import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
-import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
+import jalview.util.Format;
import jalview.util.MessageManager;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Vector;
{
Viewer viewer = null;
- public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, String inFile, String type)
- throws IOException
+ public JmolParser(String inFile, String type) throws IOException
{
super(inFile, type);
}
- public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
- boolean externalSecStr, FileParse fp) throws IOException
+ public JmolParser(FileParse fp) throws IOException
{
super(fp);
}
@Override
public void parse() throws IOException
{
- String dataName = getDataName();
- if (dataName.endsWith(".cif"))
- {
- setDbRefType(DBRefSource.MMCIF);
- }
- else
- {
- setDbRefType(DBRefSource.PDB);
- }
setChains(new Vector<PDBChain>());
Viewer jmolModel = getJmolData();
jmolModel.openReader(getDataName(), getDataName(), getReader());
*/
if (jmolModel.ms.mc > 0)
{
+ // ideally we do this
+ // try
+ // {
+ // setStructureFileType(jmolModel.evalString("show _fileType"));
+ // } catch (Exception q)
+ // {
+ // }
+ // ;
+ // instead, we distinguish .cif from non-.cif by filename
+ setStructureFileType(getDataName().toLowerCase().endsWith(".cif") ? PDBEntry.Type.MMCIF
+ .toString() : "PDB");
+
transformJmolModelToJalview(jmolModel.ms);
}
}
{
try
{
+ /*
+ * params -o (output to sysout) -n (nodisplay) -x (exit when finished)
+ * see http://wiki.jmol.org/index.php/Jmol_Application
+ */
viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
null, "-x -o -n", this);
// ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
List<SequenceI> prot = new ArrayList<SequenceI>();
PDBChain tmpchain;
String pdbId = (String) ms.getInfo(0, "title");
- setId(pdbId);
+
+ if (pdbId == null)
+ {
+ setId(safeName(getDataName()));
+ setPDBIdAvailable(false);
+ }
+ else
+ {
+ setId(pdbId);
+ setPDBIdAvailable(true);
+ }
List<Atom> significantAtoms = convertSignificantAtoms(ms);
for (Atom tmpatom : significantAtoms)
{
tmpchain.atoms.addElement(tmpatom);
} catch (Exception e)
{
- tmpchain = new PDBChain(pdbId, tmpatom.chain);
+ tmpchain = new PDBChain(getId(), tmpatom.chain);
getChains().add(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
makeResidueList();
makeCaBondList();
+ if (getId() == null)
+ {
+ // always use resource name, not the hardwired file
+ // Does the value of ID get used ? Behaviour needs to be
+ // documented and tested
+ setId(getDataName());
+ }
++
for (PDBChain chain : getChains())
{
SequenceI chainseq = postProcessChain(chain);
prot.add(chainseq);
}
- if (StructureViewSettings.isPredictSecondaryStructure())
+ if (StructureImportSettings.isProcessSecondaryStructure())
{
createAnnotation(chainseq, chain, ms.at);
}
private List<Atom> convertSignificantAtoms(ModelSet ms)
{
List<Atom> significantAtoms = new ArrayList<Atom>();
+ HashMap<String, org.jmol.modelset.Atom> chainTerMap = new HashMap<String, org.jmol.modelset.Atom>();
+ org.jmol.modelset.Atom prevAtom = null;
for (org.jmol.modelset.Atom atom : ms.at)
{
if (atom.getAtomName().equalsIgnoreCase("CA")
|| atom.getAtomName().equalsIgnoreCase("P"))
{
+ if (!atomValidated(atom, prevAtom, chainTerMap))
+ {
+ continue;
+ }
Atom curAtom = new Atom(atom.x, atom.y, atom.z);
curAtom.atomIndex = atom.getIndex();
curAtom.chain = atom.getChainIDStr();
- curAtom.insCode = atom.group.getInsertionCode();
+ curAtom.insCode = atom.group.getInsertionCode() == '\000' ? ' '
+ : atom.group.getInsertionCode();
curAtom.name = atom.getAtomName();
curAtom.number = atom.getAtomNumber();
curAtom.resName = atom.getGroup3(true);
curAtom.resNumber = atom.getResno();
curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
.getIndex()] : Float.valueOf(atom.getOccupancy100());
- curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
+ String fmt = new Format("%4i").form(curAtom.resNumber);
+ curAtom.resNumIns = (fmt + curAtom.insCode);
curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
- significantAtoms.add(curAtom);
+ // significantAtoms.add(curAtom);
+ // ignore atoms from subsequent models
+ if (!significantAtoms.contains(curAtom))
+ {
+ significantAtoms.add(curAtom);
+ }
+ prevAtom = atom;
}
}
return significantAtoms;
}
+ private boolean atomValidated(org.jmol.modelset.Atom curAtom,
+ org.jmol.modelset.Atom prevAtom,
+ HashMap<String, org.jmol.modelset.Atom> chainTerMap)
+ {
+ // System.out.println("Atom: " + curAtom.getAtomNumber()
+ // + " Last atom index " + curAtom.group.lastAtomIndex);
+ if (chainTerMap == null || prevAtom == null)
+ {
+ return true;
+ }
+ String curAtomChId = curAtom.getChainIDStr();
+ String prevAtomChId = prevAtom.getChainIDStr();
+ // new chain encoutered
+ if (!prevAtomChId.equals(curAtomChId))
+ {
+ // On chain switch add previous chain termination to xTerMap if not exists
+ if (!chainTerMap.containsKey(prevAtomChId))
+ {
+ chainTerMap.put(prevAtomChId, prevAtom);
+ }
+ // if current atom belongs to an already terminated chain and the resNum
+ // diff < 5 then mark as valid and update termination Atom
+ if (chainTerMap.containsKey(curAtomChId))
+ {
+ if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
+ {
+ return false;
+ }
+ if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+ {
+ chainTerMap.put(curAtomChId, curAtom);
+ return true;
+ }
+ return false;
+ }
+ }
+ // atom with previously terminated chain encountered
+ else if (chainTerMap.containsKey(curAtomChId))
+ {
+ if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
+ {
+ return false;
+ }
+ if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+ {
+ chainTerMap.put(curAtomChId, curAtom);
+ return true;
+ }
+ return false;
+ }
+ // HETATM with resNum jump > 2
+ return !(curAtom.isHetero() && ((curAtom.getResno() - prevAtom
+ .getResno()) > 2));
+ }
+
private void createAnnotation(SequenceI sequence, PDBChain chain,
org.jmol.modelset.Atom[] jmolAtoms)
{
{
try
{
- asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
- secstrcode[p], Float.NaN);
- ssFound = true;
+ asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
+ secstrcode[p], Float.NaN);
+ ssFound = true;
} catch (Exception e)
{
// e.printStackTrace();
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.GraphLine;
import jalview.datamodel.HiddenSequences;
+ import jalview.datamodel.PDBEntry;
+ import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
+ import jalview.structure.StructureSelectionManager;
import java.io.BufferedReader;
+ import java.io.File;
import java.io.FileReader;
+ import java.io.IOException;
import java.io.InputStreamReader;
import java.io.StringReader;
import java.net.URL;
public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
String file, String protocol)
{
+ baseUri = "";
BufferedReader in = null;
try
{
if (protocol.equals(AppletFormatAdapter.FILE))
{
in = new BufferedReader(new FileReader(file));
+ baseUri = new File(file).getParent();
+ if (baseUri == null)
+ {
+ baseUri = "";
+ }
+ else
+ {
+ baseUri += "/";
+ }
}
else if (protocol.equals(AppletFormatAdapter.URL))
{
URL url = new URL(file);
in = new BufferedReader(new InputStreamReader(url.openStream()));
+ String bs = url.toExternalForm();
+ baseUri = bs.substring(0, bs.indexOf(url.getHost())
+ + url.getHost().length());
+ baseUri += url.toURI().getPath();
+ if (baseUri.lastIndexOf("/") > -1)
+ {
+ baseUri = baseUri.substring(0, baseUri.lastIndexOf("/")) + "/";
+ }
}
else if (protocol.equals(AppletFormatAdapter.PASTE))
{
in = new BufferedReader(new StringReader(file));
+ // TODO - support mimencoded PDBs for a paste.. ?
