+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
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.event.ComponentEvent;
+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.
* Initial version created by refactoring JMol and Chimera binding models, but
* other structure viewers could in principle be accommodated in future.
* @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;
/*
/*
* 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
*
* @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.chains = chains;
+ this.nucleotide = Comparison.isNucleotide(sequenceIs);
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;
}
/**
+ * 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
return chains;
}
- public String getProtocol()
+ public DataSourceType getProtocol()
{
return protocol;
}
/**
* Construct a title string for the viewer window based on the data Jalview
* knows about
- * @param viewerName TODO
+ *
+ * @param viewerName
+ * TODO
* @param verbose
*
* @return
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();
{ Integer.valueOf(pe).toString() }));
}
final String nullChain = "TheNullChain";
- List<SequenceI> s = new ArrayList<SequenceI>();
- List<String> c = new ArrayList<String>();
+ List<SequenceI> s = new ArrayList<>();
+ List<String> c = new ArrayList<>();
if (getChains() == null)
{
setChains(new String[getPdbCount()][]);
*
* @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<PDBEntry> v = new ArrayList<PDBEntry>();
- List<int[]> rtn = new ArrayList<int[]>();
+ List<PDBEntry> v = new ArrayList<>();
+ List<int[]> rtn = new ArrayList<>();
for (int i = 0; i < getPdbCount(); i++)
{
v.add(getPdbEntry(i));
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
addSequenceAndChain(pe, seq, null);
}
-}
\ No newline at end of file
+ /**
+ * add the given sequences to the mapping scope for the given pdb file handle
+ *
+ * @param pdbFile
+ * - pdbFile identifier
+ * @param seq
+ * - set of sequences it can be mapped to
+ */
+ public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
+ {
+ for (int pe = 0; pe < getPdbCount(); pe++)
+ {
+ if (getPdbEntry(pe).getFile().equals(pdbFile))
+ {
+ addSequence(pe, seq);
+ }
+ }
+ }
+
+ @Override
+ public abstract void highlightAtoms(List<AtomSpec> atoms);
+
+ protected boolean isNucleotide()
+ {
+ 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<SequenceI> 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)))
+ {
+ 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++)
+ {
+ 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;
+ }
+
+ /**
+ * 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;
+ }
+ }
+ }
+
+ 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)
+ {
+ 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;
+ }
+
+ /**
+ * Returns a list of chains mapped in this viewer.
+ *
+ * @return
+ */
+ public abstract List<String> 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);
+}
git://source.jalview.org / jalview.git / blobdiff