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;
import javax.swing.JCheckBox;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
private static Thread initingThread = null;
- int debounceTrap = 0;
-
public JTextArea getTextArea()
{
return textArea;
{
if (guiWindow != null)
{
- guiWindow
- .setProgressBar(
- MessageManager
- .getString("status.waiting_sequence_database_fetchers_init"),
- Thread.currentThread().hashCode());
+ guiWindow.setProgressBar(
+ MessageManager.getString(
+ "status.waiting_sequence_database_fetchers_init"),
+ Thread.currentThread().hashCode());
}
// initting happening on another thread - so wait around to see if it
// finishes.
}
if (guiWindow != null)
{
- guiWindow
- .setProgressBar(
- MessageManager
- .getString("status.waiting_sequence_database_fetchers_init"),
- Thread.currentThread().hashCode());
+ guiWindow.setProgressBar(
+ MessageManager.getString(
+ "status.waiting_sequence_database_fetchers_init"),
+ Thread.currentThread().hashCode());
}
}
- if (sfetch == null
- || dasRegistry != Cache.getDasSourceRegistry()
+ if (sfetch == null || dasRegistry != Cache.getDasSourceRegistry()
|| lastDasSourceRegistry != (Cache.getDasSourceRegistry()
- .getDasRegistryURL() + Cache
- .getDasSourceRegistry().getLocalSourceString())
- .hashCode())
+ .getDasRegistryURL()
+ + Cache.getDasSourceRegistry().getLocalSourceString())
+ .hashCode())
{
_initingFetcher = true;
initingThread = Thread.currentThread();
*/
if (guiWindow != null)
{
- guiWindow.setProgressBar(MessageManager
- .getString("status.init_sequence_database_fetchers"),
+ guiWindow.setProgressBar(
+ MessageManager.getString(
+ "status.init_sequence_database_fetchers"),
Thread.currentThread().hashCode());
}
dasRegistry = Cache.getDasSourceRegistry();
{
guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
}
- lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
- .getLocalSourceString()).hashCode();
+ lastDasSourceRegistry = (dasRegistry.getDasRegistryURL()
+ + dasRegistry.getLocalSourceString()).hashCode();
sfetch = sf;
_initingFetcher = false;
initingThread = null;
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
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("warn.couldnt_create_sequence_fetcher_client"),
- MessageManager
- .getString("label.couldnt_create_sequence_fetcher"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString(
+ "warn.couldnt_create_sequence_fetcher_client"),
+ MessageManager.getString(
+ "label.couldnt_create_sequence_fetcher"),
+ 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();
private String getFrameTitle()
{
- return ((alignFrame == null) ? MessageManager
- .getString("label.new_sequence_fetcher") : MessageManager
- .getString("label.additional_sequence_fetcher"));
+ return ((alignFrame == null)
+ ? MessageManager.getString("label.new_sequence_fetcher")
+ : MessageManager
+ .getString("label.additional_sequence_fetcher"));
}
private void jbInit() throws Exception
replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
replacePunctuation
.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
- replacePunctuation.setText(MessageManager
- .getString("label.replace_commas_semicolons"));
+ replacePunctuation.setText(
+ MessageManager.getString("label.replace_commas_semicolons"));
ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
jPanel1.add(example);
jPanel1.add(clear);
jPanel1.add(close);
- jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
jPanel2.setLayout(borderLayout3);
databaseButt = /*database.getDatabaseSelectorButton();
final JButton viewdbs =*/new JButton(
@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
+ database.getSelectedSources().size() + " others)"
: ""));
String eq = database.getExampleQueries();
- dbeg.setText(MessageManager.formatMessage(
- "label.example_query_param", new String[] { eq }));
+ dbeg.setText(MessageManager.formatMessage("label.example_query_param",
+ new String[]
+ { eq }));
boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
for (DbSourceProxy dbs : database.getSelectedSources())
{
if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
{
empty = new com.stevesoft.pat.Regex(
