*/
package jalview.gui;
+import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
.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))
{
if (!en.hasNext() && nextfetch.size() > 0)
boolean rfound = false;
for (int r = 0; r < rs.length; r++)
{
- if (rs[r] != null
- && (found = DBRefUtils.searchRefs(
- rs[r].getDBRefs(), dbr)) != null
- && found.length > 0)
+ if (rs[r] != null)
{
- rfound = true;
- rs[r] = null;
+ found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
+ if (found != null && found.length > 0)
+ {
+ rfound = true;
+ rs[r] = null;
+ }
}
}
if (!rfound)
// Stack results ready for opening in alignment windows
if (aresult != null && aresult.size() > 0)
{
+ FeatureSettingsModelI proxyColourScheme = proxy
+ .getFeatureColourScheme();
+ if (proxyColourScheme != null)
+ {
+ preferredFeatureColours = proxyColourScheme;
+ }
+
AlignmentI ar = null;
if (isAliSource)
{
// process results
while (presult.size() > 0)
{
- parseResult(presult.remove(0), presultTitle.remove(0), null);
+ parseResult(presult.remove(0), presultTitle.remove(0), null,
+ preferredFeatureColours);
}
// only remove visual delay after we finished parsing.
guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
resetDialog();
}
- AlignmentI parseResult(String result, String title)
- {
- String format = new IdentifyFile().identify(result, "Paste");
- AlignmentI sequences = null;
- if (FormatAdapter.isValidFormat(format))
- {
- sequences = null;
- try
- {
- sequences = new FormatAdapter().readFile(result.toString(),
- "Paste", format);
- } catch (Exception ex)
- {
- }
-
- if (sequences != null)
- {
- return parseResult(sequences, title, format);
- }
- }
- else
- {
- showErrorMessage("Error retrieving " + textArea.getText() + " from "
- + database.getSelectedItem());
- }
-
- return null;
- }
-
/**
*
* @return a standard title for any results retrieved using the currently
}
AlignmentI parseResult(AlignmentI al, String title,
- String currentFileFormat)
+ String currentFileFormat,
+ FeatureSettingsModelI preferredFeatureColours)
{
if (al != null && al.getHeight() > 0)
}
}
+
+ if (preferredFeatureColours != null)
+ {
+ af.viewport.applyFeaturesStyle(preferredFeatureColours);
+ }
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);