * 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; @@ -245,7 +342,7 @@ public class StructureSelectionManager * the tried and tested MCview pdb mapping */ MCview.PDBfile pdb = null; - boolean parseSecStr=true; + boolean parseSecStr = processSecondaryStructure; if (isPDBFileRegistered(pdbFile)) { for (SequenceI sq : sequence) @@ -274,7 +371,8 @@ public class StructureSelectionManager } try { - pdb = new MCview.PDBfile(true, parseSecStr, pdbFile, protocol); + pdb = new MCview.PDBfile(addTempFacAnnot, parseSecStr, + secStructServices, pdbFile, protocol); if (pdb.id != null && pdb.id.trim().length() > 0 && AppletFormatAdapter.FILE.equals(protocol)) { @@ -360,11 +458,13 @@ public class StructureSelectionManager + maxChain.residues.size() + "\n\n"); PrintStream ps = new PrintStream(System.out) { + @Override public void print(String x) { mappingDetails.append(x); } + @Override public void println() { mappingDetails.append("\n"); @@ -415,19 +515,7 @@ public class StructureSelectionManager mappingDetails.toString()); if (forStructureView) { - - if (mappings == null) - { - mappings = new StructureMapping[1]; - } - else - { - StructureMapping[] tmp = new StructureMapping[mappings.length + 1]; - System.arraycopy(mappings, 0, tmp, 0, mappings.length); - mappings = tmp; - } - - mappings[mappings.length - 1] = newMapping; + mappings.add(newMapping); } maxChain.transferResidueAnnotation(newMapping, sqmpping); } @@ -455,7 +543,6 @@ public class StructureSelectionManager { return; } - boolean removeMapping = true; String[] handlepdbs; Vector pdbs = new Vector(); for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++])) @@ -480,93 +567,99 @@ public class StructureSelectionManager } } - if (pdbs.size() > 0 && mappings != null) + if (pdbs.size() > 0) { - Vector tmp = new Vector(); - for (int i = 0; i < mappings.length; i++) + List tmp = new ArrayList(); + 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 atoms = Collections.singletonList(atomSpec); + mouseOverStructure(atoms); + } + + /** + * Propagate mouseover or selection of multiple positions in a structure + * + * @param atoms + */ + public void mouseOverStructure(List 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 @@ -576,93 +669,54 @@ public class StructureSelectionManager public void mouseOverSequence(SequenceI seq, int indexpos, int index, 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; 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, index); } 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, index, + 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); + } + 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) { @@ -674,6 +728,35 @@ public class StructureSelectionManager } /** + * 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) + { + int atomNo; + List atoms = new ArrayList(); + 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 */ @@ -759,119 +842,114 @@ public class StructureSelectionManager public StructureMapping[] getMapping(String pdbfile) { - Vector tmp = new Vector(); - if (mappings != null) - { - for (int i = 0; i < mappings.length; i++) + List tmp = new ArrayList(); + for (StructureMapping sm : mappings) { - if (mappings[i].pdbfile.equals(pdbfile)) + if (sm.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) { - StringBuffer sb = new StringBuffer(); - for (int i = 0; i < mappings.length; i++) + StringBuilder sb = new StringBuilder(64); + for (StructureMapping sm : mappings) { - if (mappings[i].pdbfile.equals(pdbfile)) + if (sm.pdbfile.equals(pdbfile)) { - sb.append(mappings[i].mappingDetails); + sb.append(sm.mappingDetails); } } return sb.toString(); } - private int[] seqmappingrefs = null; // refcount for seqmappings elements - - private synchronized void modifySeqMappingList(boolean add, - AlignedCodonFrame[] codonFrames) + /** + * Decrement the reference counter for each of the given mappings, and remove + * it entirely if its reference counter reduces to zero. + * + * @param set + */ + public void removeMappings(Set set) { - if (!add && (seqmappings == null || seqmappings.size() == 0)) + if (set != null) { - return; - } - if (seqmappings == null) - { - seqmappings = new Vector(); + for (AlignedCodonFrame acf : set) + { + removeMapping(acf); + } } - if (codonFrames != null && codonFrames.length > 0) + } + + /** + * Decrement the reference counter for the given mapping, and remove it + * entirely if its reference counter reduces to zero. + * + * @param acf + */ + public void removeMapping(AlignedCodonFrame acf) + { + if (acf != null && seqmappings.contains(acf)) { - for (int cf = 0; cf < codonFrames.length; cf++) + int count = seqMappingRefCounts.get(acf); + count--; + if (count > 0) { - 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; - } - } + seqMappingRefCounts.put(acf, count); + } + else + { + seqmappings.remove(acf); + seqMappingRefCounts.remove(acf); } } } - public void removeMappings(AlignedCodonFrame[] codonFrames) + /** + * Add each of the given codonFrames to the stored set. If not aready present, + * increments its reference count instead. + * + * @param set + */ + public void addMappings(Set set) { - modifySeqMappingList(false, codonFrames); + if (set != null) + { + for (AlignedCodonFrame acf : set) + { + addMapping(acf); + } + } } - public void addMappings(AlignedCodonFrame[] codonFrames) + /** + * Add the given mapping to the stored set, or if already stored, increment + * its reference counter. + */ + public void addMapping(AlignedCodonFrame acf) { - modifySeqMappingList(true, codonFrames); + if (acf != null) + { + if (seqmappings.contains(acf)) + { + seqMappingRefCounts.put(acf, seqMappingRefCounts.get(acf) + 1); + } + else + { + seqmappings.add(acf); + seqMappingRefCounts.put(acf, 1); + } + } } - Vector sel_listeners = new Vector(); - public void addSelectionListener(SelectionListener selecter) { if (!sel_listeners.contains(selecter)) { - sel_listeners.addElement(selecter); + sel_listeners.add(selecter); } } @@ -879,7 +957,7 @@ public class StructureSelectionManager { if (sel_listeners.contains(toremove)) { - sel_listeners.removeElement(toremove); + sel_listeners.remove(toremove); } } @@ -887,18 +965,11 @@ public class StructureSelectionManager 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); } } } @@ -926,32 +997,6 @@ public class StructureSelectionManager } } - public void finalize() throws Throwable - { - if (listeners != null) - { - listeners.clear(); - listeners = null; - } - if (pdbIdFileName != null) - { - pdbIdFileName.clear(); - pdbIdFileName = 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 * @@ -975,7 +1020,6 @@ public class StructureSelectionManager } catch (Throwable x) { } - ; } } } @@ -989,4 +1033,67 @@ public class StructureSelectionManager } } + 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; + } }