import jalview.datamodel.SequenceI;
import jalview.fts.service.pdb.PDBFTSPanel;
import jalview.fts.service.uniprot.UniprotFTSPanel;
+import jalview.io.FileFormatI;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import java.awt.event.KeyEvent;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collections;
import java.util.Iterator;
import java.util.List;
private static Thread initingThread = null;
- int debounceTrap = 0;
-
public JTextArea getTextArea()
{
return textArea;
if (sfetch == null
|| dasRegistry != Cache.getDasSourceRegistry()
|| lastDasSourceRegistry != (Cache.getDasSourceRegistry()
- .getDasRegistryURL() + Cache
- .getDasSourceRegistry().getLocalSourceString())
- .hashCode())
+ .getDasRegistryURL() + Cache.getDasSourceRegistry()
+ .getLocalSourceString()).hashCode())
{
_initingFetcher = true;
initingThread = Thread.currentThread();
private IProgressIndicator progressIndicator;
+ private volatile boolean _isConstructing = false;
+
+ private List<AlignFrame> newAlframes = null;
+
public SequenceFetcher(IProgressIndicator guiIndic)
{
+ this(guiIndic, null, null);
+ }
+
+ public SequenceFetcher(IProgressIndicator guiIndic,
+ final String selectedDb, final String queryString)
+ {
+ this._isConstructing = true;
this.progressIndicator = guiIndic;
final SequenceFetcher us = this;
// launch initialiser thread
{
if (getSequenceFetcherSingleton(progressIndicator) != null)
{
- us.initGui(progressIndicator);
+ us.initGui(progressIndicator, selectedDb, queryString);
+ us._isConstructing = false;
}
else
{
@Override
public void run()
{
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(
Desktop.desktop,
MessageManager
.getString("warn.couldnt_create_sequence_fetcher_client"),
MessageManager
.getString("label.couldnt_create_sequence_fetcher"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
});
sf.start();
}
+ /**
+ * blocking call which creates a new sequence fetcher panel, configures it and
+ * presses the OK button with the given database and query.
+ *
+ * @param database
+ * @param query
+ */
+ public static List<AlignFrame> fetchAndShow(String database, String query)
+ {
+ final SequenceFetcher sf = new SequenceFetcher(Desktop.instance,
+ database, query);
+ while (sf._isConstructing)
+ {
+ try
+ {
+ Thread.sleep(50);
+ } catch (Exception q)
+ {
+ return Collections.emptyList();
+ }
+ }
+ sf.newAlframes = new ArrayList<AlignFrame>();
+ sf.run();
+ return sf.newAlframes;
+ }
+
private class DatabaseAuthority extends DefaultMutableTreeNode
{
};
/**
+ * initialise the database and query for this fetcher panel
+ *
+ * @param selectedDb
+ * - string that should correspond to a sequence fetcher
+ * @param queryString
+ * - string that will be entered in the query dialog
+ * @return true if UI was configured with valid database and query string
+ */
+ protected boolean setInitialQuery(String selectedDb, String queryString)
+ {
+ if (selectedDb == null || selectedDb.trim().length() == 0)
+ {
+ return false;
+ }
+ try
+ {
+ List<DbSourceProxy> sp = sfetch.getSourceProxy(selectedDb);
+ for (DbSourceProxy sourcep : sp)
+ {
+ if (sourcep.getTier() == 0)
+ {
+ database.selection = Arrays
+ .asList(new DbSourceProxy[] { sourcep });
+ break;
+ }
+ }
+ if (database.selection == null || database.selection.size() == 0)
+ {
+ System.err.println("Ignoring fetch parameter db='" + selectedDb
+ + "'");
+ return false;
+ }
+ textArea.setText(queryString);
+ } catch (Exception q)
+ {
+ System.err.println("Ignoring fetch parameter db='" + selectedDb
+ + "' and query='" + queryString + "'");
+ return false;
+ }
+ return true;
+ }
+
+ /**
* called by thread spawned by constructor
*
* @param guiWindow
+ * @param queryString
+ * @param selectedDb
*/
- private void initGui(IProgressIndicator guiWindow)
+ private void initGui(IProgressIndicator guiWindow, String selectedDb,
+ String queryString)
{
this.guiWindow = guiWindow;
if (guiWindow instanceof AlignFrame)
try
{
jbInit();
+ /*
+ * configure the UI with any query parameters we were called with
+ */
+ if (!setInitialQuery(selectedDb, queryString))
+ {
+ /*
+ * none provided, so show the database chooser
+ */
+ database.waitForInput();
+ }
} catch (Exception ex)
{
ex.printStackTrace();
jPanel1.add(example);
jPanel1.add(clear);
jPanel1.add(close);
- jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
jPanel2.setLayout(borderLayout3);
- databaseButt = database.getDatabaseSelectorButton();
+ databaseButt = /*database.getDatabaseSelectorButton();
+ final JButton viewdbs =*/new JButton(
+ MessageManager.getString("action.select_ddbb"));
+ databaseButt.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ hidePanel();
+ database.showDialog();
+ }
+ });
databaseButt.setFont(JvSwingUtils.getLabelFont());
database.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- debounceTrap++;
String currentSelection = database.getSelectedItem();
if (currentSelection == null)
{
showPanel();
- if (currentSelection.equalsIgnoreCase("pdb")
- && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
+ if ("pdb".equalsIgnoreCase(currentSelection))
{
pdbSourceAction();
}
- else if (currentSelection.equalsIgnoreCase("uniprot")
- && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
+ else if ("uniprot".equalsIgnoreCase(currentSelection))
{
uniprotSourceAction();
}
this.add(jPanel3, java.awt.BorderLayout.CENTER);
this.add(jPanel2, java.awt.BorderLayout.NORTH);
jScrollPane1.getViewport().add(textArea);
-
- /*
- * open the database tree
- */
- database.waitForInput();
}
private void pdbSourceAction()
new UniprotFTSPanel(this);
frame.dispose();
}
+
private void otherSourceAction()
{
try
} catch (Exception e)
{
Cache.log.info(
- "Error retrieving " + accession
- + " from " + proxy.getDbName(), e);
- } finally
- {
- return success;
+ "Error retrieving " + accession + " from "
+ + proxy.getDbName(), e);
}
+ return success;
}
/**
for (String q : queries)
{
- DBRefEntry[] found = null;
DBRefEntry dbr = new DBRefEntry();
dbr.setSource(proxy.getDbSource());
dbr.setVersion(null);
{
if (rs[r] != null)
{
- found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
- if (found != null && found.length > 0)
+ List<DBRefEntry> found = DBRefUtils.searchRefs(rs[r].getDBRefs(),
+ accId);
+ if (!found.isEmpty())
{
rfound = true;
break;
}
AlignmentI parseResult(AlignmentI al, String title,
- String currentFileFormat,
+ FileFormatI currentFileFormat,
FeatureSettingsModelI preferredFeatureColours)
{
{
af.hideFeatureColumns(SequenceOntologyI.EXON, false);
}
-
+ if (newAlframes != null)
+ {
+ newAlframes.add(af);
+ }
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
try
{
- af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
- false));
+ af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (Exception ex)
{
}
@Override
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, error,
MessageManager.getString("label.error_retrieving_data"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
{
frame.setVisible(true);
}
+
+ /**
+ * Hide this panel (on clicking the database button to open the database
+ * chooser)
+ */
+ void hidePanel()
+ {
+ frame.setVisible(false);
+ }
}
git://source.jalview.org / jalview.git / blobdiff