2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.structures.models;
23 import jalview.api.AlignmentViewPanel;
24 import jalview.api.SequenceRenderer;
25 import jalview.api.StructureSelectionManagerProvider;
26 import jalview.api.structures.JalviewStructureDisplayI;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.HiddenColumns;
29 import jalview.datamodel.PDBEntry;
30 import jalview.datamodel.SequenceI;
31 import jalview.io.DataSourceType;
32 import jalview.schemes.ColourSchemeI;
33 import jalview.structure.AtomSpec;
34 import jalview.structure.StructureListener;
35 import jalview.structure.StructureMapping;
36 import jalview.structure.StructureMappingcommandSet;
37 import jalview.structure.StructureSelectionManager;
38 import jalview.util.Comparison;
39 import jalview.util.MessageManager;
41 import java.awt.Color;
42 import java.util.ArrayList;
43 import java.util.Arrays;
44 import java.util.BitSet;
45 import java.util.List;
49 * A base class to hold common function for protein structure model binding.
50 * Initial version created by refactoring JMol and Chimera binding models, but
51 * other structure viewers could in principle be accommodated in future.
56 public abstract class AAStructureBindingModel
57 extends SequenceStructureBindingModel
58 implements StructureListener, StructureSelectionManagerProvider
61 private StructureSelectionManager ssm;
64 * distinct PDB entries (pdb files) associated
67 private PDBEntry[] pdbEntry;
70 * sequences mapped to each pdbentry
72 private SequenceI[][] sequence;
75 * array of target chains for sequences - tied to pdbentry and sequence[]
77 private String[][] chains;
80 * datasource protocol for access to PDBEntrylatest
82 DataSourceType protocol = null;
84 protected boolean colourBySequence = true;
86 private boolean nucleotide;
88 private boolean finishedInit = false;
91 * current set of model filenames loaded in the Jmol instance
93 protected String[] modelFileNames = null;
95 public String fileLoadingError;
98 * Data bean class to simplify parameterisation in superposeStructures
100 protected class SuperposeData
103 * Constructor with alignment width argument
107 public SuperposeData(int width)
109 pdbResNo = new int[width];
112 public String filename;
116 public String chain = "";
118 public boolean isRna;
121 * The pdb residue number (if any) mapped to each column of the alignment
123 public int[] pdbResNo;
132 public AAStructureBindingModel(StructureSelectionManager ssm,
136 this.sequence = seqs;
147 public AAStructureBindingModel(StructureSelectionManager ssm,
148 PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
149 DataSourceType protocol)
152 this.sequence = sequenceIs;
153 this.nucleotide = Comparison.isNucleotide(sequenceIs);
154 this.pdbEntry = pdbentry;
155 this.protocol = protocol;
159 private boolean resolveChains()
162 * final count of chain mappings discovered
165 // JBPNote: JAL-2693 - this should be a list of chain mappings per
166 // [pdbentry][sequence]
167 String[][] newchains = new String[pdbEntry.length][];
169 for (PDBEntry pdb : pdbEntry)
171 SequenceI[] seqsForPdb = sequence[pe];
172 if (seqsForPdb != null)
174 newchains[pe] = new String[seqsForPdb.length];
176 for (SequenceI asq : seqsForPdb)
178 String chain = (chains != null && chains[pe] != null)
181 SequenceI sq = (asq.getDatasetSequence() == null) ? asq
182 : asq.getDatasetSequence();
183 if (sq.getAllPDBEntries() != null)
185 for (PDBEntry pdbentry : sq.getAllPDBEntries())
187 if (pdb.getFile() != null && pdbentry.getFile() != null
188 && pdb.getFile().equals(pdbentry.getFile()))
190 String chaincode = pdbentry.getChainCode();
191 if (chaincode != null && chaincode.length() > 0)
200 newchains[pe][se] = chain;
208 return chainmaps > 0;
210 public StructureSelectionManager getSsm()
216 * Returns the i'th PDBEntry (or null)
221 public PDBEntry getPdbEntry(int i)
223 return (pdbEntry != null && pdbEntry.length > i) ? pdbEntry[i] : null;
227 * Answers true if this binding includes the given PDB id, else false
232 public boolean hasPdbId(String pdbId)
234 if (pdbEntry != null)
236 for (PDBEntry pdb : pdbEntry)
238 if (pdb.getId().equals(pdbId))
248 * Returns the number of modelled PDB file entries.
