/*
* 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 jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.Comparison;
import jalview.util.MessageManager;
import java.util.ArrayList;
import java.util.Arrays;
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
{
private StructureSelectionManager ssm;
private PDBEntry[] pdbEntry;
/*
* sequences mapped to each pdbentry
*/
private SequenceI[][] sequence;
/*
* array of target chains for sequences - tied to pdbentry and sequence[]
*/
private String[][] chains;
/*
* datasource protocol for access to PDBEntrylatest
*/
String protocol = null;
protected boolean colourBySequence = true;
private boolean nucleotide;
private boolean finishedInit = false;
/**
* 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 seqs
*/
public AAStructureBindingModel(StructureSelectionManager ssm,
SequenceI[][] seqs)
{
this.ssm = ssm;
this.sequence = seqs;
}
/**
* Constructor
*
* @param ssm
* @param pdbentry
* @param sequenceIs
* @param chains
* @param protocol
*/
public AAStructureBindingModel(StructureSelectionManager ssm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
String protocol)
{
this.ssm = ssm;
this.sequence = sequenceIs;
this.nucleotide = Comparison.isNucleotide(sequenceIs);
this.chains = chains;
this.pdbEntry = pdbentry;
this.protocol = protocol;
if (chains == null)
{
this.chains = new String[pdbentry.length][];
}
}
public StructureSelectionManager getSsm()
{
return ssm;
}
/**
* Returns the i'th PDBEntry (or null)
*
* @param i
* @return
*/
public PDBEntry getPdbEntry(int i)
{
return (pdbEntry != null && pdbEntry.length > i) ? pdbEntry[i] : null;
}
/**
* 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
*/
public int getPdbCount()
{
return pdbEntry == null ? 0 : pdbEntry.length;
}
public SequenceI[][] getSequence()
{
return sequence;
}
public String[][] getChains()
{
return chains;
}
public String getProtocol()
{
return protocol;
}
// TODO may remove this if calling methods can be pulled up here
protected void setPdbentry(PDBEntry[] pdbentry)
{
this.pdbEntry = pdbentry;
}
protected void setSequence(SequenceI[][] sequence)
{
this.sequence = sequence;
}
protected void setChains(String[][] chains)
{
this.chains = chains;
}
/**
* Construct a title string for the viewer window based on the data Jalview
* knows about
*
* @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)
{
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);
title.append(viewerName + " view for " + getSequence()[0][0].getName()
+ ":" + pdbEntry.getId());
if (verbose)
{
if (pdbEntry.getProperty() != 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"));
}
}
}
return title.toString();
}
/**
* Called by after closeViewer is called, to release any resources and
* references so they can be garbage collected. Override if needed.
*/
protected void releaseUIResources()
{
}
public boolean isColourBySequence()
{
return colourBySequence;
}
public void setColourBySequence(boolean colourBySequence)
{
this.colourBySequence = colourBySequence;
}
protected void addSequenceAndChain(int pe, SequenceI[] seq,
String[] tchain)
{
if (pe < 0 || pe >= getPdbCount())
{
throw new Error(MessageManager.formatMessage(
"error.implementation_error_no_pdbentry_from_index",
new Object[] { Integer.valueOf(pe).toString() }));
}
final String nullChain = "TheNullChain";
List s = new ArrayList();
List c = new ArrayList();
if (getChains() == null)
{
setChains(new String[getPdbCount()][]);
}
if (getSequence()[pe] != null)
{
for (int i = 0; i < getSequence()[pe].length; i++)
{
s.add(getSequence()[pe][i]);
if (getChains()[pe] != null)
{
if (i < getChains()[pe].length)
{
c.add(getChains()[pe][i]);
}
else
{
c.add(nullChain);
}
}
else
{
if (tchain != null && tchain.length > 0)
{
c.add(nullChain);
}
}
}
}
for (int i = 0; i < seq.length; i++)
{
if (!s.contains(seq[i]))
{
s.add(seq[i]);
if (tchain != null && i < tchain.length)
{
c.add(tchain[i] == null ? nullChain : tchain[i]);
}
}
}
SequenceI[] tmp = s.toArray(new SequenceI[s.size()]);
getSequence()[pe] = tmp;
if (c.size() > 0)
{
String[] tch = c.toArray(new String[c.size()]);
for (int i = 0; i < tch.length; i++)
{
if (tch[i] == nullChain)
{
tch[i] = null;
}
}
getChains()[pe] = tch;
}
else
{
getChains()[pe] = null;
}
}
/**
* add structures and any known sequence associations
*
* @returns the pdb entries added to the current set.
*/
public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
SequenceI[][] seq, String[][] chns)
{
List v = new ArrayList();
List rtn = new ArrayList();
for (int i = 0; i < getPdbCount(); i++)
{
v.add(getPdbEntry(i));
}
for (int i = 0; i < pdbe.length; i++)
{
int r = v.indexOf(pdbe[i]);
if (r == -1 || r >= getPdbCount())
{
rtn.add(new int[] { v.size(), i });
v.add(pdbe[i]);
}
else
{
// just make sure the sequence/chain entries are all up to date
addSequenceAndChain(r, seq[i], chns[i]);
}
}
pdbe = v.toArray(new PDBEntry[v.size()]);
setPdbentry(pdbe);
if (rtn.size() > 0)
{
// expand the tied sequence[] and string[] arrays
SequenceI[][] sqs = new SequenceI[getPdbCount()][];
String[][] sch = new String[getPdbCount()][];
System.arraycopy(getSequence(), 0, sqs, 0, getSequence().length);
System.arraycopy(getChains(), 0, sch, 0, this.getChains().length);
setSequence(sqs);
setChains(sch);
pdbe = new PDBEntry[rtn.size()];
for (int r = 0; r < pdbe.length; r++)
{
int[] stri = (rtn.get(r));
// record the pdb file as a new addition
pdbe[r] = getPdbEntry(stri[0]);
// and add the new sequence/chain entries
addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
}
}
else
{
pdbe = null;
}
return pdbe;
}
/**
* Add sequences to the pe'th pdbentry's sequence set.
*
* @param pe
* @param seq
*/
public void addSequence(int pe, SequenceI[] seq)
{
addSequenceAndChain(pe, seq, null);
}
/**
* 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 atoms);
protected boolean isNucleotide()
{
return this.nucleotide;
}
/**
* Returns a readable description of all mappings for the wrapped pdbfile to
* any mapped sequences
*
* @param pdbfile
* @param seqs
* @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)))
{
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
* 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)
* @param structures
* an array of data beans corresponding to pdb file index
* @return
*/
protected int findSuperposableResidues(AlignmentI alignment,
boolean[] matched, SuperposeData[] structures)
{
int refStructure = -1;
String[] files = getPdbFile();
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 < matched.length; r++)
{
if (!matched[r])
{
continue;
}
int pos = getMappedPosition(theSequence, r, mapping);
if (pos < 1 || pos == lastPos)
{
matched[r] = false;
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
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;
}
}