{
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;
@Override
public void run()
{
- JvOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("warn.couldnt_create_sequence_fetcher_client"),
- MessageManager
- .getString("label.couldnt_create_sequence_fetcher"),
- JvOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString(
+ "warn.couldnt_create_sequence_fetcher_client"),
+ MessageManager.getString(
+ "label.couldnt_create_sequence_fetcher"),
+ JvOptionPane.ERROR_MESSAGE);
}
});
if (sourcep.getTier() == 0)
{
database.selection = Arrays
- .asList(new DbSourceProxy[] { sourcep });
+ .asList(new DbSourceProxy[]
+ { sourcep });
break;
}
}
if (database.selection == null || database.selection.size() == 0)
{
- System.err.println("Ignoring fetch parameter db='" + selectedDb
- + "'");
+ System.err.println(
+ "Ignoring fetch parameter db='" + selectedDb + "'");
return false;
}
textArea.setText(queryString);
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()
{
+ 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;
}
git://source.jalview.org / jalview.git / blobdiff