- // replace commas and spaces with a semicolon
+ // replace commas and spaces with a semicolon
"(\\s|[,; ])+", ";");
}
else
}
textArea.setText(empty.replaceAll(textArea.getText()));
// see if there's anthing to search with
- if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
- .getText()))
+ if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]")
+ .search(textArea.getText()))
{
error += "Please enter a (semi-colon separated list of) database id(s)";
}
Iterator<DbSourceProxy> proxies = database.getSelectedSources()
.iterator();
String[] qries;
- List<String> nextFetch = Arrays.asList(qries = textArea.getText()
- .split(";"));
+ List<String> nextFetch = Arrays
+ .asList(qries = textArea.getText().split(";"));
Iterator<String> en = Arrays.asList(new String[0]).iterator();
int nqueries = qries.length;
try
{
// update status
- guiWindow
- .setProgressBar(MessageManager.formatMessage(
- "status.fetching_sequence_queries_from",
- new String[] {
- Integer.valueOf(nqueries).toString(),
- proxy.getDbName() }), Thread.currentThread()
- .hashCode());
+ guiWindow.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_sequence_queries_from", new String[]
+ { Integer.valueOf(nqueries).toString(),
+ proxy.getDbName() }),
+ Thread.currentThread().hashCode());
if (proxy.getMaximumQueryCount() == 1)
{
/*
}
} catch (Exception e)
{
- showErrorMessage("Error retrieving " + textArea.getText()
- + " from " + database.getSelectedItem());
+ showErrorMessage("Error retrieving " + textArea.getText() + " from "
+ + database.getSelectedItem());
// error
// +="Couldn't retrieve sequences from "+database.getSelectedItem();
System.err.println("Retrieval failed for source ='"
} catch (OutOfMemoryError e)
{
showErrorMessage("Out of Memory when retrieving "
- + textArea.getText()
- + " from "
- + database.getSelectedItem()
+ + textArea.getText() + " from " + database.getSelectedItem()
+ "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
e.printStackTrace();
} catch (Error e)
while (aresult.size() > 0)
{
presult.add(aresult.remove(0));
- presultTitle.add(aresultq.remove(0) + " "
- + getDefaultRetrievalTitle());
+ presultTitle.add(
+ aresultq.remove(0) + " " + getDefaultRetrievalTitle());
}
}
else
presultTitle.add(titl);
}
}
- guiWindow.setProgressBar(MessageManager
- .getString("status.finshed_querying"), Thread.currentThread()
- .hashCode());
+ guiWindow.setProgressBar(
+ MessageManager.getString("status.finshed_querying"),
+ Thread.currentThread().hashCode());
}
- guiWindow.setProgressBar(
- (presult.size() > 0) ? MessageManager
- .getString("status.parsing_results") : MessageManager
- .getString("status.processing"), Thread.currentThread()
- .hashCode());
+ guiWindow
+ .setProgressBar(
+ (presult.size() > 0)
+ ? MessageManager
+ .getString("status.parsing_results")
+ : MessageManager.getString("status.processing"),
+ Thread.currentThread().hashCode());
// process results
while (presult.size() > 0)
{
{
StringBuffer sb = new StringBuffer();
sb.append("Didn't retrieve the following "
- + (nextFetch.size() == 1 ? "query" : nextFetch.size()
- + " queries") + ": \n");
+ + (nextFetch.size() == 1 ? "query"
+ : nextFetch.size() + " queries")
+ + ": \n");
int l = sb.length(), lr = 0;
for (String s : nextFetch)
{
*/
void fetchMultipleAccessions(DbSourceProxy proxy,
Iterator<String> accessions, List<String> aresultq,
- List<AlignmentI> aresult, List<String> nextFetch)
- throws Exception
+ List<AlignmentI> aresult, List<String> nextFetch) throws Exception
{
StringBuilder multiacc = new StringBuilder();
List<String> tosend = new ArrayList<String>();
indres = proxy.getSequenceRecords(accession);
} catch (OutOfMemoryError oome)
{
- new OOMWarning("fetching " + accession + " from "
- + proxy.getDbName(), oome, this);
+ new OOMWarning(
+ "fetching " + accession + " from " + proxy.getDbName(),
+ oome, this);
}
if (indres != null)
{
}
} catch (Exception e)
{
- Cache.log.info(
- "Error retrieving " + accession
- + " from " + proxy.getDbName(), e);
+ Cache.log.info("Error retrieving " + accession + " from "
+ + proxy.getDbName(), e);
}
return success;
}
}
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);
}
});
}