- filteredFeatureChoice.addItemListener(listener);
-
- }
-
- /**
- * Refreshes the display to show any filters currently configured for the
- * selected feature type (editable, with 'remove' option), plus one extra row
- * for adding a condition. This should be called on change of selected feature
- * type, or after a filter has been removed, added or amended.
- */
- protected void refreshFiltersDisplay()
- {
- /*
- * clear the panel and list of filter conditions
- */
- chooseFiltersPanel.removeAll();
-
- String selectedType = (String) filteredFeatureChoice.getSelectedItem();
-
- filters.clear();
-
- /*
- * look up attributes known for feature type
- */
- List<String> attNames = FeatureAttributes.getInstance().getAttributes(
- selectedType);
-
- /*
- * if this feature type has filters set, load them first
- */
- KeyedMatcherSetI featureFilters = fr.getFeatureFilter(selectedType);
- filtersAsText.setText("");
- if (featureFilters != null)
- {
- filtersAsText.setText(featureFilters.toString());
- if (!featureFilters.isAnded())
- {
- orFilters.setSelected(true);
- }
- Iterator<KeyedMatcherI> matchers = featureFilters.getMatchers();
- while (matchers.hasNext())
- {
- filters.add(matchers.next());
- }
- }
-
- /*
- * and an empty filter for the user to populate (add)
- */
- KeyedMatcherI noFilter = new KeyedMatcher("", Condition.values()[0], "");
- filters.add(noFilter);
-
- /*
- * render the conditions in rows, each in its own JPanel
- */
- int i = 0;
- for (KeyedMatcherI filter : filters)
- {
- String key = filter.getKey();
- Condition condition = filter.getMatcher()
- .getCondition();
- String pattern = filter.getMatcher().getPattern();
- JPanel row = addFilter(key, attNames, condition, pattern, i);
- chooseFiltersPanel.add(row);
- i++;
- }
-
- filtersPane.validate();
- filtersPane.repaint();
- }
-
- /**
- * A helper method that constructs a panel with one filter condition:
- * <ul>
- * <li>a drop-down list of attribute names to choose from</li>
- * <li>a drop-down list of conditions to choose from</li>
- * <li>a text field for input of a match pattern</li>
- * <li>optionally, a 'remove' button</li>
- * </ul>
- * If attribute, condition or pattern are not null, they are set as defaults
- * for the input fields. The 'remove' button is added unless the pattern is
- * null or empty (incomplete filter condition).
- *
- * @param attribute
- * @param attNames
- * @param cond
- * @param pattern
- * @param i
- * @return
- */
- protected JPanel addFilter(String attribute, List<String> attNames,
- Condition cond, String pattern, int i)
- {
- JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT));
- filterRow.setBackground(Color.white);
-
- /*
- * inputs for attribute, condition, pattern
- */
- JComboBox<String> attCombo = new JComboBox<>();
- JComboBox<Condition> condCombo = new JComboBox<>();
- JTextField patternField = new JTextField(8);
-
- /*
- * action handlers that validate and (if valid) apply changes
- */
- ActionListener actionListener = new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (attCombo.getSelectedItem() != null)
- {
- if (validateFilter(patternField, condCombo))
- {
- updateFilter(attCombo, condCombo, patternField, i);
- filtersChanged();
- }
- }
- }
- };
- ItemListener itemListener = new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- actionListener.actionPerformed(null);
- }
- };
-
- /*
- * drop-down choice of attribute
- */
- if (attNames.isEmpty())
- {
- attCombo.addItem("---");
- attCombo.setToolTipText(MessageManager
- .getString("label.no_attributes_known"));
- }
- else
- {
- attCombo.setToolTipText("");
- for (String attName : attNames)
- {
- attCombo.addItem(attName);
- }
- if ("".equals(attribute))
- {
- attCombo.setSelectedItem(null);
- }
- else
- {
- attCombo.setSelectedItem(attribute);
- }
- attCombo.addItemListener(itemListener);
- }
- filterRow.add(attCombo);
-
- /*
- * drop-down choice of test condition
- */
- for (Condition c : Condition.values())
- {
- condCombo.addItem(c);
- }
- if (cond != null)
- {
- condCombo.setSelectedItem(cond);
- }
- condCombo.addItemListener(itemListener);
- filterRow.add(condCombo);
-
- /*
- * pattern to match against
- */
- patternField.setText(pattern);
- patternField.addActionListener(actionListener);
- patternField.addFocusListener(new FocusAdapter()
- {
- @Override
- public void focusLost(FocusEvent e)
- {
- actionListener.actionPerformed(null);
- }
- });
- filterRow.add(patternField);
-
- /*
- * add remove button if filter is populated (non-empty pattern)
