/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
import jalview.util.MessageManager;
import java.io.PrintStream;
import java.util.Enumeration;
-import java.util.Hashtable;
+import java.util.HashMap;
import java.util.IdentityHashMap;
import java.util.Vector;
StructureMapping[] mappings;
+ private boolean processSecondaryStructure = false,
+ secStructServices = false, addTempFacAnnot = false;
+
+ /**
+ * @return true if will try to use external services for processing secondary
+ * structure
+ */
+ public boolean isSecStructServices()
+ {
+ return secStructServices;
+ }
+
+ /**
+ * control use of external services for processing secondary structure
+ *
+ * @param secStructServices
+ */
+ public void setSecStructServices(boolean secStructServices)
+ {
+ this.secStructServices = secStructServices;
+ }
+
+ /**
+ * flag controlling addition of any kind of structural annotation
+ *
+ * @return true if temperature factor annotation will be added
+ */
+ public boolean isAddTempFacAnnot()
+ {
+ return addTempFacAnnot;
+ }
+
+ /**
+ * set flag controlling addition of structural annotation
+ *
+ * @param addTempFacAnnot
+ */
+ public void setAddTempFacAnnot(boolean addTempFacAnnot)
+ {
+ this.addTempFacAnnot = addTempFacAnnot;
+ }
+
+ /**
+ *
+ * @return if true, the structure manager will attempt to add secondary
+ * structure lines for unannotated sequences
+ */
+
+ public boolean isProcessSecondaryStructure()
+ {
+ return processSecondaryStructure;
+ }
+
+ /**
+ * Control whether structure manager will try to annotate mapped sequences
+ * with secondary structure from PDB data.
+ *
+ * @param enable
+ */
+ public void setProcessSecondaryStructure(boolean enable)
+ {
+ processSecondaryStructure = enable;
+ }
+
/**
* debug function - write all mappings to stdout
*/
}
}
- Hashtable mappingData = new Hashtable();
+ /**
+ * 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>();
+
+ public void registerPDBFile(String idForFile, String absoluteFile)
+ {
+ pdbIdFileName.put(idForFile, absoluteFile);
+ pdbFileNameId.put(absoluteFile, idForFile);
+ }
+
+ public String findIdForPDBFile(String idOrFile)
+ {
+ String id = pdbFileNameId.get(idOrFile);
+ return id;
+ }
+
+ public String findFileForPDBId(String idOrFile)
+ {
+ String id = pdbIdFileName.get(idOrFile);
+ return id;
+ }
+
+ public boolean isPDBFileRegistered(String idOrFile)
+ {
+ return pdbFileNameId.containsKey(idOrFile)
+ || pdbIdFileName.containsKey(idOrFile);
+ }
private static StructureSelectionManager nullProvider = null;
}
/**
+ * Import structure data and register a structure mapping for broadcasting
+ * colouring, mouseovers and selection events (convenience wrapper).
+ *
+ * @param sequence
+ * - one or more sequences to be mapped to pdbFile
+ * @param targetChains
+ * - optional chain specification for mapping each sequence to pdb
+ * (may be nill, individual elements may be nill)
+ * @param pdbFile
+ * - structure data resource
+ * @param protocol
+ * - how to resolve data from resource
+ * @return null or the structure data parsed as a pdb file
+ */
+ synchronized public MCview.PDBfile setMapping(SequenceI[] sequence,
+ String[] targetChains, String pdbFile, String protocol)
+ {
+ return setMapping(true, sequence, targetChains, pdbFile, protocol);
+ }
+
+ /**
* create sequence structure mappings between each sequence and the given
* pdbFile (retrieved via the given protocol).
