+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.gui;
-
-import jalview.jbgui.GDasSourceBrowser;
-import jalview.util.MessageManager;
-import jalview.util.TableSorter;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-
-import java.awt.BorderLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Properties;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.JCheckBox;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JTextField;
-import javax.swing.ListSelectionModel;
-import javax.swing.SwingUtilities;
-import javax.swing.event.ListSelectionEvent;
-import javax.swing.event.ListSelectionListener;
-import javax.swing.table.AbstractTableModel;
-
-import org.biodas.jdas.schema.sources.CAPABILITY;
-import org.biodas.jdas.schema.sources.COORDINATES;
-import org.biodas.jdas.schema.sources.PROP;
-import org.biodas.jdas.schema.sources.VERSION;
-
-public class DasSourceBrowser extends GDasSourceBrowser
- implements Runnable, ListSelectionListener
-{
- DasSourceRegistryI sourceRegistry = null;
-
- Vector<String> selectedSources;
-
- public DasSourceBrowser(FeatureSettings featureSettings)
- {
- fs = featureSettings;
- // TODO DasSourceRegistryProvider API
- sourceRegistry = jalview.bin.Cache.getDasSourceRegistry();
- String registry = sourceRegistry.getDasRegistryURL();
-
- registryURL.setText(registry);
-
- setSelectedFromProperties();
-
- displayFullDetails(null);
- table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-
- filter1.addListSelectionListener(this);
- filter2.addListSelectionListener(this);
- filter3.addListSelectionListener(this);
-
- // Ask to be notified of selection changes.
- ListSelectionModel rowSM = table.getSelectionModel();
- rowSM.addListSelectionListener(new ListSelectionListener()
- {
- @Override
- public void valueChanged(ListSelectionEvent e)
- {
- ListSelectionModel lsm = (ListSelectionModel) e.getSource();
- if (!lsm.isSelectionEmpty())
- {
- int selectedRow = lsm.getMinSelectionIndex();
- displayFullDetails(table.getValueAt(selectedRow, 0).toString());
- }
- }
- });
-
- table.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mouseClicked(MouseEvent evt)
- {
- if (evt.getClickCount() == 2 || evt.isPopupTrigger())
- {
- editRemoveLocalSource(evt);
- }
- }
- });
-
- if (sourceRegistry.getSources() != null)
- {
- init();
- }
- }
-
- FeatureSettings fs = null;
-
- private boolean loadingDasSources;
-
- public DasSourceBrowser()
- {
- this(null);
- }
-
- @Override
- public void paintComponent(java.awt.Graphics g)
- {
- if (sourceRegistry == null)
- {
- Thread worker = new Thread(this);
- worker.start();
- }
- }
-
- void init()
- {
- List<jalviewSourceI> sources = sourceRegistry.getSources();
- int dSize = sources.size();
- Object[][] data = new Object[dSize][2];
- for (int i = 0; i < dSize; i++)
- {
- data[i][0] = sources.get(i).getTitle(); // what's equivalent of nickname
- data[i][1] = new Boolean(
- selectedSources.contains(sources.get(i).getTitle()));
- }
-
- refreshTableData(data);
- setCapabilities(sourceRegistry);
-
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- TableSorter sorter = (TableSorter) table.getModel();
- sorter.setSortingStatus(1, TableSorter.DESCENDING);
- sorter.setSortingStatus(1, TableSorter.NOT_SORTED);
- }
- });
-
- progressBar.setIndeterminate(false);
- progressBar.setVisible(false);
- addLocal.setVisible(true);
- refresh.setVisible(true);
- }
-
- public void refreshTableData(Object[][] data)
- {
- TableSorter sorter = new TableSorter(new DASTableModel(data));
- sorter.setTableHeader(table.getTableHeader());
- table.setModel(sorter);
- }
-
- void displayFullDetails(String nickName)
