X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=252828601a738b6ebe153b142f60d438cf2b3e7c;hb=4f77328104498504339216829abf5ea87e2791ec;hp=5dc34654992f8b262cb3153415cc4ffec98a45d8;hpb=c3b8fbc19c04c2daec702a2bffdfab5d10555143;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 5dc3465..2528286 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -20,19 +20,28 @@ */ package jalview.structures.models; +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; /** @@ -44,9 +53,9 @@ import java.util.List; * @author gmcarstairs * */ -public abstract class AAStructureBindingModel extends - SequenceStructureBindingModel implements StructureListener, - StructureSelectionManagerProvider +public abstract class AAStructureBindingModel + extends SequenceStructureBindingModel + implements StructureListener, StructureSelectionManagerProvider { private StructureSelectionManager ssm; @@ -70,7 +79,7 @@ public abstract class AAStructureBindingModel extends /* * datasource protocol for access to PDBEntrylatest */ - String protocol = null; + DataSourceType protocol = null; protected boolean colourBySequence = true; @@ -83,6 +92,8 @@ public abstract class AAStructureBindingModel extends */ protected String[] modelFileNames = null; + public String fileLoadingError; + /** * Data bean class to simplify parameterisation in superposeStructures */ @@ -131,20 +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 protocol) + DataSourceType protocol) { this.ssm = ssm; this.sequence = sequenceIs; this.nucleotide = Comparison.isNucleotide(sequenceIs); this.pdbEntry = pdbentry; this.protocol = protocol; + 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) + { + 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; @@ -202,7 +264,7 @@ public abstract class AAStructureBindingModel extends return chains; } - public String getProtocol() + public DataSourceType getProtocol() { return protocol; } @@ -289,7 +351,8 @@ public abstract class AAStructureBindingModel extends { throw new Error(MessageManager.formatMessage( "error.implementation_error_no_pdbentry_from_index", - new Object[] { Integer.valueOf(pe).toString() })); + new Object[] + { Integer.valueOf(pe).toString() })); } final String nullChain = "TheNullChain"; List s = new ArrayList(); @@ -510,18 +573,18 @@ public abstract class AAStructureBindingModel extends * the sequence alignment which is the basis of structure * superposition * @param matched - * an array of booleans, indexed by alignment column, where true - * indicates that every structure has a mapped residue present in the - * column (so the column can participate in structure alignment) + * 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, - boolean[] matched, SuperposeData[] structures) + BitSet matched, SuperposeData[] structures) { int refStructure = -1; - String[] files = getPdbFile(); + String[] files = getStructureFiles(); if (files == null) { return -1; @@ -548,16 +611,16 @@ public abstract class AAStructureBindingModel extends { refStructure = pdbfnum; } - for (int r = 0; r < matched.length; r++) + for (int r = 0; r < alignment.getWidth(); r++) { - if (!matched[r]) + if (!matched.get(r)) { continue; } int pos = getMappedPosition(theSequence, r, mapping); if (pos < 1 || pos == lastPos) { - matched[r] = false; + matched.clear(r); continue; } lastPos = pos; @@ -627,8 +690,8 @@ public abstract class AAStructureBindingModel extends if (waiting) { - System.err - .println("Timed out waiting for structure viewer to load file " + System.err.println( + "Timed out waiting for structure viewer to load file " + notLoaded); return false; } @@ -646,10 +709,8 @@ public abstract class AAStructureBindingModel extends { for (SequenceI s : seqs) { - if (s == seq - || (s.getDatasetSequence() != null && s - .getDatasetSequence() == seq - .getDatasetSequence())) + if (s == seq || (s.getDatasetSequence() != null + && s.getDatasetSequence() == seq.getDatasetSequence())) { return true; } @@ -677,4 +738,89 @@ public abstract class AAStructureBindingModel extends */ 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); }