/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.structure;
-import java.io.PrintStream;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.IdentityHashMap;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.Vector;
-
-import MCview.Atom;
-import MCview.PDBChain;
-
import jalview.analysis.AlignSeq;
import jalview.api.StructureSelectionManagerProvider;
import jalview.commands.CommandI;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.IdentityHashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+
+import MCview.Atom;
+import MCview.PDBChain;
+import MCview.PDBfile;
+
public class StructureSelectionManager
{
+ public final static String NEWLINE = System.lineSeparator();
+
static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
private List<StructureMapping> mappings = new ArrayList<StructureMapping>();
/*
* Set of any registered mappings between (dataset) sequences.
*/
- Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
-
- /*
- * Reference counters for the above mappings. Remove mappings when ref count
- * goes to zero.
- */
- Map<AlignedCodonFrame, Integer> seqMappingRefCounts = new HashMap<AlignedCodonFrame, Integer>();
+ public Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
* map between the PDB IDs (or structure identifiers) used by Jalview and the
* absolute filenames for PDB data that corresponds to it
*/
- HashMap<String, String> pdbIdFileName = new HashMap<String, String>(),
- pdbFileNameId = new HashMap<String, String>();
+ Map<String, String> pdbIdFileName = new HashMap<String, String>();
+
+ Map<String, String> pdbFileNameId = new HashMap<String, String>();
public void registerPDBFile(String idForFile, String absoluteFile)
{
{
if (instances != null)
{
- throw new Error(MessageManager.getString("error.implementation_error_structure_selection_manager_null"),
- new NullPointerException(MessageManager.getString("exception.ssm_context_is_null")));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_structure_selection_manager_null"),
+ new NullPointerException(MessageManager
+ .getString("exception.ssm_context_is_null")));
}
else
{
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
- synchronized public MCview.PDBfile setMapping(SequenceI[] sequence,
+ synchronized public PDBfile setMapping(SequenceI[] sequence,
String[] targetChains, String pdbFile, String protocol)
{
return setMapping(true, sequence, targetChains, pdbFile, protocol);
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
- synchronized public MCview.PDBfile setMapping(boolean forStructureView,
- SequenceI[] sequence,
- String[] targetChains, String pdbFile, String protocol)
+ synchronized public PDBfile setMapping(boolean forStructureView,
+ SequenceI[] sequence, String[] targetChains, String pdbFile,
+ String protocol)
{
/*
* There will be better ways of doing this in the future, for now we'll use
* the tried and tested MCview pdb mapping
*/
- MCview.PDBfile pdb = null;
boolean parseSecStr = processSecondaryStructure;
if (isPDBFileRegistered(pdbFile))
{
// false if any annotation present from this structure
// JBPNote this fails for jmol/chimera view because the *file* is
// passed, not the structure data ID -
- if (MCview.PDBfile.isCalcIdForFile(ala,
- findIdForPDBFile(pdbFile)))
+ if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
{
parseSecStr = false;
}
}
}
}
+ PDBfile pdb = null;
try
{
- pdb = new MCview.PDBfile(addTempFacAnnot, parseSecStr,
- secStructServices, pdbFile, protocol);
+ pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
+ pdbFile, protocol);
if (pdb.id != null && pdb.id.trim().length() > 0
&& AppletFormatAdapter.FILE.equals(protocol))
{
for (int s = 0; s < sequence.length; s++)
{
boolean infChain = true;
+ final SequenceI seq = sequence[s];
if (targetChains != null && targetChains[s] != null)
{
infChain = false;
targetChain = targetChains[s];
}
- else if (sequence[s].getName().indexOf("|") > -1)
+ else if (seq.getName().indexOf("|") > -1)
{
- targetChain = sequence[s].getName().substring(
- sequence[s].getName().lastIndexOf("|") + 1);
+ targetChain = seq.getName().substring(
+ seq.getName().lastIndexOf("|") + 1);
if (targetChain.length() > 1)
{
if (targetChain.trim().length() == 0)
targetChain = "";
}
+ /*
+ * Attempt pairwise alignment of the sequence with each chain in the PDB,
+ * and remember the highest scoring chain
+ */
int max = -10;
AlignSeq maxAlignseq = null;
String maxChainId = " ";
PDBChain maxChain = null;
boolean first = true;
- for (int i = 0; i < pdb.chains.size(); i++)
+ for (PDBChain chain : pdb.chains)
{
- PDBChain chain = (pdb.chains.elementAt(i));