252 public int getPdbCount()
254 return pdbEntry == null ? 0 : pdbEntry.length;
257 public SequenceI[][] getSequence()
262 public String[][] getChains()
267 public DataSourceType getProtocol()
272 // TODO may remove this if calling methods can be pulled up here
273 protected void setPdbentry(PDBEntry[] pdbentry)
275 this.pdbEntry = pdbentry;
278 protected void setSequence(SequenceI[][] sequence)
280 this.sequence = sequence;
283 protected void setChains(String[][] chains)
285 this.chains = chains;
289 * Construct a title string for the viewer window based on the data Jalview
298 public String getViewerTitle(String viewerName, boolean verbose)
300 if (getSequence() == null || getSequence().length < 1
301 || getPdbCount() < 1 || getSequence()[0].length < 1)
303 return ("Jalview " + viewerName + " Window");
305 // TODO: give a more informative title when multiple structures are
307 StringBuilder title = new StringBuilder(64);
308 final PDBEntry pdbe = getPdbEntry(0);
309 title.append(viewerName + " view for " + getSequence()[0][0].getName()
310 + ":" + pdbe.getId());
314 String method = (String) pdbe.getProperty("method");
317 title.append(" Method: ").append(method);
319 String chain = (String) pdbe.getProperty("chains");
322 title.append(" Chain:").append(chain);
325 return title.toString();
329 * Called by after closeViewer is called, to release any resources and
330 * references so they can be garbage collected. Override if needed.
332 protected void releaseUIResources()
337 public boolean isColourBySequence()
339 return colourBySequence;
342 public void setColourBySequence(boolean colourBySequence)
344 this.colourBySequence = colourBySequence;
347 protected void addSequenceAndChain(int pe, SequenceI[] seq,
350 if (pe < 0 || pe >= getPdbCount())
352 throw new Error(MessageManager.formatMessage(
353 "error.implementation_error_no_pdbentry_from_index",
355 { Integer.valueOf(pe).toString() }));
357 final String nullChain = "TheNullChain";
358 List<SequenceI> s = new ArrayList<>();
359 List<String> c = new ArrayList<>();
360 if (getChains() == null)
362 setChains(new String[getPdbCount()][]);
364 if (getSequence()[pe] != null)
366 for (int i = 0; i < getSequence()[pe].length; i++)
368 s.add(getSequence()[pe][i]);
369 if (getChains()[pe] != null)
371 if (i < getChains()[pe].length)
373 c.add(getChains()[pe][i]);
382 if (tchain != null && tchain.length > 0)
389 for (int i = 0; i < seq.length; i++)
391 if (!s.contains(seq[i]))
394 if (tchain != null && i < tchain.length)
396 c.add(tchain[i] == null ? nullChain : tchain[i]);
400 SequenceI[] tmp = s.toArray(new SequenceI[s.size()]);
401 getSequence()[pe] = tmp;
404 String[] tch = c.toArray(new String[c.size()]);
405 for (int i = 0; i < tch.length; i++)
407 if (tch[i] == nullChain)
412 getChains()[pe] = tch;
416 getChains()[pe] = null;
421 * add structures and any known sequence associations
423 * @returns the pdb entries added to the current set.