- */
- if (pattern != null && pattern.trim().length() > 0)
- {
- // todo: gif for - button
- JButton removeCondition = new BasicArrowButton(SwingConstants.WEST);
- removeCondition.setToolTipText(MessageManager
- .getString("label.delete_row"));
- removeCondition.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- filters.remove(i);
- filtersChanged();
- }
- });
- filterRow.add(removeCondition);
- }
-
- return filterRow;
- }
-
- /**
- * Action on any change to feature filtering, namely
- * <ul>
- * <li>change of selected attribute</li>
- * <li>change of selected condition</li>
- * <li>change of match pattern</li>
- * <li>removal of a condition</li>
- * </ul>
- * The action should be to
- * <ul>
- * <li>parse and validate the filters</li>
- * <li>if valid, update the filter text box</li>
- * <li>and apply the filters to the viewport</li>
- * </ul>
- */
- protected void filtersChanged()
- {
- /*
- * update the filter conditions for the feature type
- */
- String featureType = (String) filteredFeatureChoice.getSelectedItem();
- boolean anded = andFilters.isSelected();
- KeyedMatcherSetI combined = new KeyedMatcherSet();
-
- for (KeyedMatcherI filter : filters)
- {
- String pattern = filter.getMatcher().getPattern();
- if (pattern.trim().length() > 0)
- {
- if (anded)
- {
- combined.and(filter);
- }
- else
- {
- combined.or(filter);
- }
- }
- }
-
- /*
- * save the filter conditions in the FeatureRenderer
- * (note this might now be an empty filter with no conditions)
- */
- fr.setFeatureFilter(featureType, combined);
-
- filtersAsText.setText(combined.toString());
-
- refreshFiltersDisplay();
-
- af.alignPanel.paintAlignment(true, true);
- }
-
- /**
- * Constructs a filter condition from the given input fields, and replaces the
- * condition at filterIndex with the new one
- *
- * @param attCombo
- * @param condCombo
- * @param valueField
- * @param filterIndex
- */
- protected void updateFilter(JComboBox<String> attCombo,
- JComboBox<Condition> condCombo, JTextField valueField,
- int filterIndex)
- {
- String attName = (String) attCombo.getSelectedItem();
- Condition cond = (Condition) condCombo.getSelectedItem();
- String pattern = valueField.getText();
- KeyedMatcherI km = new KeyedMatcher(attName, cond, pattern);
-
- filters.set(filterIndex, km);
- }
-
- public void fetchDAS_actionPerformed(ActionEvent e)
- {
- fetchDAS.setEnabled(false);
- cancelDAS.setEnabled(true);
- dassourceBrowser.setGuiEnabled(false);
- Vector<jalviewSourceI> selectedSources = dassourceBrowser
- .getSelectedSources();
- doDasFeatureFetch(selectedSources, true, true);
- }
-
- /**
- * get the features from selectedSources for all or the current selection
- *
- * @param selectedSources
- * @param checkDbRefs
- * @param promptFetchDbRefs
- */
- private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
- boolean checkDbRefs, boolean promptFetchDbRefs)
- {
- SequenceI[] dataset, seqs;
- int iSize;
- AlignmentViewport vp = af.getViewport();
- if (vp.getSelectionGroup() != null
- && vp.getSelectionGroup().getSize() > 0)
- {
- iSize = vp.getSelectionGroup().getSize();
- dataset = new SequenceI[iSize];
- seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment());
- }
- else
- {
- 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;
- }
- }
-
- return true;
- }
-
- // ///////////////////////////////////////////////////////////////////////
- // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
- // ///////////////////////////////////////////////////////////////////////
- class FeatureTableModel extends AbstractTableModel
- {
- FeatureTableModel(Object[][] data)
- {
- this.data = data;
- }
-
- private String[] columnNames = {
- MessageManager.getString("label.feature_type"),
- MessageManager.getString("action.colour"),
- MessageManager.getString("label.display") };
-
- private Object[][] data;
-
- public Object[][] getData()
- {
- return data;
- }
-
- public void setData(Object[][] data)
- {
- this.data = data;
- }
-
- @Override
- public int getColumnCount()
- {
- return columnNames.length;
- }
-
- public Object[] getRow(int row)
- {
- return data[row];
- }
-
- @Override
- public int getRowCount()
- {
- return data.length;
- }
-
- @Override
- public String getColumnName(int col)
- {
- return columnNames[col];
- }
-
- @Override
- public Object getValueAt(int row, int col)
- {
- return data[row][col];
- }
-
- @Override
- public Class getColumnClass(int c)
- {
- return getValueAt(0, c).getClass();
- }