X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=56d2e9bdc462c386dd6d9afca01e28d43032682d;hb=27555f103dbf71e346da16206f784f14e20af3d0;hp=3602056673d41ead4f7a3ed9490a54c7460a826f;hpb=17fe82c9d7f9da1b17f3091e4b3992a35e3e411e;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 3602056..56d2e9b 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -1,17 +1,49 @@ +/* + * 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.structures.models; -import java.util.ArrayList; -import java.util.List; - +import jalview.api.AlignmentViewPanel; +import jalview.api.SequenceRenderer; import jalview.api.StructureSelectionManagerProvider; +import jalview.api.structures.JalviewStructureDisplayI; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.io.DataSourceType; +import jalview.schemes.ColourSchemeI; import jalview.structure.AtomSpec; import jalview.structure.StructureListener; +import jalview.structure.StructureMapping; +import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; import jalview.util.Comparison; import jalview.util.MessageManager; +import java.awt.Color; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.BitSet; +import java.util.List; + /** * * A base class to hold common function for protein structure model binding. @@ -21,13 +53,17 @@ import jalview.util.MessageManager; * @author gmcarstairs * */ -public abstract class AAStructureBindingModel extends - SequenceStructureBindingModel implements StructureListener, - StructureSelectionManagerProvider +public abstract class AAStructureBindingModel + extends SequenceStructureBindingModel + implements StructureListener, StructureSelectionManagerProvider { private StructureSelectionManager ssm; + /* + * distinct PDB entries (pdb files) associated + * with sequences + */ private PDBEntry[] pdbEntry; /* @@ -43,12 +79,50 @@ public abstract class AAStructureBindingModel extends /* * datasource protocol for access to PDBEntrylatest */ - String protocol = null; + DataSourceType protocol = null; protected boolean colourBySequence = true; private boolean nucleotide; + private boolean finishedInit = false; + + /** + * current set of model filenames loaded in the Jmol instance + */ + protected String[] modelFileNames = null; + + public String fileLoadingError; + + /** + * Data bean class to simplify parameterisation in superposeStructures + */ + protected class SuperposeData + { + /** + * Constructor with alignment width argument + * + * @param width + */ + public SuperposeData(int width) + { + pdbResNo = new int[width]; + } + + public String filename; + + public String pdbId; + + public String chain = ""; + + public boolean isRna; + + /* + * The pdb residue number (if any) mapped to each column of the alignment + */ + public int[] pdbResNo; + } + /** * Constructor * @@ -68,25 +142,71 @@ public abstract class AAStructureBindingModel extends * @param ssm * @param pdbentry * @param sequenceIs - * @param chains * @param protocol */ public AAStructureBindingModel(StructureSelectionManager ssm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, - String protocol) + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, + DataSourceType protocol) { this.ssm = ssm; this.sequence = sequenceIs; this.nucleotide = Comparison.isNucleotide(sequenceIs); - this.chains = chains; this.pdbEntry = pdbentry; this.protocol = protocol; - if (chains == null) + resolveChains(); + } + + private boolean resolveChains() + { + /** + * final count of chain mappings discovered + */ + int chainmaps = 0; + // JBPNote: JAL-2693 - this should be a list of chain mappings per + // [pdbentry][sequence] + String[][] newchains = new String[pdbEntry.length][]; + int pe = 0; + for (PDBEntry pdb : pdbEntry) { - this.chains = new String[pdbentry.length][]; + SequenceI[] seqsForPdb = sequence[pe]; + if (seqsForPdb != null) + { + newchains[pe] = new String[seqsForPdb.length]; + int se = 0; + for (SequenceI asq : seqsForPdb) + { + String chain = (chains != null && chains[pe] != null) + ? chains[pe][se] + : null; + SequenceI sq = (asq.getDatasetSequence() == null) ? asq + : asq.getDatasetSequence(); + if (sq.getAllPDBEntries() != null) + { + for (PDBEntry pdbentry : sq.getAllPDBEntries()) + { + if (pdb.getFile() != null && pdbentry.getFile() != null + && pdb.getFile().equals(pdbentry.getFile())) + { + String chaincode = pdbentry.getChainCode(); + if (chaincode != null && chaincode.length() > 0) + { + chain = chaincode; + chainmaps++; + break; + } + } + } + } + newchains[pe][se] = chain; + se++; + } + pe++; + } } - } + chains = newchains; + return chainmaps > 0; + } public StructureSelectionManager getSsm() { return ssm; @@ -104,6 +224,27 @@ public abstract class AAStructureBindingModel extends } /** + * Answers true if this binding includes the given PDB id, else false + * + * @param pdbId + * @return + */ + public boolean hasPdbId(String pdbId) + { + if (pdbEntry != null) + { + for (PDBEntry pdb : pdbEntry) + { + if (pdb.getId().equals(pdbId)) + { + return true; + } + } + } + return false; + } + + /** * Returns the number of modelled PDB file entries. * * @return @@ -123,7 +264,7 @@ public abstract class AAStructureBindingModel extends return chains; } - public String getProtocol() + public DataSourceType getProtocol() { return protocol; } @@ -147,7 +288,9 @@ public abstract class AAStructureBindingModel extends /** * Construct a title string for the viewer window based on the data Jalview * knows about - * @param viewerName TODO + * + * @param viewerName + * TODO * @param verbose * * @return @@ -155,33 +298,28 @@ public abstract class AAStructureBindingModel extends public String getViewerTitle(String viewerName, boolean verbose) { if (getSequence() == null || getSequence().length < 1 - || getPdbCount() < 1 - || getSequence()[0].length < 1) + || getPdbCount() < 1 || getSequence()[0].length < 1) { return ("Jalview " + viewerName + " Window"); } // TODO: give a more informative title when multiple structures are // displayed. StringBuilder title = new StringBuilder(64); - final PDBEntry pdbEntry = getPdbEntry(0); + final PDBEntry pdbe = getPdbEntry(0); title.append(viewerName + " view for " + getSequence()[0][0].getName() - + ":" - + pdbEntry.getId()); - + + ":" + pdbe.getId()); + if (verbose) { - if (pdbEntry.getProperty() != null) + String method = (String) pdbe.getProperty("method"); + if (method != null) { - if (pdbEntry.getProperty().get("method") != null) - { - title.append(" Method: "); - title.append(pdbEntry.getProperty().get("method")); - } - if (pdbEntry.getProperty().get("chains") != null) - { - title.append(" Chain:"); - title.append(pdbEntry.getProperty().get("chains")); - } + title.append(" Method: ").append(method); + } + String chain = (String) pdbe.getProperty("chains"); + if (chain != null) + { + title.append(" Chain:").append(chain); } } return title.toString(); @@ -217,8 +355,8 @@ public abstract class AAStructureBindingModel extends { Integer.valueOf(pe).toString() })); } final String nullChain = "TheNullChain"; - List s = new ArrayList(); - List c = new ArrayList(); + List s = new ArrayList<>(); + List c = new ArrayList<>(); if (getChains() == null) { setChains(new String[getPdbCount()][]); @@ -284,11 +422,11 @@ public abstract class AAStructureBindingModel extends * * @returns the pdb entries added to the current set. */ - public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, SequenceI[][] seq, - String[][] chns) + public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, + SequenceI[][] seq, String[][] chns) { - List v = new ArrayList(); - List rtn = new ArrayList(); + List v = new ArrayList<>(); + List rtn = new ArrayList<>(); for (int i = 0; i < getPdbCount(); i++) { v.add(getPdbEntry(i)); @@ -298,8 +436,7 @@ public abstract class AAStructureBindingModel extends int r = v.indexOf(pdbe[i]); if (r == -1 || r >= getPdbCount()) { - rtn.add(new int[] - { v.size(), i }); + rtn.add(new int[] { v.size(), i }); v.add(pdbe[i]); } else @@ -367,23 +504,321 @@ public abstract class AAStructureBindingModel extends } @Override - public