X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=10a2b282ddaefeefa447880c2f494ede691cf325;hb=4b2392caa53f1de3400e7916d1d9c7b815d446f4;hp=37946b1f38d2a104d286e1b867d1b3ffb74629fa;hpb=45a15211723195c363f1798dd9f0907ea6c28f08;p=jalview.git diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java index 37946b1..10a2b28 100644 --- a/src/jalview/ws/SequenceFetcher.java +++ b/src/jalview/ws/SequenceFetcher.java @@ -20,156 +20,116 @@ */ package jalview.ws; +import jalview.bin.ApplicationSingletonProvider; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; +import jalview.datamodel.DBRefSource; import jalview.ext.ensembl.EnsemblGene; -import jalview.ext.ensembl.EnsemblGenomes; -import jalview.ws.dbsources.EmblCdsSource; -import jalview.ws.dbsources.EmblSource; -import jalview.ws.dbsources.Pdb; -import jalview.ws.dbsources.PfamFull; -import jalview.ws.dbsources.PfamSeed; -import jalview.ws.dbsources.RfamSeed; import jalview.ws.dbsources.Uniprot; -import jalview.ws.dbsources.das.api.jalviewSourceI; import jalview.ws.seqfetcher.ASequenceFetcher; import jalview.ws.seqfetcher.DbSourceProxy; import java.util.ArrayList; +import java.util.Collections; import java.util.List; /** - * This implements the run-time discovery of sequence database clients. + * Thread safe construction of database proxies. This implements the run-time + * discovery of sequence database clients. * + * TODO: extend to a configurable database plugin mechanism where classes are + * instantiated by reflection and queried for their DbRefSource and version + * association. */ -public class SequenceFetcher extends ASequenceFetcher +public class SequenceFetcher extends ASequenceFetcher implements ApplicationSingletonI { + /* + * set a mock fetcher here for testing only - reset to null afterwards + */ + private static SequenceFetcher mockFetcher; + /** - * Thread safe construction of database proxies TODO: extend to a configurable - * database plugin mechanism where classes are instantiated by reflection and - * queried for their DbRefSource and version association. + * Returns a new SequenceFetcher singleton, or a mock object if one has been + * set. * + * @return */ - public SequenceFetcher() + public static SequenceFetcher getInstance() { - this(true); + return mockFetcher != null ? mockFetcher + : (SequenceFetcher) ApplicationSingletonProvider + .getInstance(SequenceFetcher.class); } - public SequenceFetcher(boolean addDas) + /** + * Set the instance object to use (intended for unit testing with mock + * objects). + * + * Be sure to reset to null in the tearDown method of any tests! + * + * @param sf + */ + public static void setSequenceFetcher(SequenceFetcher sf) { - addDBRefSourceImpl(EnsemblGene.class); - addDBRefSourceImpl(EnsemblGenomes.class); - addDBRefSourceImpl(EmblSource.class); - addDBRefSourceImpl(EmblCdsSource.class); - addDBRefSourceImpl(Uniprot.class); - addDBRefSourceImpl(Pdb.class); - addDBRefSourceImpl(PfamFull.class); - addDBRefSourceImpl(PfamSeed.class); - addDBRefSourceImpl(RfamSeed.class); - - if (addDas) - { - registerDasSequenceSources(); - } + mockFetcher = sf; } /** - * return an ordered list of database sources where non-das database classes - * appear before das database classes + * + * This public constructor is only is for use by testng to anonymously + * subclass SequenceFetcher. + * + * */ - public String[] getOrderedSupportedSources() + public SequenceFetcher() { - String[] srcs = this.getSupportedDb(); - ArrayList dassrc = new ArrayList(), nondas = new ArrayList(); - for (int i = 0; i < srcs.length; i++) - { - boolean das = false, skip = false; - String nm; - for (DbSourceProxy dbs : getSourceProxy(srcs[i])) - { - // Skip the alignment databases for the moment - they're not useful for - // verifying a single sequence against its reference source - if (dbs.isAlignmentSource()) - { - skip = true; - } - else - { - nm = dbs.getDbName(); - if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource) - { - if (nm.startsWith("das:")) - { - nm = nm.substring(4); - das = true; - } - break; - } - } - } - if (skip) - { - continue; - } - if (das) - { - dassrc.add(srcs[i]); - } - else - { - nondas.add(srcs[i]); - } - } - String[] tosort = nondas.toArray(new String[0]), sorted = nondas - .toArray(new String[0]); - for (int j = 0, jSize = sorted.length; j < jSize; j++) - { - tosort[j] = tosort[j].toLowerCase(); - } - jalview.util.QuickSort.sort(tosort, sorted); - // construct array with all sources listed - - srcs = new String[sorted.length + dassrc.size()]; - int i = 0; - for (int j = sorted.length - 1; j >= 0; j--, i++) - { - srcs[i] = sorted[j]; - sorted[j] = null; - } + addAllDatabases(); + } - sorted = dassrc.toArray(new String[0]); - tosort = dassrc.toArray(new String[0]); - for (int j = 0, jSize = sorted.length; j < jSize; j++) - { - tosort[j] = tosort[j].toLowerCase(); - } - jalview.util.QuickSort.sort(tosort, sorted); - for (int j = sorted.length - 1; j >= 0; j--, i++) - { - srcs[i] = sorted[j]; - } - return srcs; + public void addAllDatabases() + { + addDBRefSourceImpl(EnsemblGene.class); // includes EnsemblGenomes.class + addDBRefSourceImpl(Uniprot.class); // includes UniprotName.class + // addDBRefSourceImpl(EmblSource.class); + // addDBRefSourceImpl(EmblCdsSource.class); + // addDBRefSourceImpl(Pdb.class); + // addDBRefSourceImpl(PfamFull.class); + // addDBRefSourceImpl(PfamSeed.class); + // addDBRefSourceImpl(RfamSeed.class); + addDBRefSourceImpl(DBRefSource.EMBL, + "jalview.ws.dbsources.EmblSource"); + addDBRefSourceImpl(DBRefSource.EMBLCDS, + "jalview.ws.dbsources.EmblCdsSource"); + addDBRefSourceImpl(DBRefSource.PDB, "jalview.ws.dbsources.Pdb"); + addDBRefSourceImpl(DBRefSource.PFAM_FULL, + "jalview.ws.dbsources.PfamFull"); + addDBRefSourceImpl(DBRefSource.PFAM_SEED, + "jalview.ws.dbsources.PfamSeed"); + addDBRefSourceImpl(DBRefSource.RFAM_SEED, + "jalview.ws.dbsources.RfamSeed"); } /** - * query the currently defined DAS source registry for sequence sources and - * add a DasSequenceSource instance for each source to the SequenceFetcher - * source list. + * return an ordered list of database sources excluding alignment only + * databases */ - public void registerDasSequenceSources() + public String[] getNonAlignmentSources() { - // TODO: define a context as a registry provider (either desktop, - // jalview.bin.cache, or something else). - for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry() - .getSources()) + String[] srcs = this.getSupportedDb(); + List src = new ArrayList<>(); + outer: for (int i = 0; i < srcs.length; i++) { - if (source.isSequenceSource()) + for (DbSourceProxy dbs : getSourceProxy(srcs[i])) { - List dassources = source.getSequenceSourceProxies(); - for (DbSourceProxy seqsrc : dassources) + // Skip the alignment databases for the moment - they're not useful for + // verifying a single sequence against its reference source + if (dbs.isAlignmentSource()) { - addDbRefSourceImpl(seqsrc); + continue outer; } } + src.add(srcs[i]); } + Collections.sort(src, String.CASE_INSENSITIVE_ORDER); + return src.toArray(new String[src.size()]); } - }