*
+ * @param forStructureView
+ * when true, record the mapping for use in mouseOvers
+ *
* @param sequence
* - one or more sequences to be mapped to pdbFile
* @param targetChains
* - 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 MCview.PDBfile setMapping(boolean forStructureView,
+ SequenceI[] sequence,
String[] targetChains, String pdbFile, String protocol)
{
/*
* the tried and tested MCview pdb mapping
*/
MCview.PDBfile pdb = null;
- boolean parseSecStr=true;
- for (SequenceI sq:sequence)
+ boolean parseSecStr = processSecondaryStructure;
+ if (isPDBFileRegistered(pdbFile))
{
- SequenceI ds = sq;while (ds.getDatasetSequence()!=null) { ds = ds.getDatasetSequence();};
- if (ds.getAnnotation()!=null)
+ for (SequenceI sq : sequence)
{
- for (AlignmentAnnotation ala:ds.getAnnotation())
+ SequenceI ds = sq;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ ;
+ if (ds.getAnnotation() != null)
{
- // false if any annotation present from this structure
- if (MCview.PDBfile.isCalcIdForFile(ala.getCalcId(), pdbFile))
+ for (AlignmentAnnotation ala : ds.getAnnotation())
{
- parseSecStr = false;
+ // 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)))
+ {
+ parseSecStr = false;
+ }
}
}
}
}
try
{
- pdb = new MCview.PDBfile(true, parseSecStr, pdbFile, protocol);
-
+ pdb = new MCview.PDBfile(addTempFacAnnot, parseSecStr,
+ secStructServices, pdbFile, protocol);
+ if (pdb.id != null && pdb.id.trim().length() > 0
+ && AppletFormatAdapter.FILE.equals(protocol))
+ {
+ registerPDBFile(pdb.id.trim(), pdbFile);
+ }
} catch (Exception ex)
{
ex.printStackTrace();
boolean first = true;
for (int i = 0; i < pdb.chains.size(); i++)
{
- PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
+ 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],
- ((PDBChain) pdb.chains.elementAt(i)).sequence,
- ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+ pdb.chains.elementAt(i).sequence,
+ pdb.chains.elementAt(i).isNa ? AlignSeq.DNA
: AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
+ maxChain.residues.size() + "\n\n");
PrintStream ps = new PrintStream(System.out)
{
+ @Override
public void print(String x)
{
mappingDetails.append(x);
}
+ @Override
public void println()
{
mappingDetails.append("\n");
+ (maxAlignseq.seq1end + sequence[s].getEnd() - 1));
maxChain.makeExactMapping(maxAlignseq, sequence[s]);
-
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .getMappingFromS1(false);
+ jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping(
+ sqmpping.getMap().getInverse());
maxChain.transferRESNUMFeatures(sequence[s], null);
// allocate enough slots to store the mapping from positions in
index++;
} while (index < maxChain.atoms.size());
- if (mappings == null)
- {
- mappings = new StructureMapping[1];
- }
- else
- {
- StructureMapping[] tmp = new StructureMapping[mappings.length + 1];
- System.arraycopy(mappings, 0, tmp, 0, mappings.length);
- mappings = tmp;
- }
-
if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
{
pdbFile = "INLINE" + pdb.id;
}
-
- mappings[mappings.length - 1] = new StructureMapping(sequence[s],
+ StructureMapping newMapping = new StructureMapping(sequence[s],
pdbFile, pdb.id, maxChainId, mapping,
mappingDetails.toString());
- maxChain.transferResidueAnnotation(mappings[mappings.length - 1]);
+ if (forStructureView)
+ {
+
+ if (mappings == null)
+ {
+ mappings = new StructureMapping[1];
+ }
+ else
+ {
+ StructureMapping[] tmp = new StructureMapping[mappings.length + 1];
+ System.arraycopy(mappings, 0, tmp, 0, mappings.length);
+ mappings = tmp;
+ }
+
+ mappings[mappings.length - 1] = newMapping;
+ }
+ maxChain.transferResidueAnnotation(newMapping, sqmpping);
}
// ///////
{
return;
}
- boolean removeMapping = true;
String[] handlepdbs;
Vector pdbs = new Vector();
for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++]))
listeners.clear();
listeners = null;
}
- if (mappingData != null)
+ if (pdbIdFileName != null)
{
- mappingData.clear();
- mappingData = null;
+ pdbIdFileName.clear();
+ pdbIdFileName = null;
}
if (sel_listeners != null)
{
}
}
+ public void registerPDBEntry(PDBEntry pdbentry)
+ {
+ if (pdbentry.getFile() != null
+ && pdbentry.getFile().trim().length() > 0)
+ {
+ registerPDBFile(pdbentry.getId(), pdbentry.getFile());
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff