package jalview.ws;\r
\r
import jalview.analysis.AlignSeq;\r
+import jalview.bin.Cache;\r
import jalview.datamodel.AlignmentI;\r
import jalview.datamodel.DBRefEntry;\r
import jalview.datamodel.DBRefSource;\r
StringBuffer sbuffer = new StringBuffer();\r
\r
boolean running = false;\r
+\r
/**\r
* picr client instance\r
*/\r
\r
SequenceFetcher sfetcher;\r
\r
+ private SequenceI[] alseqs;\r
+\r
public DBRefFetcher()\r
{\r
}\r
\r
/**\r
- * Creates a new SequenceFeatureFetcher object and fetches from the\r
- * currently selected set of databases.\r
+ * Creates a new SequenceFeatureFetcher object and fetches from the currently\r
+ * selected set of databases.\r
* \r
* @param seqs\r
- * fetch references for these sequences\r
+ * fetch references for these sequences\r
* @param af\r
- * the parent alignframe for progress bar monitoring.\r
+ * the parent alignframe for progress bar monitoring.\r
*/\r
public DBRefFetcher(SequenceI[] seqs, AlignFrame af)\r
{\r
this(seqs, af, null);\r
}\r
+\r
/**\r
- * Creates a new SequenceFeatureFetcher object and fetches from the\r
- * currently selected set of databases.\r
+ * Creates a new SequenceFeatureFetcher object and fetches from the currently\r
+ * selected set of databases.\r
* \r
* @param seqs\r
- * fetch references for these sequences\r
+ * fetch references for these sequences\r
* @param af\r
- * the parent alignframe for progress bar monitoring.\r
- * @param sources array of database source strings to query references from\r
+ * the parent alignframe for progress bar monitoring.\r
+ * @param sources\r
+ * array of database source strings to query references from\r
*/\r
public DBRefFetcher(SequenceI[] seqs, AlignFrame af, String[] sources)\r
{\r
this.af = af;\r
+ alseqs = new SequenceI[seqs.length];\r
SequenceI[] ds = new SequenceI[seqs.length];\r
for (int i = 0; i < seqs.length; i++)\r
{\r
+ alseqs[i] = seqs[i];\r
if (seqs[i].getDatasetSequence() != null)\r
ds[i] = seqs[i].getDatasetSequence();\r
else\r
this.dataset = ds;\r
// TODO Jalview 2.5 lots of this code should be in the gui package!\r
sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);\r
- if (sources==null)\r
+ if (sources == null)\r
{\r
// af.featureSettings_actionPerformed(null);\r
- String[] defdb=null,otherdb = sfetcher.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
- Vector selsources = new Vector(), dasselsrc= (af.featureSettings!=null) ? af.featureSettings.getSelectedSources()\r
+ String[] defdb = null, otherdb = sfetcher\r
+ .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
+ Vector selsources = new Vector(), dasselsrc = (af.featureSettings != null) ? af.featureSettings\r
+ .getSelectedSources()\r
: new jalview.gui.DasSourceBrowser().getSelectedSources();\r
Enumeration en = dasselsrc.elements();\r
while (en.hasMoreElements())\r
selsources.addElement(src.getNickname());\r
}\r
int osel = 0;\r
- for (int o=0;otherdb!=null && o<otherdb.length;o++)\r
+ for (int o = 0; otherdb != null && o < otherdb.length; o++)\r
{\r
if (!selsources.contains(otherdb[o]))\r
{\r
otherdb[o] = null;\r
- } else {\r
+ }\r
+ else\r
+ {\r
osel++;\r
}\r
}\r
{\r
defdb = DBRefSource.PROTEINDBS;\r
}\r
- // append the selected sequence sources to the default dbs \r
- dbSources = new String[defdb.length+osel];\r
+ // append the selected sequence sources to the default dbs\r
+ dbSources = new String[defdb.length + osel];\r
System.arraycopy(defdb, 0, dbSources, 0, defdb.length);\r
- for (int o=0,op=defdb.length; otherdb!=null && o<otherdb.length; o++)\r
+ for (int o = 0, op = defdb.length; otherdb != null\r
+ && o < otherdb.length; o++)\r
{\r
- if (otherdb[o]!=null)\r
+ if (otherdb[o] != null)\r
{\r
dbSources[op++] = otherdb[o];\r
}\r
}\r
- } else {\r
- // we assume the caller knows what they're doing and ensured that all the db source names are valid\r
+ }\r
+ else\r
+ {\r
+ // we assume the caller knows what they're doing and ensured that all the\r
+ // db source names are valid\r
dbSources = sources;\r
}\r
}\r
+\r
/**\r
- * retrieve all the das sequence sources and add them to the list of db sources to retrieve from \r
+ * retrieve all the das sequence sources and add them to the list of db\r
+ * sources to retrieve from\r
*/\r
public void appendAllDasSources()\r
{\r
if (dbSources == null)\r
{\r
- dbSources = new String[] {};\r
+ dbSources = new String[]\r
+ {};\r
}\r
// append additional sources\r
- String[] otherdb = sfetcher.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
- if (otherdb!=null && otherdb.length>0)\r
+ String[] otherdb = sfetcher\r
+ .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
+ if (otherdb != null && otherdb.length > 0)\r
{\r
- String[] newsrc = new String[dbSources.length+otherdb.length];\r
- System.arraycopy(dbSources, 0, newsrc,0,dbSources.length);\r
- System.arraycopy(otherdb, 0, newsrc,dbSources.length, otherdb.length);\r
+ String[] newsrc = new String[dbSources.length + otherdb.length];\r
+ System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);\r
+ System\r
+ .arraycopy(otherdb, 0, newsrc, dbSources.length,\r
+ otherdb.length);\r
dbSources = newsrc;\r
}\r
}\r
+\r
/**\r
* start the fetcher thread\r
* \r
* @param waitTillFinished\r
- * true to block until the fetcher has finished\r
+ * true to block until the fetcher has finished\r
*/\r
public void fetchDBRefs(boolean waitTillFinished)\r
{\r
* could be either seq name or dbref id\r
* \r
* @param seq\r
- * SequenceI\r
+ * SequenceI\r
* @param key\r
- * String\r
+ * String\r
*/\r
void addSeqId(SequenceI seq, String key)\r
{\r
running = true;\r
long startTime = System.currentTimeMillis();\r
af.setProgressBar("Fetching db refs", startTime);\r
- try {\r
- picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator().getAccessionMapperPort(); \r
+ try\r
+ {\r
+ if (Cache.getDefault("DBREFFETCH_USEPICR", false))\r
+ {\r
+ picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator()\r
+ .getAccessionMapperPort();\r
+ }\r
} catch (Exception e)\r
{\r
System.err.println("Couldn't locate PICR service instance.\n");\r
{\r
// Still queries to make for current seqIndex\r
StringBuffer queryString = new StringBuffer("");\r
- int numq=0,nqSize = (maxqlen > queries.size()) ? queries.size()\r
- : maxqlen;\r
- \r
- while (queries.size()>0 && numq < nqSize)\r
+ int numq = 0, nqSize = (maxqlen > queries.size()) ? queries\r
+ .size() : maxqlen;\r
+\r
+ while (queries.size() > 0 && numq < nqSize)\r
{\r
String query = (String) queries.elementAt(0);\r
if (dbsource.isValidReference(query))\r
{\r
if (jalview.bin.Cache.log.isDebugEnabled())\r
{\r
- jalview.bin.Cache.log.debug("Querying "+dbsource.getDbName()+" with : '"+queryString.toString()+"'");\r
+ jalview.bin.Cache.log.debug("Querying "\r
+ + dbsource.getDbName() + " with : '"\r
+ + queryString.toString() + "'");\r
}\r
retrieved = dbsource.getSequenceRecords(queryString.toString());\r
} catch (Exception ex)\r
{ dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT\r
// });\r
// check for existing dbrefs to use\r
- if (uprefs != null && uprefs.length>0)\r
+ if (uprefs != null && uprefs.length > 0)\r
{\r
for (int j = 0; j < uprefs.length; j++)\r
{\r
{\r
String token = st.nextToken();\r
UPEntry[] presp = null;\r
- try {\r
- presp=picrClient.getUPIForAccession(token, null, picrClient.getMappedDatabaseNames(), null, true);\r
- } catch (Exception e) {\r
- System.err.println("Exception with Picr for '"+token+"'\n");\r
- e.printStackTrace();\r
+ if (picrClient != null)\r
+ {\r
+ // resolve the string against PICR to recover valid IDs\r
+ try\r
+ {\r
+ presp = picrClient\r
+ .getUPIForAccession(token, null, picrClient\r
+ .getMappedDatabaseNames(), null, true);\r
+ } catch (Exception e)\r
+ {\r
+ System.err.println("Exception with Picr for '" + token\r
+ + "'\n");\r
+ e.printStackTrace();\r
+ }\r
}\r
- if (presp!=null && presp.length>0)\r
+ if (presp != null && presp.length > 0)\r
{\r
- for (int id=0;id<presp.length; id++)\r
+ for (int id = 0; id < presp.length; id++)\r
{\r
- // construct sequences from response if sequences are present, and do a transferReferences\r
+ // construct sequences from response if sequences are\r
+ // present, and do a transferReferences\r
// otherwise transfer non sequence x-references directly.\r
}\r
- System.out.println("Validated ID against PICR... (for what its worth):"+token);\r
+ System.out\r
+ .println("Validated ID against PICR... (for what its worth):"\r
+ + token);\r
addSeqId(sequence, token);\r
queries.addElement(token.toUpperCase());\r
- } else {\r
- //if ()\r
- //System.out.println("Not querying source with token="+token+"\n");\r
+ }\r
+ else\r
+ {\r
+ // if ()\r
+ // System.out.println("Not querying source with token="+token+"\n");\r
addSeqId(sequence, token);\r
queries.addElement(token.toUpperCase());\r
}\r
AlignmentI retrievedAl) // File\r
// file)\r
{\r
-\r
if (retrievedAl == null || retrievedAl.getHeight() == 0)\r
{\r
return;\r
}\r
- SequenceI[] retrieved = recoverDbSequences(retrievedAl.getSequencesArray());\r
+ SequenceI[] retrieved = recoverDbSequences(retrievedAl\r
+ .getSequencesArray());\r
SequenceI sequence = null;\r
+ boolean transferred = false;\r
+ StringBuffer messages = new StringBuffer();\r
\r
// Vector entries = new Uniprot().getUniprotEntries(file);\r
\r
absStart = nonGapped.indexOf(entrySeq);\r
if (absStart == -1)\r
{ // verification failed.\r
- sbuffer.append(sequence.getName()\r
+ messages.append(sequence.getName()\r
+ " SEQUENCE NOT %100 MATCH \n");\r
continue;\r
}\r
-\r
+ transferred = true;\r
sbuffer.append(sequence.getName() + " HAS " + absStart\r
+ " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n");\r
//\r
}\r
else\r
{\r
+ transferred = true;\r
// update start and end of local sequence to place it in entry's\r
// reference frame.\r
// apply identity map map from whole of local sequence to matching\r
// absStart+sequence.getStart()+entrySeq.length()-1},\r
// new int[] { entry.getStart(), entry.getEnd() }, 1, 1);\r
// relocate local features for updated start\r
- if (updateRefFrame && sequence.getSequenceFeatures() != null)\r
- {\r
+ if (updateRefFrame) {\r
+ if (sequence.getSequenceFeatures() != null)\r
+ {\r
SequenceFeature[] sf = sequence.getSequenceFeatures();\r
int start = sequence.getStart();\r
int end = sequence.getEnd();\r
sf[sfi].setEnd(sf[sfi].getEnd() + startShift);\r
}\r
}\r
+ }\r
}\r
}\r
\r
// finally, update local sequence reference frame if we're allowed\r
sequence.setStart(absStart);\r
sequence.setEnd(absEnd);\r
+ // search for alignment sequences to update coordinate frame for\r
+ for (int alsq = 0; alsq<alseqs.length; alsq++)\r
+ {\r
+ if (alseqs[alsq].getDatasetSequence()==sequence)\r
+ {\r
+ String ngAlsq = AlignSeq.extractGaps("-. ",\r
+ alseqs[alsq].getSequenceAsString()).toUpperCase();\r
+ int oldstrt = alseqs[alsq].getStart();\r
+ alseqs[alsq].setStart(sequence.getSequenceAsString().toUpperCase().indexOf(ngAlsq)+sequence.getStart());\r
+ if (oldstrt != alseqs[alsq].getStart()) {\r
+ alseqs[alsq].setEnd(ngAlsq.length()+alseqs[alsq].getStart()-1);\r
+ }\r
+ }\r
+ }\r
+ // TODO: search for all other references to this dataset sequence, and update start/end\r
+ // TODO: update all AlCodonMappings which involve this alignment sequence (e.g. Q30167 cdna translation from exon2 product (vamsas demo)\r
}\r
// and remove it from the rest\r
// TODO: decide if we should remove annotated sequence from set\r
sdataset.remove(sequence);\r
- // TODO: should we make a note of sequences that have received new DB ids, so we can query all enabled DAS servers for them ?\r
+ // TODO: should we make a note of sequences that have received new DB\r
+ // ids, so we can query all enabled DAS servers for them ?\r
}\r
}\r
+ if (!transferred)\r
+ {\r
+ // report the ID/sequence mismatches\r
+ sbuffer.append(messages);\r
+ }\r
}\r
\r
/**\r
* loop thru and collect additional sequences in Map.\r
+ * \r
* @param sequencesArray\r
* @return\r
*/\r
private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)\r
{\r
Vector nseq = new Vector();\r
- for (int i=0;sequencesArray!=null && i<sequencesArray.length;i++)\r
+ for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++)\r
{\r
nseq.addElement(sequencesArray[i]);\r
DBRefEntry dbr[] = sequencesArray[i].getDBRef();\r
jalview.datamodel.Mapping map = null;\r
- for (int r=0;(dbr!=null) && r<dbr.length; r++) {\r
- if ((map=dbr[r].getMap())!=null)\r
+ for (int r = 0; (dbr != null) && r < dbr.length; r++)\r
+ {\r
+ if ((map = dbr[r].getMap()) != null)\r
{\r
- if (!nseq.contains(map.getTo()))\r
+ if (map.getTo() != null && !nseq.contains(map.getTo()))\r
{\r
nseq.addElement(map.getTo());\r
}\r
}\r
}\r
}\r
- if (nseq.size()>0) {\r
+ if (nseq.size() > 0)\r
+ {\r
sequencesArray = new SequenceI[nseq.size()];\r
nseq.toArray(sequencesArray);\r
}\r
git://source.jalview.org / jalview.git / blobdiff