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 String[][] newchains = new String[pdbEntry.length][];
167 for (PDBEntry pdb : pdbEntry)
169 SequenceI[] seqsForPdb = sequence[pe];
170 if (seqsForPdb != null)
172 newchains[pe] = new String[seqsForPdb.length];
174 for (SequenceI asq : seqsForPdb)
176 String chain = (chains != null && chains[pe] != null)
179 SequenceI sq = asq.getDatasetSequence();
180 if (sq.getAllPDBEntries() != null)
182 for (PDBEntry pdbentry : sq.getAllPDBEntries())
184 if (pdb.getFile() != null && pdbentry.getFile() != null
185 && pdb.getFile().equals(pdbentry.getFile()))
187 String chaincode = pdbentry.getChainCode();
188 if (chaincode != null && chaincode.length() > 0)
197 newchains[pe][se] = chain;
205 return chainmaps > 0;
207 public StructureSelectionManager getSsm()
213 * Returns the i'th PDBEntry (or null)
218 public PDBEntry getPdbEntry(int i)
220 return (pdbEntry != null && pdbEntry.length > i) ? pdbEntry[i] : null;
224 * Answers true if this binding includes the given PDB id, else false
229 public boolean hasPdbId(String pdbId)
231 if (pdbEntry != null)
233 for (PDBEntry pdb : pdbEntry)
235 if (pdb.getId().equals(pdbId))
245 * Returns the number of modelled PDB file entries.
249 public int getPdbCount()
251 return pdbEntry == null ? 0 : pdbEntry.length;
254 public SequenceI[][] getSequence()
259 public String[][] getChains()
264 public DataSourceType getProtocol()
269 // TODO may remove this if calling methods can be pulled up here
270 protected void setPdbentry(PDBEntry[] pdbentry)
272 this.pdbEntry = pdbentry;
275 protected void setSequence(SequenceI[][] sequence)
277 this.sequence = sequence;
280 protected void setChains(String[][] chains)
282 this.chains = chains;
286 * Construct a title string for the viewer window based on the data Jalview
295 public String getViewerTitle(String viewerName, boolean verbose)
297 if (getSequence() == null || getSequence().length < 1
298 || getPdbCount() < 1 || getSequence()[0].length < 1)
300 return ("Jalview " + viewerName + " Window");
302 // TODO: give a more informative title when multiple structures are
304 StringBuilder title = new StringBuilder(64);
305 final PDBEntry pdbe = getPdbEntry(0);
306 title.append(viewerName + " view for " + getSequence()[0][0].getName()
307 + ":" + pdbe.getId());
311 String method = (String) pdbe.getProperty("method");
314 title.append(" Method: ").append(method);
316 String chain = (String) pdbe.getProperty("chains");
319 title.append(" Chain:").append(chain);
322 return title.toString();
326 * Called by after closeViewer is called, to release any resources and
327 * references so they can be garbage collected. Override if needed.
329 protected void releaseUIResources()
334 public boolean isColourBySequence()
336 return colourBySequence;
339 public void setColourBySequence(boolean colourBySequence)
341 this.colourBySequence = colourBySequence;
344 protected void addSequenceAndChain(int pe, SequenceI[] seq,
347 if (pe < 0 || pe >= getPdbCount())
349 throw new Error(MessageManager.formatMessage(
350 "error.implementation_error_no_pdbentry_from_index",
352 { Integer.valueOf(pe).toString() }));
354 final String nullChain = "TheNullChain";
355 List<SequenceI> s = new ArrayList<SequenceI>();
356 List<String> c = new ArrayList<String>();
357 if (getChains() == null)
359 setChains(new String[getPdbCount()][]);
361 if (getSequence()[pe] != null)
363 for (int i = 0; i < getSequence()[pe].length; i++)
365 s.add(getSequence()[pe][i]);
366 if (getChains()[pe] != null)
368 if (i < getChains()[pe].length)
370 c.add(getChains()[pe][i]);
379 if (tchain != null && tchain.length > 0)
386 for (int i = 0; i < seq.length; i++)
388 if (!s.contains(seq[i]))
391 if (tchain != null && i < tchain.length)
393 c.add(tchain[i] == null ? nullChain : tchain[i]);
397 SequenceI[] tmp = s.toArray(new SequenceI[s.size()]);
398 getSequence()[pe] = tmp;
401 String[] tch = c.toArray(new String[c.size()]);
402 for (int i = 0; i < tch.length; i++)
404 if (tch[i] == nullChain)
409 getChains()[pe] = tch;
413 getChains()[pe] = null;
418 * add structures and any known sequence associations
420 * @returns the pdb entries added to the current set.
422 public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
423 SequenceI[][] seq, String[][] chns)
425 List<PDBEntry> v = new ArrayList<PDBEntry>();
426 List<int[]> rtn = new ArrayList<int[]>();
427 for (int i = 0; i < getPdbCount(); i++)
429 v.add(getPdbEntry(i));
431 for (int i = 0; i < pdbe.length; i++)
433 int r = v.indexOf(pdbe[i]);
434 if (r == -1 || r >= getPdbCount())
436 rtn.add(new int[] { v.size(), i });
441 // just make sure the sequence/chain entries are all up to date
442 addSequenceAndChain(r, seq[i], chns[i]);
445 pdbe = v.toArray(new PDBEntry[v.size()]);
449 // expand the tied sequence[] and string[] arrays
450 SequenceI[][] sqs = new SequenceI[getPdbCount()][];
451 String[][] sch = new String[getPdbCount()][];
452 System.arraycopy(getSequence(), 0, sqs, 0, getSequence().length);
453 System.arraycopy(getChains(), 0, sch, 0, this.getChains().length);
456 pdbe = new PDBEntry[rtn.size()];
457 for (int r = 0; r < pdbe.length; r++)
459 int[] stri = (rtn.get(r));
460 // record the pdb file as a new addition
461 pdbe[r] = getPdbEntry(stri[0]);
462 // and add the new sequence/chain entries
463 addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
474 * Add sequences to the pe'th pdbentry's sequence set.
479 public void addSequence(int pe, SequenceI[] seq)
481 addSequenceAndChain(pe, seq, null);
485 * add the given sequences to the mapping scope for the given pdb file handle
488 * - pdbFile identifier
490 * - set of sequences it can be mapped to
492 public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
494 for (int pe = 0; pe < getPdbCount(); pe++)
496 if (getPdbEntry(pe).getFile().equals(pdbFile))
498 addSequence(pe, seq);
504 public abstract void highlightAtoms(List<AtomSpec> atoms);
506 protected boolean isNucleotide()
508 return this.nucleotide;
512 * Returns a readable description of all mappings for the wrapped pdbfile to
513 * any mapped sequences
519 public String printMappings()
521 if (pdbEntry == null)
525 StringBuilder sb = new StringBuilder(128);
526 for (int pdbe = 0; pdbe < getPdbCount(); pdbe++)
528 String pdbfile = getPdbEntry(pdbe).getFile();
529 List<SequenceI> seqs = Arrays.asList(getSequence()[pdbe]);
530 sb.append(getSsm().printMappings(pdbfile, seqs));
532 return sb.toString();
536 * Returns the mapped structure position for a given aligned column of a given
537 * sequence, or -1 if the column is gapped, beyond the end of the sequence, or
538 * not mapped to structure.
545 protected int getMappedPosition(SequenceI seq, int alignedPos,
546 StructureMapping mapping)
548 if (alignedPos >= seq.getLength())
553 if (Comparison.isGap(seq.getCharAt(alignedPos)))
557 int seqPos = seq.findPosition(alignedPos);
558 int pos = mapping.getPDBResNum(seqPos);
563 * Helper method to identify residues that can participate in a structure
564 * superposition command. For each structure, identify a sequence in the
565 * alignment which is mapped to the structure. Identify non-gapped columns in
566 * the sequence which have a mapping to a residue in the structure. Returns
567 * the index of the first structure that has a mapping to the alignment.