if (targetChain.length() > 0 && !targetChain.equals(chain.id)
&& !infChain)
{
}
// TODO: correctly determine sequence type for mixed na/peptide
// structures
- AlignSeq as = new AlignSeq(sequence[s],
- pdb.chains.elementAt(i).sequence,
- pdb.chains.elementAt(i).isNa ? AlignSeq.DNA
- : AlignSeq.PEP);
- as.calcScoreMatrix();
- as.traceAlignment();
+ final String type = chain.isNa ? AlignSeq.DNA : AlignSeq.PEP;
+ AlignSeq as = AlignSeq.doGlobalNWAlignment(seq, chain.sequence,
+ type);
+ // equivalent to:
+ // AlignSeq as = new AlignSeq(sequence[s], chain.sequence, type);
+ // as.calcScoreMatrix();
+ // as.traceAlignment();
if (first || as.maxscore > max
|| (as.maxscore == max && chain.id.equals(targetChain)))
{
continue;
}
- final StringBuffer mappingDetails = new StringBuffer();
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + maxChain.sequence.getSequenceAsString());
- mappingDetails.append("\nNo of residues = "
- + maxChain.residues.size() + "\n\n");
+ final StringBuilder mappingDetails = new StringBuilder(128);
+ mappingDetails.append(NEWLINE).append("PDB Sequence is :")
+ .append(NEWLINE).append("Sequence = ")
+ .append(maxChain.sequence.getSequenceAsString());
+ mappingDetails.append(NEWLINE).append("No of residues = ")
+ .append(maxChain.residues.size()).append(NEWLINE)
+ .append(NEWLINE);
PrintStream ps = new PrintStream(System.out)
{
@Override
@Override
public void println()
{
- mappingDetails.append("\n");
+ mappingDetails.append(NEWLINE);
}
};
maxAlignseq.printAlignment(ps);
- mappingDetails.append("\nPDB start/end " + maxAlignseq.seq2start
- + " " + maxAlignseq.seq2end);
- mappingDetails.append("\nSEQ start/end "
- + (maxAlignseq.seq1start + sequence[s].getStart() - 1) + " "
- + (maxAlignseq.seq1end + sequence[s].getEnd() - 1));
+ mappingDetails.append(NEWLINE).append("PDB start/end ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq2start)).append(
+ " ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
+
+ mappingDetails.append(NEWLINE).append("SEQ start/end ");
+ mappingDetails.append(
+ String.valueOf(maxAlignseq.seq1start + seq.getStart() - 1))
+ .append(" ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq1end
+ + seq.getEnd() - 1));
- maxChain.makeExactMapping(maxAlignseq, sequence[s]);
+ maxChain.makeExactMapping(maxAlignseq, seq);
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping(
sqmpping.getMap().getInverse());
- maxChain.transferRESNUMFeatures(sequence[s], null);
+ maxChain.transferRESNUMFeatures(seq, null);
// allocate enough slots to store the mapping from positions in
// sequence[s] to the associated chain
- int[][] mapping = new int[sequence[s].findPosition(sequence[s]
- .getLength()) + 2][2];
+ int[][] mapping = new int[seq.findPosition(seq.getLength()) + 2][2];
int resNum = -10000;
int index = 0;
do
{
- Atom tmp = (Atom) maxChain.atoms.elementAt(index);
+ Atom tmp = maxChain.atoms.elementAt(index);
if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
{
resNum = tmp.resNumber;
- mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
- mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
+ if (tmp.alignmentMapping >= -1)
+ {
+ // TODO (JAL-1836) address root cause: negative residue no in PDB
+ // file
+ mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
+ mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
+ }
}
index++;
{
pdbFile = "INLINE" + pdb.id;
}
- StructureMapping newMapping = new StructureMapping(sequence[s],
- pdbFile, pdb.id, maxChainId, mapping,
- mappingDetails.toString());
+ StructureMapping newMapping = new StructureMapping(seq, pdbFile,
+ pdb.id, maxChainId, mapping, mappingDetails.toString());
if (forStructureView)
{
mappings.add(newMapping);
{
return;
}
- String[] handlepdbs;
- Vector pdbs = new Vector();
- for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++]))
- {
- ;
- }
+
+ /*
+ * Remove mappings to the closed listener's PDB files, but first check if
+ * another listener is still interested
+ */
+ List<String> pdbs = new ArrayList<String>(Arrays.asList(pdbfiles));
+
StructureListener sl;
for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof StructureListener)
{
sl = (StructureListener) listeners.elementAt(i);
- handlepdbs = sl.getPdbFile();
- for (int j = 0; j < handlepdbs.length; j++)
+ for (String pdbfile : sl.getPdbFile())
{
- if (pdbs.contains(handlepdbs[j]))
- {
- pdbs.removeElement(handlepdbs[j]);
- }
+ pdbs.remove(pdbfile);
}
-
}
}
+ /*
+ * Rebuild the mappings set, retaining only those which are for 'other' PDB
+ * files
+ */
if (pdbs.size() > 0)
{
List<StructureMapping> tmp = new ArrayList<StructureMapping>();
}
}
}
- if (!results.isEmpty())