void highlightAtoms(List atoms) + public abstract void highlightAtoms(List atoms); + + protected boolean isNucleotide() { - if (atoms != null) + return this.nucleotide; + } + + /** + * Returns a readable description of all mappings for the wrapped pdbfile to + * any mapped sequences + * + * @return + */ + public String printMappings() + { + if (pdbEntry == null) + { + return ""; + } + StringBuilder sb = new StringBuilder(128); + for (int pdbe = 0; pdbe < getPdbCount(); pdbe++) + { + String pdbfile = getPdbEntry(pdbe).getFile(); + List seqs = Arrays.asList(getSequence()[pdbe]); + sb.append(getSsm().printMappings(pdbfile, seqs)); + } + return sb.toString(); + } + + /** + * Returns the mapped structure position for a given aligned column of a given + * sequence, or -1 if the column is gapped, beyond the end of the sequence, or + * not mapped to structure. + * + * @param seq + * @param alignedPos + * @param mapping + * @return + */ + protected int getMappedPosition(SequenceI seq, int alignedPos, + StructureMapping mapping) + { + if (alignedPos >= seq.getLength()) + { + return -1; + } + + if (Comparison.isGap(seq.getCharAt(alignedPos))) { - for (AtomSpec atom : atoms) + return -1; + } + int seqPos = seq.findPosition(alignedPos); + int pos = mapping.getPDBResNum(seqPos); + return pos; + } + + /** + * Helper method to identify residues that can participate in a structure + * superposition command. For each structure, identify a sequence in the + * alignment which is mapped to the structure. Identify non-gapped columns in + * the sequence which have a mapping to a residue in the structure. Returns + * the index of the first structure that has a mapping to the alignment. + * + * @param alignment + * the sequence alignment which is the basis of structure + * superposition + * @param matched + * a BitSet, where bit j is set to indicate that every structure has + * a mapped residue present in column j (so the column can + * participate in structure alignment) + * @param structures + * an array of data beans corresponding to pdb file index + * @return + */ + protected int findSuperposableResidues(AlignmentI alignment, + BitSet matched, SuperposeData[] structures) + { + int refStructure = -1; + String[] files = getStructureFiles(); + if (files == null) + { + return -1; + } + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + { + StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]); + int lastPos = -1; + + /* + * Find the first mapped sequence (if any) for this PDB entry which is in + * the alignment + */ + final int seqCountForPdbFile = getSequence()[pdbfnum].length; + for (int s = 0; s < seqCountForPdbFile; s++) { - highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(), - atom.getChain(), atom.getPdbFile()); + for (StructureMapping mapping : mappings) + { + final SequenceI theSequence = getSequence()[pdbfnum][s]; + if (mapping.getSequence() == theSequence + && alignment.findIndex(theSequence) > -1) + { + if (refStructure < 0) + { + refStructure = pdbfnum; + } + for (int r = 0; r < alignment.getWidth(); r++) + { + if (!matched.get(r)) + { + continue; + } + int pos = getMappedPosition(theSequence, r, mapping); + if (pos < 1 || pos == lastPos) + { + matched.clear(r); + continue; + } + lastPos = pos; + structures[pdbfnum].pdbResNo[r] = pos; + } + String chain = mapping.getChain(); + if (chain != null && chain.trim().length() > 0) + { + structures[pdbfnum].chain = chain; + } + structures[pdbfnum].pdbId = mapping.getPdbId(); + structures[pdbfnum].isRna = theSequence.getRNA() != null; + + /* + * move on to next pdb file (ignore sequences for other chains + * for the same structure) + */ + s = seqCountForPdbFile; + break; + } + } } } + return refStructure; } - protected abstract void highlightAtom(int atomIndex, int pdbResNum, - String chain, String pdbFile); + /** + * Returns true if the structure viewer has loaded all of the files of + * interest (identified by the file mapping having been set up), or false if + * any are still not