/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.FeatureSettings;
+import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
import jalview.util.UrlLink;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.dbsources.das.api.jalviewSourceI;
int refCount = 0;
for (int i = 0; i < sequences.length; i++)
{
- DBRefEntry[] dbref = sequences[i].getDBRef();
+ DBRefEntry[] dbref = sequences[i].getDBRefs();
if (dbref != null)
{
for (int j = 0; j < dbref.length; j++)
{
- if (dbref[j].getSource().equals(
- jalview.datamodel.DBRefSource.UNIPROT))
+ if (dbref[j].getSource().equals(DBRefSource.UNIPROT))
{
refCount++;
break;
reply = JOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
- "Do you want Jalview to find\n"
- + "Uniprot Accession ids for given sequence names?",
- "Find Uniprot Accession Ids",
+ MessageManager
+ .getString("info.you_want_jalview_to_find_uniprot_accessions"),
+ MessageManager
+ .getString("label.find_uniprot_accession_ids"),
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
}
class FetchSeqFeatures implements Runnable
{
+ @Override
public void run()
{
startFetching();
class FetchDBRefs implements Runnable
{
+ @Override
public void run()
{
running = true;
- new DBRefFetcher(sequences, af).fetchDBRefs(true);
+ boolean isNucleotide = af.getViewport().getAlignment().isNucleotide();
+ new DBRefFetcher(sequences, af, null, af.featureSettings,
+ isNucleotide).fetchDBRefs(true);
+
startFetching();
setGuiFetchComplete();
}
startTime = System.currentTimeMillis();
if (af != null)
{
- af.setProgressBar("Fetching DAS Sequence Features", startTime);
+ af.setProgressBar(MessageManager
+ .getString("status.fetching_das_sequence_features"),
+ startTime);
}
if (sourceRegistry == null)
{
{
jalviewSourceI[] sources = sourceRegistry.getSources().toArray(
new jalviewSourceI[0]);
- String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
- "uniprot");
+ String active = Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
StringTokenizer st = new StringTokenizer(active, "\t");
selectedSources = new Vector();
String token;
source));
for (String id : idl)
{
- List<String> qid = Arrays.asList(new String[]
- { id });
+ List<String> qid = Arrays.asList(new String[] { id });
try
{
DasGFFAdapter dga = featuresc.fetchData(source, qid);
} catch (Exception ex)
{
Cache.log
- .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");
- Cache.log.info("Mapping feature from " + f.getBegin()
+ .warn("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");
+ Cache.log.warn("Mapping feature from " + f.getBegin()
+ " to " + f.getEnd() + " in dbref "
+ dbref.getAccessionId() + " in "
+ dbref.getSource());
- Cache.log.info("using das Source " + source);
- Cache.log.info("Exception", ex);
+ Cache.log.warn("using das Source " + source);
+ Cache.log.warn("Exception", ex);
}
if (vf != null)
if (af != null)
{
- af.setProgressBar("No DAS Sources Active", startTime);
+ af.setProgressBar(
+ MessageManager.getString("status.no_das_sources_active"),
+ startTime);
}
if (getFeatSettings() != null)
{
{
if (af != null)
{
- af.setProgressBar("DAS Feature Fetching Cancelled", startTime);
+ af.setProgressBar(MessageManager
+ .getString("status.das_feature_fetching_cancelled"),
+ startTime);
}
cancelled = true;
}
if (!cancelled && af != null)
{
// only update the progress bar if we've completed the fetch normally
- af.setProgressBar("DAS Feature Fetching Complete", startTime);
+ af.setProgressBar(MessageManager
+ .getString("status.das_feature_fetching_complete"), startTime);
}
if (af != null && af.featureSettings != null)
{
- af.featureSettings.setTableData();
+ af.featureSettings.discoverAllFeatureData();
}
if (getFeatSettings() != null)
Object[] nextSequence(jalviewSourceI dasSource, SequenceI seq)
{
if (cancelled)
+ {
return null;
- DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
- seq.getDBRef(), new String[]
- {
+ }
+ DBRefEntry[] uprefs = DBRefUtils.selectRefs(seq.getDBRefs(),
+ new String[] {
// jalview.datamodel.DBRefSource.PDB,
- jalview.datamodel.DBRefSource.UNIPROT,
+ DBRefSource.UNIPROT,
// jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
// sys sources
});
for (COORDINATES csys : dasSource.getVersion().getCOORDINATES())
{
- if (jalview.util.DBRefUtils.isDasCoordinateSystem(
- csys.getAuthority(), uprefs[j]))
+ if (DBRefUtils.isDasCoordinateSystem(csys.getAuthority(),
+ uprefs[j]))
{
debug("Launched fetcher for coordinate system "
+ csys.getAuthority());
qstring.add(uprefs[j].getAccessionId());
}
else
+ {
System.out.println("IGNORE " + csys.getAuthority());
+ }
}
}
}
}
}
- return new Object[]
- { ids, qstring };
+ return new Object[] { ids, qstring };
}
/**
{
for (String note : feat.getNOTE())
{
- desc += (String) note;
+ desc += note;
}
}
git://source.jalview.org / jalview.git / blobdiff