570 * the sequence alignment which is the basis of structure
573 * a BitSet, where bit j is set to indicate that every structure has
574 * a mapped residue present in column j (so the column can
575 * participate in structure alignment)
577 * an array of data beans corresponding to pdb file index
580 protected int findSuperposableResidues(AlignmentI alignment,
581 BitSet matched, SuperposeData[] structures)
583 int refStructure = -1;
584 String[] files = getStructureFiles();
589 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
591 StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
595 * Find the first mapped sequence (if any) for this PDB entry which is in
598 final int seqCountForPdbFile = getSequence()[pdbfnum].length;
599 for (int s = 0; s < seqCountForPdbFile; s++)
601 for (StructureMapping mapping : mappings)
603 final SequenceI theSequence = getSequence()[pdbfnum][s];
604 if (mapping.getSequence() == theSequence
605 && alignment.findIndex(theSequence) > -1)
607 if (refStructure < 0)
609 refStructure = pdbfnum;
611 for (int r = 0; r < alignment.getWidth(); r++)
617 int pos = getMappedPosition(theSequence, r, mapping);
618 if (pos < 1 || pos == lastPos)
624 structures[pdbfnum].pdbResNo[r] = pos;
626 String chain = mapping.getChain();
627 if (chain != null && chain.trim().length() > 0)
629 structures[pdbfnum].chain = chain;
631 structures[pdbfnum].pdbId = mapping.getPdbId();
632 structures[pdbfnum].isRna = theSequence.getRNA() != null;
635 * move on to next pdb file (ignore sequences for other chains
636 * for the same structure)
638 s = seqCountForPdbFile;
648 * Returns true if the structure viewer has loaded all of the files of
649 * interest (identified by the file mapping having been set up), or false if
650 * any are still not loaded after a timeout interval.
654 protected boolean waitForFileLoad(String[] files)
657 * give up after 10 secs plus 1 sec per file
659 long starttime = System.currentTimeMillis();
660 long endTime = 10000 + 1000 * files.length + starttime;
661 String notLoaded = null;
663 boolean waiting = true;
664 while (waiting && System.currentTimeMillis() < endTime)
667 for (String file : files)
676 StructureMapping[] sm = getSsm().getMapping(file);
677 if (sm == null || sm.length == 0)
681 } catch (Throwable x)
691 "Timed out waiting for structure viewer to load file "
699 public boolean isListeningFor(SequenceI seq)
701 if (sequence != null)
703 for (SequenceI[] seqs : sequence)
707 for (SequenceI s : seqs)
709 if (s == seq || (s.getDatasetSequence() != null
710 && s.getDatasetSequence() == seq.getDatasetSequence()))
721 public boolean isFinishedInit()
726 public void setFinishedInit(boolean fi)
728 this.finishedInit = fi;
732 * Returns a list of chains mapped in this viewer.
736 public abstract List<String> getChainNames();
739 * Returns the Jalview panel hosting the structure viewer (if any)
743 public JalviewStructureDisplayI getViewer()
748 public abstract void setJalviewColourScheme(ColourSchemeI cs);
751 * Constructs and sends a command to align structures against a reference
752 * structure, based on one or more sequence alignments. May optionally return
753 * an error or warning message for the alignment command.
756 * an array of alignments to process
757 * @param structureIndices
758 * an array of corresponding reference structures (index into pdb
759 * file array); if a negative value is passed, the first PDB file
760 * mapped to an alignment sequence is used as the reference for
763 * an array of corresponding hidden columns for each alignment
766 public abstract String superposeStructures(AlignmentI[] alignments,
767 int[] structureIndices, HiddenColumns[] hiddenCols);
769 public abstract void setBackgroundColour(Color col);
771 protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
772 String[] files, SequenceRenderer sr, AlignmentViewPanel avp);
775 * returns the current sequenceRenderer that should be used to colour the
782 public abstract SequenceRenderer getSequenceRenderer(
783 AlignmentViewPanel alignment);
785 protected abstract void colourBySequence(
786 StructureMappingcommandSet[] colourBySequenceCommands);
788 public abstract void colourByChain();
790 public abstract void colourByCharge();
793 * colour any structures associated with sequences in the given alignment
794 * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
795 * if colourBySequence is enabled.
797 public void colourBySequence(AlignmentViewPanel alignmentv)
799 if (!colourBySequence || !isLoadingFinished())
803 if (getSsm() == null)
807 String[] files = getStructureFiles();
809 SequenceRenderer sr = getSequenceRenderer(alignmentv);
811 StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
812 files, sr, alignmentv);
813 colourBySequence(colourBySequenceCommands);
816 public boolean hasFileLoadingError()
818 return fileLoadingError != null && fileLoadingError.length() > 0;
821 public abstract jalview.api.FeatureRenderer getFeatureRenderer(
822 AlignmentViewPanel alignment);