- {
-
- StringBuffer text = new StringBuffer(
- "<HTML><font size=\"2\" face=\"Verdana, Arial, Helvetica, sans-serif\">");
-
- if (nickName == null)
- {
- fullDetails.setText(text + MessageManager
- .getString("label.select_das_service_from_table"));
- return;
- }
-
- int dSize = sourceRegistry.getSources().size();
- for (jalviewSourceI ds : sourceRegistry.getSources())
- {
- if (!ds.getTitle().equals(nickName))
- {
- continue;
- }
-
- VERSION latest = ds.getVersion();
- text.append(
- "<font color=\"#0000FF\">Id:</font> " + ds.getUri() + "<br>");
- text.append("<font color=\"#0000FF\">Nickname:</font> "
- + ds.getTitle() + "<br>");
-
- text.append("<font color=\"#0000FF\">URL:</font> <a href=\""
- + ds.getSourceURL() + "\">" + ds.getSourceURL() + "</a>"
- + "<br>");
- if (!ds.isLocal())
- {
- if (ds.getDocHref() != null && ds.getDocHref().length() > 0)
- {
- text.append("<font color=\"#0000FF\">Site:</font> <a href=\""
- + ds.getDocHref() + "\">" + ds.getDocHref() + "</a>"
- + "<br>");
- }
-
- text.append("<font color=\"#0000FF\">Description:</font> "
- + ds.getDescription() + "<br>");
-
- text.append(
- "<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"
- + ds.getEmail() + "\">" + ds.getEmail() + "</a>"
- + "<br>");
-
- text.append("<font color=\"#0000FF\">Registered at:</font> "
- + latest.getCreated() + "<br>");
-
- // TODO: Identify last successful test date
- // text.append("<font color=\"#0000FF\">Last successful test:</font> "
- // + latest.dasSources[i].getLeaseDate() + "<br>");
- }
- else
- {
- text.append("Source was added manually.<br/>");
- }
- text.append("<font color=\"#0000FF\">Labels:</font> ");
- boolean b = false;
- for (PROP labl : latest.getPROP())
- {
- if (labl.getName().equalsIgnoreCase("LABEL"))
- {
- if (b)
- {
- text.append(",");
- }
- text.append(" ");
-
- text.append(labl.getValue());
- b = true;
- }
- ;
- }
- text.append("<br>");
-
- text.append("<font color=\"#0000FF\">Capabilities:</font> ");
- CAPABILITY[] scap = latest.getCAPABILITY().toArray(new CAPABILITY[0]);
- for (int j = 0; j < scap.length; j++)
- {
- text.append(scap[j].getType());
- if (j < scap.length - 1)
- {
- text.append(", ");
- }
- }
- text.append("<br>");
-
- text.append("<font color=\"#0000FF\">Coordinates:</font>");
- int i = 1;
- for (COORDINATES dcs : latest.getCOORDINATES())
- {
- text.append("<br/>" + i++ + ". ");
- text.append(dcs.getAuthority() + " : " + dcs.getSource());
- if (dcs.getTaxid() != null && dcs.getTaxid().trim().length() > 0)
- {
- text.append(" [TaxId:" + dcs.getTaxid() + "]");
- }
- if (dcs.getVersion() != null
- && dcs.getVersion().trim().length() > 0)
- {
- {
- text.append(" {v. " + dcs.getVersion() + "}");
- }
- }
- text.append(" (<a href=\"" + dcs.getUri() + "\">" + dcs.getUri()
- + "</a>)");
- }
- text.append("</font></html>");
-
- break;
- }
-
- fullDetails.setText(text.toString());
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- fullDetailsScrollpane.getVerticalScrollBar().setValue(0);
- }
- });
- }
-
- @Override
- public void run()
- {
- loadingDasSources = true;
-
- addLocal.setVisible(false);
- refresh.setVisible(false);
- progressBar.setVisible(true);
- progressBar.setIndeterminate(true);
- setParentGuiEnabled(false);
- // Refresh the source list.
- sourceRegistry.refreshSources();
-
- init();
-
- setParentGuiEnabled(true);
- loadingDasSources = false;
-
- }
-
- private void setParentGuiEnabled(boolean b)
- {
- if (fs != null)
- {
- fs.fetchDAS.setEnabled(b);
- fs.saveDAS.setEnabled(b);
- }
- }
-
- public Vector<jalviewSourceI> getSelectedSources()
- {
- // wait around if we're still loading.