+ for (Object li : listeners)
{
- for (Object li : listeners)
+ if (li instanceof SequenceListener)
{
- if (li instanceof SequenceListener)
- {
- ((SequenceListener) li).highlightSequence(results);
- }
+ ((SequenceListener) li).highlightSequence(results);
}
}
}
results.addResult(seq, index, index);
}
- seqListener.highlightSequence(results);
+ if (!results.isEmpty())
+ {
+ seqListener.highlightSequence(results);
+ }
}
}
}
else if (listener instanceof SecondaryStructureListener)
{
((SecondaryStructureListener) listener).mouseOverSequence(seq,
- indexpos);
+ indexpos, index);
}
}
}
protected void highlightStructure(StructureListener sl, SequenceI seq,
int index)
{
+ if (!sl.isListeningFor(seq))
+ {
+ return;
+ }
int atomNo;
List<AtomSpec> atoms = new ArrayList<AtomSpec>();
for (StructureMapping sm : mappings)
{
List<StructureMapping> tmp = new ArrayList<StructureMapping>();
for (StructureMapping sm : mappings)
- {
+ {
if (sm.pdbfile.equals(pdbfile))
- {
+ {
tmp.add(sm);
- }
+ }
}
return tmp.toArray(new StructureMapping[tmp.size()]);
}
- public String printMapping(String pdbfile)
+ /**
+ * Returns a readable description of all mappings for the given pdbfile to any
+ * of the given sequences
+ *
+ * @param pdbfile
+ * @param seqs
+ * @return
+ */
+ public String printMappings(String pdbfile, List<SequenceI> seqs)
{
+ if (pdbfile == null || seqs == null || seqs.isEmpty())
+ {
+ return "";
+ }
+
StringBuilder sb = new StringBuilder(64);
for (StructureMapping sm : mappings)
{
- if (sm.pdbfile.equals(pdbfile))
+ if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence))
{
sb.append(sm.mappingDetails);
+ sb.append(NEWLINE);
+ // separator makes it easier to read multiple mappings
+ sb.append("=====================");
+ sb.append(NEWLINE);
}
}
+ sb.append(NEWLINE);
return sb.toString();
}
/**
- * Decrement the reference counter for each of the given mappings, and remove
- * it entirely if its reference counter reduces to zero.
+ * Remove the given mapping
*
- * @param set
+ * @param acf
*/
- public void removeMappings(Set<AlignedCodonFrame> set)
+ public void deregisterMapping(AlignedCodonFrame acf)
{
- if (set != null)
+ if (acf != null)
{
- for (AlignedCodonFrame acf : set)
- {
- removeMapping(acf);
+ boolean removed = seqmappings.remove(acf);
+ if (removed && seqmappings.isEmpty())
+ { // debug
+ System.out.println("All mappings removed");
}
}
}
/**
- * Decrement the reference counter for the given mapping, and remove it
- * entirely if its reference counter reduces to zero.
+ * Add each of the given codonFrames to the stored set, if not aready present.
*
- * @param acf
+ * @param set
*/
- public void removeMapping(AlignedCodonFrame acf)
+ public void registerMappings(Set<AlignedCodonFrame> set)
{
- if (acf != null && seqmappings.contains(acf))
+ if (set != null)
{
- int count = seqMappingRefCounts.get(acf);
- count--;
- if (count > 0)
- {
- seqMappingRefCounts.put(acf, count);
- }
- else
+ for (AlignedCodonFrame acf : set)
{
- seqmappings.remove(acf);
- seqMappingRefCounts.remove(acf);
+ registerMapping(acf);
}
}
}
/**
- * Add each of the given codonFrames to the stored set. If not aready present,
- * increments its reference count instead.
- *
- * @param set
+ * Add the given mapping to the stored set, unless already stored.
*/
- public void addMappings(Set<AlignedCodonFrame> set)
+ public void registerMapping(AlignedCodonFrame acf)
{
- if (set != null)
+ if (acf != null)
{
- for (AlignedCodonFrame acf : set)
+ if (!seqmappings.contains(acf))
{
- addMapping(acf);
+ seqmappings.add(acf);
}
}
}
/**
- * Add the given mapping to the stored set, or if already stored, increment
- * its reference counter.
+ * Resets this object to its initial state by removing all registered
+ * listeners, codon mappings, PDB file mappings
*/
- public void addMapping(AlignedCodonFrame acf)
+ public void resetAll()
{
- if (acf != null)
+ if (mappings != null)
{
- if (seqmappings.contains(acf))
- {
- seqMappingRefCounts.put(acf, seqMappingRefCounts.get(acf) + 1);
- }
- else
- {
- seqmappings.add(acf);
- seqMappingRefCounts.put(acf, 1);
- }
+ mappings.clear();
+ }
+ if (seqmappings != null)
+ {
+ seqmappings.clear();
+ }
+ if (sel_listeners != null)
+ {
+ sel_listeners.clear();
+ }
+ if (listeners != null)
+ {
+ listeners.clear();
+ }
+ if (commandListeners != null)
+ {
+ commandListeners.clear();
+ }
+ if (view_listeners != null)
+ {
+ view_listeners.clear();
+ }
+ if (pdbFileNameId != null)
+ {
+ pdbFileNameId.clear();
+ }
+ if (pdbIdFileName != null)
+ {
+ pdbIdFileName.clear();
}
}
git://source.jalview.org / jalview.git / blobdiff