- iSize = vp.getAlignment().getHeight();
- seqs = vp.getAlignment().getSequencesArray();
- }
-
- dataset = new SequenceI[iSize];
- for (int i = 0; i < iSize; i++)
- {
- dataset[i] = seqs[i].getDatasetSequence();
- }
-
- cancelDAS.setEnabled(true);
- dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset,
- this, selectedSources, checkDbRefs, promptFetchDbRefs);
- af.getViewport().setShowSequenceFeatures(true);
- af.showSeqFeatures.setSelected(true);
- }
-
- /**
- * blocking call to initialise the das source browser
- */
- public void initDasSources()
- {
- dassourceBrowser.initDasSources();
- }
-
- /**
- * examine the current list of das sources and return any matching the given
- * nicknames in sources
- *
- * @param sources
- * Vector of Strings to resolve to DAS source nicknames.
- * @return sources that are present in source list.
- */
- public List<jalviewSourceI> resolveSourceNicknames(Vector<String> sources)
- {
- return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
- }
-
- /**
- * get currently selected das sources. ensure you have called initDasSources
- * before calling this.
- *
- * @return vector of selected das source nicknames
- */
- public Vector<jalviewSourceI> getSelectedSources()
- {
- return dassourceBrowser.getSelectedSources();
- }
-
- /**
- * properly initialise DAS fetcher and then initiate a new thread to fetch
- * features from the named sources (rather than any turned on by default)
- *
- * @param sources
- * @param block
- * if true then runs in same thread, otherwise passes to the Swing
- * executor
- */
- public void fetchDasFeatures(Vector<String> sources, boolean block)
- {
- initDasSources();
- List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
- .resolveSourceNicknames(sources);
- if (resolved.size() == 0)
- {
- resolved = dassourceBrowser.getSelectedSources();
- }
- if (resolved.size() > 0)
- {
- final List<jalviewSourceI> dassources = resolved;
- fetchDAS.setEnabled(false);
- // cancelDAS.setEnabled(true); doDasFetch does this.
- Runnable fetcher = new Runnable()
- {
-
- @Override
- public void run()
- {
- doDasFeatureFetch(dassources, true, false);
-
- }
- };
- if (block)
- {
- fetcher.run();
- }
- else
- {
- SwingUtilities.invokeLater(fetcher);
- }
- }
- }
-
- public void saveDAS_actionPerformed(ActionEvent e)
- {
- dassourceBrowser
- .saveProperties(jalview.bin.Cache.applicationProperties);
- }
-
- public void complete()
- {
- fetchDAS.setEnabled(true);
- cancelDAS.setEnabled(false);
- dassourceBrowser.setGuiEnabled(true);
-
- }
-
- public void cancelDAS_actionPerformed(ActionEvent e)
- {
- if (dasFeatureFetcher != null)
- {
- dasFeatureFetcher.cancel();
- }
- complete();
- }
-
- public void noDasSourceActive()
- {
- complete();
- JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.getString("label.no_das_sources_selected_warn"),
- MessageManager.getString("label.no_das_sources_selected_title"),
- JvOptionPane.DEFAULT_OPTION, JvOptionPane.INFORMATION_MESSAGE);
- }
-
- /**
- * Answers true unless a numeric condition has been selected with a
- * non-numeric value. Sets the value field to RED with a tooltip if in error.
- * <p>
- * If the pattern entered is empty, this method returns false, but does not
- * mark the field as invalid. This supports selecting an attribute for a new
- * condition before a match pattern has been entered.
- *
- * @param value
- * @param condCombo
- */
- protected boolean validateFilter(JTextField value,
- JComboBox<Condition> condCombo)
- {
- if (value == null || condCombo == null)
- {
- return true; // fields not populated
- }
-
- Condition cond = (Condition) condCombo.getSelectedItem();
- value.setBackground(Color.white);
- value.setToolTipText("");
- String v1 = value.getText().trim();
- if (v1.length() == 0)
- {
- return false;
- }
-
- if (cond.isNumeric())
- {
- try
- {
- Float.valueOf(v1);
- } catch (NumberFormatException e)
- {
- value.setBackground(Color.red);
- value.setToolTipText(MessageManager
- .getString("label.numeric_required"));
- return false;
- }