+ baseUri = "";
}
else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
{
if (is != null)
{
in = new BufferedReader(new java.io.InputStreamReader(is));
+ // TODO: this probably doesn't work for classloader - needs a test
+ baseUri = new File("/" + file).getParent() + "/";
}
}
if (in != null)
String lastread = "";
- private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
+ /**
+ * used for resolving absolute references to resources relative to
+ * annotationFile location
+ */
+ String baseUri = "";
+
+ private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE",
+ STRUCTMODEL = "STRUCTMODEL";
public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
BufferedReader in) throws Exception
modified = true;
continue;
}
-
+ else if (token.equalsIgnoreCase(STRUCTMODEL))
+ {
+ boolean failedtoadd = true;
+ // expect
+ // STRUCTMODEL <QUERYID> <TemplateID> <URL to model> <URL to
+ // alignment>
+ if (st.hasMoreTokens()) {
+ refSeq = al.findName(refSeqId = st.nextToken());
+ if (refSeq == null)
+ {
+ System.err.println("Couldn't locate " + refSeqId
+ + " in the alignment for STRUCTMODEL");
+ refSeqId = null;
+ }
+ else
+ {
+ String tempId = st.nextToken();
+ String urlToModel = st.nextToken();
+ String urlToPairwise = st.hasMoreTokens() ? st.nextToken()
+ : "";
+ if (add_structmodel(al, refSeq, tempId, urlToModel,
+ urlToPairwise))
+ {
+ failedtoadd = false;
+ }
+ }
+ }
+ if (failedtoadd)
+ {
+ System.err
+ .println("Need <QueryId> <TemplateId> <URL to Model> [<URL to pairwise alignment>] as tab separated fields after "
+ + STRUCTMODEL);
+ } else {
+ modified = true;
+ }
+ continue;
+ }
// Parse out the annotation row
graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
label = st.nextToken();
return modified;
}
+ /**
+ * resolve a structural model and generate and add an alignment sequence for
+ * it
+ *
+ * @param refSeq2
+ * @param tempId
+ * @param urlToModel
+ * @param urlToPairwise
+ * @return true if model and sequence was added
+ */
+ private boolean add_structmodel(AlignmentI al, SequenceI refSeq2, String tempId,
+ String urlToModel, String urlToPairwise)
+ {
+ String warningMessage = null, modelPath = null, modelProt = null, aliPath = null, aliProt = null;
+ boolean added = false;
+ try {
+ // locate tempId. if it exists, will need to merge, otherwise:
+ SequenceI templateSeq = al.findName(tempId);
+ // 1. load urlToModel
+ modelPath = resolveAbsolute(urlToModel);
+ modelProt = AppletFormatAdapter.checkProtocol(modelPath);
+ // need to transfer to local temp file ?
+ PDBEntry modelpe = new PDBEntry(tempId, null, Type.FILE, modelPath);
+ PDBEntry templpe = new PDBEntry(tempId, null, Type.FILE, modelPath);
+ refSeq2.addPDBId(modelpe);
+ aliPath = resolveAbsolute(urlToPairwise);
+ aliProt = AppletFormatAdapter.checkProtocol(aliPath);
+ // 2. load urlToPairwise
+ AlignmentI pwa = new AppletFormatAdapter().readFile(aliPath, aliProt,
+ "FASTA");
+ SequenceI qPw = null, tPw = null;
+ if (pwa != null)
+ {
+ // resolve query/template sequences in provided alignment
+ qPw = pwa.findName(refSeqId);
+ tPw = pwa.findName(tempId);
+ }
+ if (false)
+ // (qPw != null && tPw != null)
+ {
+ // not yet complete
+ // refalQ vvva--addrvvvtttddd
+ // refalT ---aaaa---sss---ddd
+ // profalQ ---v-v-v-a.-.-a---dd--r--vvvtt--td--dd
+ // profalT ---.-.-.-aa-a-a---..--.--sss..--.d--dd
+ // Pragmatic solution here:
+ // Map templpe onto refalT only where refalT and refalQ are both
+ // non-gaps
+
+ // columns for start..end in refSeq2
+ int[] gapMap = refSeq2.gapMap();
+ // insert gaps in tPw
+ int curi = 0, width = refSeq2.getLength();
+ // TBC
+ }
+ else
+ {
+ // assume 1:1 - so synthesise sequences to use to construct mapping
+ StructureFile pdbf = StructureSelectionManager
+ .getStructureSelectionManager().setMapping(false,
+ new SequenceI[] { refSeq2.getDatasetSequence() },
+ null, modelPath, modelProt);
+ refSeq2.getDatasetSequence().addPDBId(modelpe);
+ if (templateSeq == null && tPw != null)
+ {
+ tPw.createDatasetSequence();
+ tPw.getDatasetSequence().addPDBId(templpe); // needs to set mapping based on model yet...
+ al.addSequence(tPw);
+ added = true;
+ }
+ }
+ // 3. pad/insert gaps in urlToPairwise according to gaps already present in
+ // refSeq2
+ // 4. add padded tempId sequence to alignment
+ // 4. associate urlToModel with refSeq2 based on position map provided by
+ // urlToPairwise
+ // 5. associate urlToModel with tempId based on position map provided by
+ // urlToPairwise
+ // start a thread to load urlToModel and process/annotate sequences.