- while (sourceRegistry == null)
- {
- if (!loadingDasSources)
- {
- new Thread(this).start();
- try
- {
- Thread.sleep(5);
- } catch (Exception e)
- {
- }
- ;
- while (loadingDasSources)
- {
- try
- {
- Thread.sleep(5);
- } catch (Exception e)
- {
- }
- ;
- }
- ;
- }
- }
-
- Vector<jalviewSourceI> selected = new Vector<jalviewSourceI>();
- for (String source : selectedSources)
- {
- jalviewSourceI srce = sourceRegistry.getSource(source);
- if (srce != null)
- {
- selected.addElement(srce);
- }
- }
- return selected;
- }
-
- @Override
- public void refresh_actionPerformed(ActionEvent e)
- {
- saveProperties(jalview.bin.Cache.applicationProperties);
-
- Thread worker = new Thread(this);
- worker.start();
- }
-
- private void setCapabilities(DasSourceRegistryI sourceRegistry2)
- {
- Vector<String> authority = new Vector<String>();
- Vector<String> type = new Vector<String>();
- Vector<String> label = new Vector<String>();
- Vector<String> taxIds = new Vector<String>();
- authority.add("Any");
- type.add("Any");
- label.add("Any");
-
- for (jalviewSourceI ds : sourceRegistry2.getSources())
- {
- VERSION latest = ds.getVersion();
-
- for (COORDINATES cs : latest.getCOORDINATES())
- {
- if (!type.contains(cs.getSource()))
- {
- type.add(cs.getSource()); // source==category
- }
-
- if (!authority.contains(cs.getAuthority()))
- {
- authority.add(cs.getAuthority());
- }
- }
-
- for (PROP slabel : latest.getPROP())
- {
- if (slabel.getName().equalsIgnoreCase("LABEL")
- && !label.contains(slabel.getValue()))
- {
- label.add(slabel.getValue());
- }
- }
-
- }
-
- filter1.setListData(authority);
- filter2.setListData(type);
- filter3.setListData(label);
- // filter4 taxIds
-
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- filter1.setSelectedIndex(0);
- filter2.setSelectedIndex(0);
- filter3.setSelectedIndex(0);
- }
- });
- }
-
- @Override
- public void amendLocal(boolean newSource)
- {
- String url = "http://localhost:8080/", nickname = "";
- boolean seqsrc = false;
- if (!newSource)
- {
- int selectedRow = table.getSelectionModel().getMinSelectionIndex();
- nickname = table.getValueAt(selectedRow, 0).toString();
- jalviewSourceI source = sourceRegistry.getSource(nickname);
- url = source.getUri();
- seqsrc = source.isSequenceSource();
- }
-
- JTextField nametf = new JTextField(nickname, 40);
- JTextField urltf = new JTextField(url, 40);
- JCheckBox seqs = new JCheckBox(
- MessageManager.getString("label.sequence_source"));
- seqs.setSelected(seqsrc);
- JPanel panel = new JPanel(new BorderLayout());
- JPanel pane12 = new JPanel(new BorderLayout());
- pane12.add(new JLabel(MessageManager.getString("label.name:")),
- BorderLayout.CENTER);
- pane12.add(nametf, BorderLayout.EAST);
- panel.add(pane12, BorderLayout.NORTH);
- pane12 = new JPanel(new BorderLayout());
- pane12.add(new JLabel(MessageManager.getString("label.url:")),
- BorderLayout.NORTH);
- pane12.add(seqs, BorderLayout.SOUTH);
- pane12.add(urltf, BorderLayout.EAST);
- panel.add(pane12, BorderLayout.SOUTH);
-
- int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
- panel, MessageManager.getString("label.enter_local_das_source"),
- JvOptionPane.OK_CANCEL_OPTION);
-
- if (reply != JvOptionPane.OK_OPTION)
- {
- return;
- }
-
- if (!urltf.getText().endsWith("/"))
- {
- urltf.setText(urltf.getText() + "/");
- }
-
- jalviewSourceI local = sourceRegistry.createLocalSource(urltf.getText(),
- nametf.getText(), seqs.isSelected(), true);
- List sources = sourceRegistry.getSources();
- int osize = sources.size();
- int size = osize + (newSource ? 1 : 0);
-
- Object[][] data = new Object[size][2];
- DASTableModel dtm = (table != null)
- ? (DASTableModel) ((TableSorter) table.getModel())
- .getTableModel()
- : null;
- for (int i = 0; i < osize; i++)
- {
- String osrc = (dtm == null || i >= osize) ? null
- : (String) dtm.getValueAt(i, 0);
- if (!newSource && osrc != null
- && dtm.getValueAt(i, 0).equals(nickname))
- {
- data[i][0] = local.getTitle();
- data[i][1] = new Boolean(true);
- }
- else
- {
- data[i][0] = osrc;
- data[i][1] = new Boolean(selectedSources.contains(osrc));
- }
- }
- // Always add a new source at the end
- if (newSource)
- {
- data[osize][0] = local.getTitle();
- data[osize][1] = new Boolean(true);
- selectedSources.add(local.getTitle());
- }
-
- refreshTableData(data);
-
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- scrollPane.getVerticalScrollBar()
- .setValue(scrollPane.getVerticalScrollBar().getMaximum());
- }
- });
-
- displayFullDetails(local.getTitle());
- }
-
- public void editRemoveLocalSource(MouseEvent evt)
- {
- int selectedRow = table.getSelectionModel().getMinSelectionIndex();
- if (selectedRow == -1)
- {
- return;
- }
-
- String nickname = table.getValueAt(selectedRow, 0).toString();
-
- if (!sourceRegistry.getSource(nickname).isLocal())
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString(
- "label.you_can_only_edit_or_remove_local_das_sources"),
- MessageManager.getString("label.public_das_source"),
- JvOptionPane.WARNING_MESSAGE);
- return;
- }
-
- Object[] options = { "Edit", "Remove", "Cancel" };
- int choice = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
- "Do you want to edit or remove " + nickname + "?",
- "Edit / Remove Local DAS Source",
- JvOptionPane.YES_NO_CANCEL_OPTION,
- JvOptionPane.QUESTION_MESSAGE, null, options, options[2]);
-
- switch (choice)
- {
- case 0:
- amendLocal(false);
- break;
- case 1:
- sourceRegistry.removeLocalSource(sourceRegistry.getSource(nickname));
- selectedSources.remove(nickname);
- Object[][] data = new Object[sourceRegistry.getSources().size()][2];
- int index = 0, l = table.getRowCount();
-
- for (int i = 0; i < l; i++)
- {
- String nm;
- if ((nm = (String) table.getValueAt(i, 0)).equals(nickname))
- {
- continue;
- }
- else
- {
- data[index][0] = nm;
- data[index][1] = new Boolean(selectedSources.contains(nm));
- index++;
- }
- }
- refreshTableData(data);
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- scrollPane.getVerticalScrollBar()
- .setValue(scrollPane.getVerticalScrollBar().getMaximum());
- }
- });
-
- break;
- }
- }
-
- @Override
- public void valueChanged(ListSelectionEvent evt)
- {
- // Called when the MainTable selection changes
- if (evt.getValueIsAdjusting())
- {
- return;
- }
-
- displayFullDetails(null);
-
- // Filter the displayed data sources
-
- ArrayList names = new ArrayList();
- ArrayList selected = new ArrayList();
-
- // The features filter is not visible, but we must still
- // filter the das source list here.
- // July 2006 - only 6 sources fo not serve features
- Object[] dummyFeatureList = new Object[] { "features" };
- List<jalviewSourceI> srcs = sourceRegistry.getSources();
- for (jalviewSourceI ds : srcs)
- {
-
- VERSION v = ds.getVersion();
- List<COORDINATES> coords = v.getCOORDINATES();
- if (ds.isLocal() || ((coords == null || coords.size() == 0)
- && filter1.getSelectedIndex() == 0
- && filter2.getSelectedIndex() == 0
- && filter3.getSelectedIndex() == 0))
- {
- // THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT
- // HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT
- // IS ADDED FROM THE REGISTRY
- names.add(ds.getTitle());
- selected.add(new Boolean(selectedSources.contains(ds.getTitle())));
- continue;
- }
-
- if (!selectedInList(dummyFeatureList, ds.getCapabilityList(v))
- || !selectedInList(filter3.getSelectedValues(),
- ds.getLabelsFor(v)))
- {
- continue;
- }
-
- for (int j = 0; j < coords.size(); j++)
- {
- if (selectedInList(filter1.getSelectedValues(),
- new String[]
- { coords.get(j).getAuthority() })
- && selectedInList(filter2.getSelectedValues(), new String[]
- { coords.get(j).getSource() }))
- {
- names.add(ds.getTitle());
- selected.add(
- new Boolean(selectedSources.contains(ds.getTitle())));
- break;
- }
- }
- }
-
- int dSize = names.size();
- Object[][] data = new Object[dSize][2];
- for (int d = 0; d < dSize; d++)
- {
- data[d][0] = names.get(d);
- data[d][1] = selected.get(d);
- }
-
- refreshTableData(data);
- }
-
- private boolean selectedInList(Object[] selection, String[] items)
- {
- for (int i = 0; i < selection.length; i++)
- {
- if (selection[i].equals("Any"))
- {
- return true;
- }
- if (items == null || items.length == 0)
- {
- return false;
- }
- String sel = (items[0].startsWith("das1:") ? "das1:" : "")
- + selection[i];
- for (int j = 0; j < items.length; j++)
- {
- if (sel.equals(items[j]))
- {
- return true;
- }
- }
- }
-
- return false;
- }
-
- void setSelectedFromProperties()
- {
- String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
- "uniprot");
- StringTokenizer st = new StringTokenizer(active, "\t");
- selectedSources = new Vector();
- while (st.hasMoreTokens())
- {
- selectedSources.addElement(st.nextToken());
- }
- }
-
- @Override
- public void reset_actionPerformed(ActionEvent e)
- {
- registryURL.setText(sourceRegistry.getDasRegistryURL());
- }
-
- /**
- * set the DAS source settings in the given jalview properties.
- *
- * @param properties
- */
- public void saveProperties(Properties properties)
- {
- if (registryURL.getText() == null || registryURL.getText().length() < 1)
- {
- properties.remove(jalview.bin.Cache.DAS_REGISTRY_URL);
- }
- else
- {
- properties.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL,
- registryURL.getText());
- }
-
- StringBuffer sb = new StringBuffer();
- for (int r = 0; r < table.getModel().getRowCount(); r++)
- {
- if (((Boolean) table.getValueAt(r, 1)).booleanValue())
- {
- sb.append(table.getValueAt(r, 0) + "\t");
- }
- }
-
- properties.setProperty(jalview.bin.Cache.DAS_ACTIVE_SOURCE,
- sb.toString());
-
- String sourceprop = sourceRegistry.getLocalSourceString();
- properties.setProperty(jalview.bin.Cache.DAS_LOCAL_SOURCE, sourceprop);
- }
-
- class DASTableModel extends AbstractTableModel
- {
-
- public DASTableModel(Object[][] data)
- {
- this.data = data;
- }
-
- private String[] columnNames = new String[] {
- MessageManager.getString("label.nickname"),
- MessageManager.getString("label.use_source") };
-
- private Object[][] data;
-
- @Override
- public int getColumnCount()
- {
- return columnNames.length;
- }
-
- @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];
- }
-
- /*
- * JTable uses this method to determine the default renderer/ editor for
- * each cell. If we didn't implement this method, then the last column would
- * contain text ("true"/"false"), rather than a check box.
- */
- @Override
- public Class getColumnClass(int c)
- {
- return getValueAt(0, c).getClass();
- }
-
- /*
- * Don't need to implement this method unless your table's editable.
- */
- @Override
- public boolean isCellEditable(int row, int col)
- {
- // Note that the data/cell address is constant,
- // no matter where the cell appears onscreen.
- return col == 1;
-
- }
-
- /*
- * Don't need to implement this method unless your table's data can change.
- */
- @Override
- public void setValueAt(Object value, int row, int col)
- {
- data[row][col] = value;
- fireTableCellUpdated(row, col);
-
- String name = getValueAt(row, 0).toString();
- boolean selected = ((Boolean) value).booleanValue();
-
- if (selectedSources.contains(name) && !selected)
- {
- selectedSources.remove(name);
- }
-
- if (!selectedSources.contains(name) && selected)
- {
- selectedSources.add(name);
- }
- }
- }
-
- public void initDasSources()
- {
-
- Thread thr = new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- // this actually initialises the das source list
- paintComponent(null); // yuk
- }
- });
- thr.start();
- while (loadingDasSources || sourceRegistry == null)
- {
- try
- {
- Thread.sleep(10);
- } catch (Exception e)
- {
- }
- ;
- }
- }
-
- /**
- * disable or enable the buttons on the source browser
- *
- * @param b
- */
- public void setGuiEnabled(boolean b)
- {
- refresh.setEnabled(b);
- addLocal.setEnabled(b);
- }
-}
git://source.jalview.org / jalview.git / blobdiff