import jalview.schemes.FeatureColourAdapter;
import jalview.schemes.FeatureSettingsAdapter;
import jalview.util.MapList;
-import jalview.util.StringUtils;
import java.awt.Color;
import java.io.UnsupportedEncodingException;
public AlignmentI getSequenceRecords(String query) throws Exception
{
/*
- * if given a transcript id, look up its gene parent
+ * convert to a non-duplicated list of gene identifiers
*/
- if (isTranscriptIdentifier(query))
+ List<String> geneIds = getGeneIds(query);
+
+ AlignmentI al = null;
+ for (String geneId : geneIds)
{
- query = new EnsemblLookup(getDomain()).getParent(query);
- if (query == null)
+ /*
+ * fetch the gene sequence(s) with features and xrefs
+ */
+ AlignmentI geneAlignment = super.getSequenceRecords(geneId);
+
+ if (geneAlignment.getHeight() == 1)
{
- return null;
+ getTranscripts(geneAlignment, geneId);
+ }
+ if (al == null)
+ {
+ al = geneAlignment;
+ }
+ else
+ {
+ al.append(geneAlignment);
}
}
+ return al;
+ }
- /*
- * if given a gene or other external name, lookup and fetch
- * the corresponding gene for all model organisms
- */
- if (!isGeneIdentifier(query))
+ /**
+ * Converts a query, which may contain one or more gene or transcript
+ * identifiers, into a non-redundant list of gene identifiers.
+ *
+ * @param accessions
+ * @return
+ */
+ List<String> getGeneIds(String accessions)
+ {
+ List<String> geneIds = new ArrayList<String>();
+
+ for (String acc : accessions.split(getAccessionSeparator()))
{
- List<String> geneIds = new EnsemblSymbol(getDomain()).getIds(query);
- if (geneIds.isEmpty())
+ if (isGeneIdentifier(acc))
{
- return null;
+ if (!geneIds.contains(acc))
+ {
+ geneIds.add(acc);
+ }
}
- String theIds = StringUtils.listToDelimitedString(geneIds,
- getAccessionSeparator());
- return getSequenceRecords(theIds);
- }
- /*
- * fetch the gene sequence(s) with features and xrefs
- */
- AlignmentI al = super.getSequenceRecords(query);
+ /*
+ * if given a transcript id, look up its gene parent
+ */
+ else if (isTranscriptIdentifier(acc))
+ {
+ String geneId = new EnsemblLookup(getDomain()).getParent(acc);
+ if (geneId != null && !geneIds.contains(geneId))
+ {
+ geneIds.add(geneId);
+ }
+ }
- /*
- * if we retrieved a single gene, get its transcripts as well
- */
- if (al.getHeight() == 1)
- {
- getTranscripts(al, query);
+ /*
+ * if given a gene or other external name, lookup and fetch
+ * the corresponding gene for all model organisms
+ */
+ else
+ {
+ List<String> ids = new EnsemblSymbol(getDomain()).getIds(acc);
+ for (String geneId : ids)
+ {
+ if (!geneIds.contains(geneId))
+ {
+ geneIds.add(geneId);
+ }
+ }
+ }
}
-
- return al;
+ return geneIds;
}
/**
};
}
- @Override
- public int getMaximumQueryCount()
- {
- return 1;
- }
-
}
// TODO: Refactor to GUI independent code and write tests.
// indicate if successive sources should be merged into one alignment.
boolean addToLast = false;
- ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
- ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
+ List<String> aresultq = new ArrayList<String>();
+ List<String> presultTitle = new ArrayList<String>();
+ List<AlignmentI> presult = new ArrayList<AlignmentI>();
+ List<AlignmentI> aresult = new ArrayList<AlignmentI>();
Iterator<DbSourceProxy> proxies = database.getSelectedSources()
.iterator();
String[] qries;
- List<String> nextfetch = Arrays.asList(qries = textArea.getText()
+ List<String> nextFetch = Arrays.asList(qries = textArea.getText()
.split(";"));
Iterator<String> en = Arrays.asList(new String[0]).iterator();
int nqueries = qries.length;
FeatureSettingsModelI preferredFeatureColours = null;
- while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
+ while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0))
{
- if (!en.hasNext() && nextfetch.size() > 0)
+ if (!en.hasNext() && nextFetch.size() > 0)
{
- en = nextfetch.iterator();
- nqueries = nextfetch.size();
+ en = nextFetch.iterator();
+ nqueries = nextFetch.size();
// save the remaining queries in the original array
- qries = nextfetch.toArray(new String[nqueries]);
- nextfetch = new ArrayList<String>();
+ qries = nextFetch.toArray(new String[nqueries]);
+ nextFetch = new ArrayList<String>();
}
DbSourceProxy proxy = proxies.next();
- boolean isAliSource = false;
try
{
// update status
Integer.valueOf(nqueries).toString(),
proxy.getDbName() }), Thread.currentThread()
.hashCode());
- isAliSource = proxy.isAlignmentSource();
if (proxy.getMaximumQueryCount() == 1)
{
+ /*
+ * proxy only handles one accession id at a time
+ */
while (en.hasNext())
{
- String item = en.next();
- try
+ String acc = en.next();
+ if (!fetchSingleAccession(proxy, acc, aresultq, aresult))
{
- if (aresult != null)
- {
- try
- {
- // give the server a chance to breathe
- Thread.sleep(5);
- } catch (Exception e)
- {
- //
- }
-
- }
-
- AlignmentI indres = null;
- try
- {
- indres = proxy.getSequenceRecords(item);
- } catch (OutOfMemoryError oome)
- {
- new OOMWarning("fetching " + item + " from "
- + proxy.getDbName(), oome, this);
- }
- if (indres != null)
- {
- aresultq.add(item);
- aresult.add(indres);
- }
- else
- {
- nextfetch.add(item);
- }
- } catch (Exception e)
- {
- Cache.log.info(
- "Error retrieving " + item
- + " from " + proxy.getDbName(), e);
- nextfetch.add(item);
+ nextFetch.add(acc);
}
}
}
else
{
- StringBuffer multiacc = new StringBuffer();
- ArrayList<String> tosend = new ArrayList<String>();
- while (en.hasNext())
- {
- String nel = en.next();
- tosend.add(nel);
- multiacc.append(nel);
- if (en.hasNext())
- {
- multiacc.append(proxy.getAccessionSeparator());
- }
- }
- try
- {
- AlignmentI rslt;
- SequenceI[] rs;
- List<String> nores = new ArrayList<String>();
- rslt = proxy.getSequenceRecords(multiacc.toString());
- if (rslt == null || rslt.getHeight() == 0)
- {
- // no results - pass on all queries to next source
- nextfetch.addAll(tosend);
- }
- else
- {
- aresultq.add(multiacc.toString());
- aresult.add(rslt);
-
- rs = rslt.getSequencesArray();
- // search for each query in the dbrefs associated with each
- // sequence
- // returned.
- // ones we do not find will be used to query next source (if any)
- for (String q : tosend)
- {
- DBRefEntry dbr = new DBRefEntry(), found[] = null;
- dbr.setSource(proxy.getDbSource());
- dbr.setVersion(null);
- String accId = proxy.getAccessionIdFromQuery(q);
- dbr.setAccessionId(accId);
- boolean rfound = false;
- for (int r = 0; r < rs.length; r++)
- {
- if (rs[r] != null)
- {
- found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
- if (found != null && found.length > 0)
- {
- rfound = true;
- rs[r] = null;
- }
- }
- }
- if (!rfound)
- {
- nextfetch.add(q);
- }
- }
- }
- } catch (OutOfMemoryError oome)
- {
- new OOMWarning("fetching " + multiacc + " from "
- + database.getSelectedItem(), oome, this);
- }
+ /*
+ * proxy can fetch multiple accessions at one time
+ */
+ fetchMultipleAccessions(proxy, en, aresultq, aresult, nextFetch);
}
-
} catch (Exception e)
{
showErrorMessage("Error retrieving " + textArea.getText()
e.printStackTrace();
} catch (OutOfMemoryError e)
{
- // resets dialog box - so we don't use OOMwarning here.
showErrorMessage("Out of Memory when retrieving "
+ textArea.getText()
+ " from "
+ " from " + database.getSelectedItem());
e.printStackTrace();
}
+
// Stack results ready for opening in alignment windows
if (aresult != null && aresult.size() > 0)
{
}
AlignmentI ar = null;
- if (isAliSource)
+ if (proxy.isAlignmentSource())
{
addToLast = false;
// new window for each result
{
ar.append(aresult.remove(0));
}
- ;
}
addToLast = true;
presult.add(ar);
}
// only remove visual delay after we finished parsing.
guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
- if (nextfetch.size() > 0)
+ if (nextFetch.size() > 0)
{
StringBuffer sb = new StringBuffer();
sb.append("Didn't retrieve the following "
- + (nextfetch.size() == 1 ? "query" : nextfetch.size()
+ + (nextFetch.size() == 1 ? "query" : nextFetch.size()
+ " queries") + ": \n");
int l = sb.length(), lr = 0;
- for (String s : nextfetch)
+ for (String s : nextFetch)
{
if (l != sb.length())
{
}
/**
+ * Tries to fetch one or more accession ids from the database proxy
+ *
+ * @param proxy
+ * @param accessions
+ * the queries to fetch
+ * @param aresultq
+ * a successful queries list to add to
+ * @param aresult
+ * a list of retrieved alignments to add to
+ * @param nextFetch
+ * failed queries are added to this list
+ * @throws Exception
+ */
+ void fetchMultipleAccessions(DbSourceProxy proxy,
+ Iterator<String> accessions, List<String> aresultq,
+ List<AlignmentI> aresult, List<String> nextFetch)
+ throws Exception
+ {
+ StringBuilder multiacc = new StringBuilder();
+ List<String> tosend = new ArrayList<String>();
+ while (accessions.hasNext())
+ {
+ String nel = accessions.next();
+ tosend.add(nel);
+ multiacc.append(nel);
+ if (accessions.hasNext())
+ {
+ multiacc.append(proxy.getAccessionSeparator());
+ }
+ }
+
+ try
+ {
+ String query = multiacc.toString();
+ AlignmentI rslt = proxy.getSequenceRecords(query);
+ if (rslt == null || rslt.getHeight() == 0)
+ {
+ // no results - pass on all queries to next source
+ nextFetch.addAll(tosend);
+ }
+ else
+ {
+ aresultq.add(query);
+ aresult.add(rslt);
+ if (tosend.size() > 1)
+ {
+ checkResultForQueries(rslt, tosend, nextFetch, proxy);
+ }
+ }
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + multiacc + " from "
+ + database.getSelectedItem(), oome, this);
+ }
+ }
+
+ /**
+ * Query for a single accession id via the database proxy
+ *
+ * @param proxy
+ * @param accession
+ * @param aresultq
+ * a list of successful queries to add to
+ * @param aresult
+ * a list of retrieved alignments to add to
+ * @return true if the fetch was successful, else false
+ */
+ boolean fetchSingleAccession(DbSourceProxy proxy, String accession,
+ List<String> aresultq, List<AlignmentI> aresult)
+ {
+ boolean success = false;
+ try
+ {
+ if (aresult != null)
+ {
+ try
+ {
+ // give the server a chance to breathe
+ Thread.sleep(5);
+ } catch (Exception e)
+ {
+ //
+ }
+ }
+
+ AlignmentI indres = null;
+ try
+ {
+ indres = proxy.getSequenceRecords(accession);
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + accession + " from "
+ + proxy.getDbName(), oome, this);
+ }
+ if (indres != null)
+ {
+ aresultq.add(accession);
+ aresult.add(indres);
+ success = true;
+ }
+ } catch (Exception e)
+ {
+ Cache.log.info(
+ "Error retrieving " + accession
+ + " from " + proxy.getDbName(), e);
+ } finally
+ {
+ return success;
+ }
+ }
+
+ /**
+ * Checks which of the queries were successfully retrieved by searching the
+ * DBRefs of the retrieved sequences for a match. Any not found are added to
+ * the 'nextFetch' list.
+ *
+ * @param rslt
+ * @param queries
+ * @param nextFetch
+ * @param proxy
+ */
+ void checkResultForQueries(AlignmentI rslt, List<String> queries,
+ List<String> nextFetch, DbSourceProxy proxy)
+ {
+ SequenceI[] rs = rslt.getSequencesArray();
+
+ for (String q : queries)
+ {
+ DBRefEntry[] found = null;
+ DBRefEntry dbr = new DBRefEntry();
+ dbr.setSource(proxy.getDbSource());
+ dbr.setVersion(null);
+ String accId = proxy.getAccessionIdFromQuery(q);
+ dbr.setAccessionId(accId);
+ boolean rfound = false;
+ for (int r = 0; r < rs.length; r++)
+ {
+ if (rs[r] != null)
+ {
+ found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
+ if (found != null && found.length > 0)
+ {
+ rfound = true;
+ break;
+ }
+ }
+ }
+ if (!rfound)
+ {
+ nextFetch.add(q);
+ }
+ }
+ }
+
+ /**
*
* @return a standard title for any results retrieved using the currently
* selected source and settings
git://source.jalview.org / jalview.git / commitdiff