+ } catch (IOException x)
+ {
+ warningMessage = x.toString();
+ } finally {
+ if (warningMessage !=null)
+ {
+ System.err.println("Warnings whilst processing STRUCTMODEL: "+warningMessage);
+ }
+ return added;
+ }
+ }
+
+ private String resolveAbsolute(String relURI)
+ {
+ if (relURI.indexOf(":/") > -1 || relURI.startsWith("/")
+ || "".equals(baseUri) || relURI.startsWith(baseUri))
+ {
+ return relURI;
+ }
+ return baseUri + relURI;
+ }
+
private void parseHideCols(ColumnSelection colSel, String nextToken)
{
StringTokenizer inval = new StringTokenizer(nextToken, ",");
else if (key.equalsIgnoreCase("consThreshold"))
{
sg.cs.setConservationInc(Integer.parseInt(value));
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null),
- sg.getStartRes(), sg.getEndRes() + 1);
+ Conservation c = new Conservation("Group", 3,
+ sg.getSequences(null), sg.getStartRes(),
+ sg.getEndRes() + 1);
c.calculate();
c.verdict(false, 25); // TODO: refer to conservation percent threshold
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
import jalview.gui.IProgressIndicator;
import jalview.io.AppletFormatAdapter;
import jalview.io.StructureFile;
return setMapping(true, sequence, targetChains, pdbFile, protocol);
}
-
/**
* create sequence structure mappings between each sequence and the given
* pdbFile (retrieved via the given protocol).
*/
synchronized public StructureFile setMapping(boolean forStructureView,
SequenceI[] sequenceArray, String[] targetChainIds,
- String pdbFile,
- String protocol)
+ String pdbFile, String protocol)
{
/*
* There will be better ways of doing this in the future, for now we'll use
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
-
- if (pdbFile != null && isCIFFile(pdbFile))
- {
- pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
- secStructServices, pdbFile, protocol);
- }
- else
- {
- pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
- pdbFile, protocol);
- }
+ pdb = new JmolParser(pdbFile, protocol);
if (pdb.getId() != null && pdb.getId().trim().length() > 0
&& AppletFormatAdapter.FILE.equals(protocol))
{
registerPDBFile(pdb.getId().trim(), pdbFile);
}
+ // if PDBId is unavailable then skip SIFTS mapping execution path
+ isMapUsingSIFTs = pdb.isPPDBIdAvailable();
+
} catch (Exception ex)
{
ex.printStackTrace();
{
boolean infChain = true;
final SequenceI seq = sequenceArray[s];
+ SequenceI ds = seq;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+
if (targetChainIds != null && targetChainIds[s] != null)
{
infChain = false;
}
ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
- if (isMapUsingSIFTs)
+ if (isMapUsingSIFTs && seq.isProtein())
{
setProgressBar(null);
setProgressBar(MessageManager
pdb, maxChain, sqmpping, maxAlignseq);
seqToStrucMapping.add(siftsMapping);
maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
+ // "IEA:SIFTS" ?
maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+
} catch (SiftsException e)
{
// fall back to NW alignment
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
targetChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+ // "IEA:Jalview" ?
+ maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
}
else
try
{
StructureMapping siftsMapping = getStructureMapping(seq,
- pdbFile,
- chain.id, pdb, chain, sqmpping, maxAlignseq);
+ pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
foundSiftsMappings.add(siftsMapping);
} catch (SiftsException e)
{
{
seqToStrucMapping.addAll(foundSiftsMappings);
maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
+ // "IEA:SIFTS" ?
maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
sqmpping);
+ ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
}
else
{
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
maxChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
+ maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+ // "IEA:Jalview" ?
+ maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
}
}
setProgressBar(null);
setProgressBar(MessageManager
.getString("status.obtaining_mapping_with_nw_alignment"));
- seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
- maxChain, pdb, maxAlignseq));
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+ maxChainId, maxChain, pdb, maxAlignseq);
+ seqToStrucMapping.add(nwMapping);
+ ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+
}
if (forStructureView)
return "cif".equalsIgnoreCase(fileExt);
}
+ /**
+ * retrieve a mapping for seq from SIFTs using associated DBRefEntry for
+ * uniprot or PDB
+ *
+ * @param seq
+ * @param pdbFile
+ * @param targetChainId
+ * @param pdb
+ * @param maxChain
+ * @param sqmpping
+ * @param maxAlignseq
+ * @return
+ * @throws SiftsException
+ */
private StructureMapping getStructureMapping(SequenceI seq,
String pdbFile, String targetChainId, StructureFile pdb,
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
AlignSeq maxAlignseq) throws SiftsException
{
- StructureMapping curChainMapping = siftsClient
- .getSiftsStructureMapping(seq, pdbFile, targetChainId);
- try
- {
+ StructureMapping curChainMapping = siftsClient
+ .getSiftsStructureMapping(seq, pdbFile, targetChainId);
+ try
+ {
PDBChain chain = pdb.findChain(targetChainId);
if (chain != null)
{
chain.transferResidueAnnotation(curChainMapping, sqmpping);
}
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- return curChainMapping;
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ return curChainMapping;
}
- private StructureMapping getNWMappings(SequenceI seq,
- String pdbFile,
+ private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
String maxChainId, PDBChain maxChain, StructureFile pdb,
AlignSeq maxAlignseq)
{
return seqmappings;
}
+ public static StructureSelectionManager getStructureSelectionManager()
+ {
+ return instances.values().iterator().next();
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff