*/
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;
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();
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:"))
{
{
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()];
{
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];
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:"))
{
{
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()];
{
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];
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
|| 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: "
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 "
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
{
// 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())
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())