X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=bf9693795c6b93ddbd83a04dbf0a2ee3bc89e8a5;hb=8edebdd9789b2d93fb8f9db24b8be2c1e6317690;hp=caf5b5e5209a5a2b8d191864dcc28e2aa287a757;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java index caf5b5e..bf96937 100644 --- a/src/jalview/ws/SequenceFetcher.java +++ b/src/jalview/ws/SequenceFetcher.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,11 +20,24 @@ */ package jalview.ws; +import jalview.analysis.CrossRef; +import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefSource; import jalview.datamodel.SequenceI; +import jalview.util.QuickSort; +import jalview.ws.dbsources.EmblCdsSouce; +import jalview.ws.dbsources.EmblSource; +import jalview.ws.dbsources.Pdb; +import jalview.ws.dbsources.PfamFull; +import jalview.ws.dbsources.PfamSeed; +import jalview.ws.dbsources.RfamFull; +import jalview.ws.dbsources.RfamSeed; +import jalview.ws.dbsources.Uniprot; +import jalview.ws.dbsources.UnprotName; import jalview.ws.dbsources.das.api.jalviewSourceI; +import jalview.ws.dbsources.das.datamodel.DasSequenceSource; import jalview.ws.seqfetcher.ASequenceFetcher; import jalview.ws.seqfetcher.DbSourceProxy; @@ -55,18 +68,16 @@ public class SequenceFetcher extends ASequenceFetcher public SequenceFetcher(boolean addDas) { - addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class); - addDBRefSourceImpl(jalview.ws.dbsources.EmblCdsSouce.class); - addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class); - addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class); - addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class); - addDBRefSourceImpl(jalview.ws.dbsources.PfamFull.class); - addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed - // alignment is - // 'default' for - // PFAM - addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class); - addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class); + addDBRefSourceImpl(EmblSource.class); + addDBRefSourceImpl(EmblCdsSouce.class); + addDBRefSourceImpl(Uniprot.class); + addDBRefSourceImpl(UnprotName.class); + addDBRefSourceImpl(Pdb.class); + addDBRefSourceImpl(PfamFull.class); + addDBRefSourceImpl(PfamSeed.class); + // ensures Seed alignment is 'default' for PFAM + addDBRefSourceImpl(RfamFull.class); + addDBRefSourceImpl(RfamSeed.class); if (addDas) { registerDasSequenceSources(); @@ -96,7 +107,7 @@ public class SequenceFetcher extends ASequenceFetcher else { nm = dbs.getDbName(); - if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource) + if (getSourceProxy(srcs[i]) instanceof DasSequenceSource) { if (nm.startsWith("das:")) { @@ -126,7 +137,7 @@ public class SequenceFetcher extends ASequenceFetcher { tosort[j] = tosort[j].toLowerCase(); } - jalview.util.QuickSort.sort(tosort, sorted); + QuickSort.sort(tosort, sorted); // construct array with all sources listed srcs = new String[sorted.length + dassrc.size()]; @@ -143,7 +154,7 @@ public class SequenceFetcher extends ASequenceFetcher { tosort[j] = tosort[j].toLowerCase(); } - jalview.util.QuickSort.sort(tosort, sorted); + QuickSort.sort(tosort, sorted); for (int j = sorted.length - 1; j >= 0; j--, i++) { srcs[i] = sorted[j]; @@ -163,7 +174,7 @@ public class SequenceFetcher extends ASequenceFetcher for (DbSourceProxy dbs : getSourceProxy(srcs[i])) { String nm = dbs.getDbName(); - if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource) + if (getSourceProxy(srcs[i]) instanceof DasSequenceSource) { if (nm.startsWith("das:")) { @@ -186,7 +197,7 @@ public class SequenceFetcher extends ASequenceFetcher { tosort[j] = ((String[]) sorted[j])[1]; } - jalview.util.QuickSort.sort(tosort, sorted); + QuickSort.sort(tosort, sorted); int i = 0; // construct array with all sources listed srcs = new String[sorted.length + dassrc.size()]; @@ -203,7 +214,7 @@ public class SequenceFetcher extends ASequenceFetcher { tosort[j] = ((String[]) sorted[j])[1]; } - jalview.util.QuickSort.sort(tosort, sorted); + QuickSort.sort(tosort, sorted); for (int j = sorted.length - 1; j >= 0; j--, i++) { srcs[i] = ((String[]) sorted[j])[0]; @@ -285,7 +296,9 @@ public class SequenceFetcher extends ASequenceFetcher String db = dbSources[dbsource]; // skip me if (db.equals(DBRefSource.PDB)) + { continue; + } for (DbSourceProxy sp : sfetcher.getSourceProxy(db)) { System.out.println("Source: " + sp.getDbName() + " (" + db @@ -304,8 +317,8 @@ public class SequenceFetcher extends ASequenceFetcher || sp.getDbSourceProperties().containsKey( DBRefSource.CODINGSEQDB); // try and find products - String types[] = jalview.analysis.CrossRef - .findSequenceXrefTypes(dna, al.getSequencesArray()); + String types[] = CrossRef.findSequenceXrefTypes(dna, + al.getSequencesArray()); if (types != null) { System.out.println("Xref Types for: " @@ -313,7 +326,7 @@ public class SequenceFetcher extends ASequenceFetcher for (int t = 0; t < types.length; t++) { System.out.println("Type: " + types[t]); - SequenceI[] prod = jalview.analysis.CrossRef + SequenceI[] prod = CrossRef .findXrefSequences(al.getSequencesArray(), dna, types[t]).getSequencesArray(); System.out.println("Found " @@ -348,9 +361,13 @@ public class SequenceFetcher extends ASequenceFetcher System.out.println("ERROR:No alignment retrieved."); StringBuffer raw = sp.getRawRecords(); if (raw != null) + { System.out.println(raw.toString()); + } else + { System.out.println("ERROR:No Raw results."); + } } else { @@ -395,7 +412,8 @@ public class SequenceFetcher extends ASequenceFetcher // have a bash at finding the products amongst all the retrieved // sequences. SequenceI[] seqs = al.getSequencesArray(); - Alignment prodal = jalview.analysis.CrossRef.findXrefSequences( + Alignment prodal = CrossRef + .findXrefSequences( seqs, dna, null, ds); System.out.println("Found " + ((prodal == null) ? "no" : "" + prodal.getHeight()) @@ -434,8 +452,8 @@ public class SequenceFetcher extends ASequenceFetcher public void registerDasSequenceSources() { // TODO: define a context as a registry provider (either desktop, - // jalview.bin.cache, or something else). - for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry() + // Cache, or something else). + for (jalviewSourceI source : Cache.getDasSourceRegistry() .getSources()) { if (source.isSequenceSource())