loaded after a timeout interval. + * + * @param files + */ + protected boolean waitForFileLoad(String[] files) + { + /* + * give up after 10 secs plus 1 sec per file + */ + long starttime = System.currentTimeMillis(); + long endTime = 10000 + 1000 * files.length + starttime; + String notLoaded = null; + + boolean waiting = true; + while (waiting && System.currentTimeMillis() < endTime) + { + waiting = false; + for (String file : files) + { + notLoaded = file; + if (file == null) + { + continue; + } + try + { + StructureMapping[] sm = getSsm().getMapping(file); + if (sm == null || sm.length == 0) + { + waiting = true; + } + } catch (Throwable x) + { + waiting = true; + } + } + } - protected boolean isNucleotide() + if (waiting) + { + System.err.println( + "Timed out waiting for structure viewer to load file " + + notLoaded); + return false; + } + return true; + } + + @Override + public boolean isListeningFor(SequenceI seq) { - return this.nucleotide; + if (sequence != null) + { + for (SequenceI[] seqs : sequence) + { + if (seqs != null) + { + for (SequenceI s : seqs) + { + if (s == seq || (s.getDatasetSequence() != null + && s.getDatasetSequence() == seq.getDatasetSequence())) + { + return true; + } + } + } + } + } + return false; + } + + public boolean isFinishedInit() + { + return finishedInit; + } + + public void setFinishedInit(boolean fi) + { + this.finishedInit = fi; } -} \ No newline at end of file + + /** + * Returns a list of chains mapped in this viewer. + * + * @return + */ + public abstract List getChainNames(); + + /** + * Returns the Jalview panel hosting the structure viewer (if any) + * + * @return + */ + public JalviewStructureDisplayI getViewer() + { + return null; + } + + public abstract void setJalviewColourScheme(ColourSchemeI cs); + + /** + * Constructs and sends a command to align structures against a reference + * structure, based on one or more sequence alignments. May optionally return + * an error or warning message for the alignment command. + * + * @param alignments + * an array of alignments to process + * @param structureIndices + * an array of corresponding reference structures (index into pdb + * file array); if a negative value is passed, the first PDB file + * mapped to an alignment sequence is used as the reference for + * superposition + * @param hiddenCols + * an array of corresponding hidden columns for each alignment + * @return + */ + public abstract String superposeStructures(AlignmentI[] alignments, + int[] structureIndices, HiddenColumns[] hiddenCols); + + public abstract void setBackgroundColour(Color col); + + protected abstract StructureMappingcommandSet[] getColourBySequenceCommands( + String[] files, SequenceRenderer sr, AlignmentViewPanel avp); + + /** + * returns the current sequenceRenderer that should be used to colour the + * structures + * + * @param alignment + * + * @return + */ + public abstract SequenceRenderer getSequenceRenderer( + AlignmentViewPanel alignment); + + protected abstract void colourBySequence( + StructureMappingcommandSet[] colourBySequenceCommands); + + public abstract void colourByChain(); + + public abstract void colourByCharge(); + + /** + * colour any structures associated with sequences in the given alignment + * using the getFeatureRenderer() and getSequenceRenderer() renderers but only + * if colourBySequence is enabled. + */ + public void colourBySequence(AlignmentViewPanel alignmentv) + { + if (!colourBySequence || !isLoadingFinished()) + { + return; + } + if (getSsm() == null) + { + return; + } + String[] files = getStructureFiles(); + + SequenceRenderer sr = getSequenceRenderer(alignmentv); + + StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands( + files, sr, alignmentv); + colourBySequence(colourBySequenceCommands); + } + + public boolean hasFileLoadingError() + { + return fileLoadingError != null && fileLoadingError.length() > 0; + } + + public abstract jalview.api.FeatureRenderer getFeatureRenderer( + AlignmentViewPanel alignment); +}