425 public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
426 SequenceI[][] seq, String[][] chns)
428 List<PDBEntry> v = new ArrayList<>();
429 List<int[]> rtn = new ArrayList<>();
430 for (int i = 0; i < getPdbCount(); i++)
432 v.add(getPdbEntry(i));
434 for (int i = 0; i < pdbe.length; i++)
436 int r = v.indexOf(pdbe[i]);
437 if (r == -1 || r >= getPdbCount())
439 rtn.add(new int[] { v.size(), i });
444 // just make sure the sequence/chain entries are all up to date
445 addSequenceAndChain(r, seq[i], chns[i]);
448 pdbe = v.toArray(new PDBEntry[v.size()]);
452 // expand the tied sequence[] and string[] arrays
453 SequenceI[][] sqs = new SequenceI[getPdbCount()][];
454 String[][] sch = new String[getPdbCount()][];
455 System.arraycopy(getSequence(), 0, sqs, 0, getSequence().length);
456 System.arraycopy(getChains(), 0, sch, 0, this.getChains().length);
459 pdbe = new PDBEntry[rtn.size()];
460 for (int r = 0; r < pdbe.length; r++)
462 int[] stri = (rtn.get(r));
463 // record the pdb file as a new addition
464 pdbe[r] = getPdbEntry(stri[0]);
465 // and add the new sequence/chain entries
466 addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
477 * Add sequences to the pe'th pdbentry's sequence set.
482 public void addSequence(int pe, SequenceI[] seq)
484 addSequenceAndChain(pe, seq, null);
488 * add the given sequences to the mapping scope for the given pdb file handle
491 * - pdbFile identifier
493 * - set of sequences it can be mapped to
495 public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
497 for (int pe = 0; pe < getPdbCount(); pe++)
499 if (getPdbEntry(pe).getFile().equals(pdbFile))
501 addSequence(pe, seq);
507 public abstract void highlightAtoms(List<AtomSpec> atoms);
509 protected boolean isNucleotide()
511 return this.nucleotide;
515 * Returns a readable description of all mappings for the wrapped pdbfile to
516 * any mapped sequences
520 public String printMappings()
522 if (pdbEntry == null)
526 StringBuilder sb = new StringBuilder(128);
527 for (int pdbe = 0; pdbe < getPdbCount(); pdbe++)
529 String pdbfile = getPdbEntry(pdbe).getFile();
530 List<SequenceI> seqs = Arrays.asList(getSequence()[pdbe]);
531 sb.append(getSsm().printMappings(pdbfile, seqs));
533 return sb.toString();
537 * Returns the mapped structure position for a given aligned column of a given
538 * sequence, or -1 if the column is gapped, beyond the end of the sequence, or
539 * not mapped to structure.
546 protected int getMappedPosition(SequenceI seq, int alignedPos,
547 StructureMapping mapping)
549 if (alignedPos >= seq.getLength())
554 if (Comparison.isGap(seq.getCharAt(alignedPos)))
558 int seqPos = seq.findPosition(alignedPos);
559 int pos = mapping.getPDBResNum(seqPos);
564 * Helper method to identify residues that can participate in a structure
565 * superposition command. For each structure, identify a sequence in the
566 * alignment which is mapped to the structure. Identify non-gapped columns in
567 * the sequence which have a mapping to a residue in the structure. Returns
568 * the index of the first structure that has a mapping to the alignment.
571 * the sequence alignment which is the basis of structure
574 * a BitSet, where bit j is set to indicate that every structure has
575 * a mapped residue present in column j (so the column can
576 * participate in structure alignment)
578 * an array of data beans corresponding to pdb file index
581 protected int findSuperposableResidues(AlignmentI alignment,
582 BitSet matched, SuperposeData[] structures)
584 int refStructure = -1;
585 String[] files = getStructureFiles();
590 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
592 StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
596 * Find the first mapped sequence (if any) for this PDB entry which is in
599 final int seqCountForPdbFile = getSequence()[pdbfnum].length;
600 for (int s = 0; s < seqCountForPdbFile; s++)
602 for (StructureMapping mapping : mappings)
604 final SequenceI theSequence = getSequence()[pdbfnum][s];
605 if (mapping.getSequence() == theSequence
606 && alignment.findIndex(theSequence) > -1)
608 if (refStructure < 0)
610 refStructure = pdbfnum;
612 for (int r = 0; r < alignment.getWidth(); r++)
618 int pos = getMappedPosition(theSequence, r, mapping);
619 if (pos < 1 || pos == lastPos)
625 structures[pdbfnum].pdbResNo[r] = pos;
627 String chain = mapping.getChain();
628 if (chain != null && chain.trim().length() > 0)
630 structures[pdbfnum].chain = chain;
632 structures[pdbfnum].pdbId = mapping.getPdbId();
633 structures[pdbfnum].isRna = theSequence.getRNA() != null;
636 * move on to next pdb file (ignore sequences for other chains
637 * for the same structure)
639 s = seqCountForPdbFile;
649 * Returns true if the structure viewer has loaded all of the files of
650 * interest (identified by the file mapping having been set up), or false if
651 * any are still not loaded after a timeout interval.
655 protected boolean waitForFileLoad(String[] files)
658 * give up after 10 secs plus 1 sec per file
660 long starttime = System.currentTimeMillis();
661 long endTime = 10000 + 1000 * files.length + starttime;
662 String notLoaded = null;
664 boolean waiting = true;
665 while (waiting && System.currentTimeMillis() < endTime)
668 for (String file : files)
677 StructureMapping[] sm = getSsm().getMapping(file);
678 if (sm == null || sm.length == 0)
682 } catch (Throwable x)
692 "Timed out waiting for structure viewer to load file "
700 public boolean isListeningFor(SequenceI seq)
702 if (sequence != null)
704 for (SequenceI[] seqs : sequence)
708 for (SequenceI s : seqs)
710 if (s == seq || (s.getDatasetSequence() != null
711 && s.getDatasetSequence() == seq.getDatasetSequence()))
722 public boolean isFinishedInit()
727 public void setFinishedInit(boolean fi)
729 this.finishedInit = fi;
733 * Returns a list of chains mapped in this viewer.
737 public abstract List<String> getChainNames();
740 * Returns the Jalview panel hosting the structure viewer (if any)
744 public JalviewStructureDisplayI getViewer()
749 public abstract void setJalviewColourScheme(ColourSchemeI cs);
752 * Constructs and sends a command to align structures against a reference
753 * structure, based on one or more sequence alignments. May optionally return
754 * an error or warning message for the alignment command.
757 * an array of alignments to process
758 * @param structureIndices
759 * an array of corresponding reference structures (index into pdb
760 * file array); if a negative value is passed, the first PDB file
761 * mapped to an alignment sequence is used as the reference for
764 * an array of corresponding hidden columns for each alignment
767 public abstract String superposeStructures(AlignmentI[] alignments,
768 int[] structureIndices, HiddenColumns[] hiddenCols);
770 public abstract void setBackgroundColour(Color col);
772 protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
773 String[] files, SequenceRenderer sr, AlignmentViewPanel avp);
776 * returns the current sequenceRenderer that should be used to colour the
783 public abstract SequenceRenderer getSequenceRenderer(
784 AlignmentViewPanel alignment);
786 protected abstract void colourBySequence(
787 StructureMappingcommandSet[] colourBySequenceCommands);
789 public abstract void colourByChain();
791 public abstract void colourByCharge();
794 * colour any structures associated with sequences in the given alignment
795 * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
796 * if colourBySequence is enabled.
798 public void colourBySequence(AlignmentViewPanel alignmentv)
800 if (!colourBySequence || !isLoadingFinished())
804 if (getSsm() == null)
808 String[] files = getStructureFiles();
810 SequenceRenderer sr = getSequenceRenderer(alignmentv);
812 StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
813 files, sr, alignmentv);
814 colourBySequence(colourBySequenceCommands);
817 public boolean hasFileLoadingError()
819 return fileLoadingError != null && fileLoadingError.length() > 0;
822 public abstract jalview.api.FeatureRenderer getFeatureRenderer(
823 AlignmentViewPanel alignment);