/* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program 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 2 * of the License, or (at your option) any later version. * * This program 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 this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.gui; import jalview.jbgui.*; import javax.swing.table.AbstractTableModel; import javax.swing.event.*; import jalview.util.TableSorter; import java.awt.event.*; import javax.swing.*; import java.util.*; import org.biojava.dasobert.dasregistry.DasCoordinateSystem; import org.biojava.dasobert.dasregistry.DasSource; import org.biojava.dasobert.dasregistry.Das1Source; import java.awt.BorderLayout; public class DasSourceBrowser extends GDasSourceBrowser implements Runnable, ListSelectionListener { static DasSource[] dasSources = null; Hashtable localSources = null; Vector selectedSources; public DasSourceBrowser() { registryURL.setText(jalview.bin.Cache.getDefault("DAS_REGISTRY_URL", "http://das.sanger.ac.uk/registry/das1/sources/") ); 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() { public void valueChanged(ListSelectionEvent e) { //Ignore extra messages. if (e.getValueIsAdjusting()) return; ListSelectionModel lsm = (ListSelectionModel) e.getSource(); if (!lsm.isSelectionEmpty()) { int selectedRow = lsm.getMinSelectionIndex(); displayFullDetails(table.getValueAt(selectedRow, 0).toString()); } } }); table.addMouseListener(new MouseAdapter() { public void mouseClicked(MouseEvent evt) { if(evt.getClickCount()==2 || SwingUtilities.isRightMouseButton(evt)) editRemoveLocalSource(evt); } }); if(dasSources==null) { Thread worker = new Thread(this); worker.start(); } else { init(); } } void init() { int dSize = dasSources.length; Object[][] data = new Object[dSize][2]; for (int i = 0; i < dSize; i++) { data[i][0] = dasSources[i].getNickname(); data[i][1] = new Boolean(selectedSources.contains(dasSources[i]. getNickname())); } refreshTableData(data); setCapabilities(dasSources); javax.swing.SwingUtilities.invokeLater(new Runnable() { 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( ""); if (nickName == null) { fullDetails.setText(text + "Select a DAS service from the table" + " to read a full description here."); return; } int dSize = dasSources.length; for (int i = 0; i < dSize; i++) { if (!dasSources[i].getNickname().equals(nickName)) continue; DasSource ds = dasSources[i]; text.append("Id: " + dasSources[i].getId() + "
"); text.append("Nickname: " + dasSources[i].getNickname() + "
"); text.append("URL: " + dasSources[i].getUrl() + "
"); text.append("Admin Email: "+dasSources[i].getAdminemail()+"" + "
"); text.append("Registered at: " + dasSources[i].getRegisterDate() + "
"); text.append("Last successful test: " + dasSources[i].getLeaseDate() + "
"); text.append("Labels: "); for(int s=0; s"); text.append("Capabilities: "); String[] scap = dasSources[i].getCapabilities(); for (int j = 0; j < scap.length; j++) { text.append(scap[j]); if (j < scap.length - 1) text.append(", "); } text.append("
"); text.append("Coordinates: "); DasCoordinateSystem[] dcs = ds.getCoordinateSystem(); for (int j = 0; j < dcs.length; j++) { text.append("(" + dcs[j].getUniqueId() + ") " + dcs[j].getCategory() + ", " + dcs[j].getName()); if (dcs[j].getNCBITaxId() != 0) text.append(", " + dcs[j].getNCBITaxId()); if (dcs[j].getOrganismName().length() > 0) text.append(", " + dcs[j].getOrganismName()); text.append("
"); } text.append("Description: " + dasSources[i].getDescription() + "
"); if (dasSources[i].getHelperurl()!=null && dasSources[i].getHelperurl().length() > 0) { text.append("Go to site"); } text.append(""); break; } fullDetails.setText(text.toString()); javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { fullDetailsScrollpane.getVerticalScrollBar().setValue(0); } }); } public void run() { addLocal.setVisible(false); refresh.setVisible(false); progressBar.setVisible(true); progressBar.setIndeterminate(true); dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources(); appendLocalSources(); init(); } public Vector getSelectedSources() { Vector selected = new Vector(); for (int r = 0; r < selectedSources.size(); r++) { for (int i = 0; i < dasSources.length; i++) { if (dasSources[i].getNickname().equals( selectedSources.elementAt(r))) { selected.addElement(dasSources[i]); break; } } } return selected; } public DasSource[] getDASSource() { if(dasSources==null) { dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources(); appendLocalSources(); } return dasSources; } public void refresh_actionPerformed(ActionEvent e) { saveProperties(jalview.bin.Cache.applicationProperties); Thread worker = new Thread(this); worker.start(); } private void setCapabilities(DasSource[] sources) { Vector authority = new Vector(); Vector type = new Vector(); Vector label = new Vector(); authority.addElement("Any"); type.addElement("Any"); label.addElement("Any"); for (int i = 0; i < sources.length; i++) { DasSource ds = sources[i]; DasCoordinateSystem[] dcs = ds.getCoordinateSystem(); for (int j = 0; j < dcs.length; j++) { if (!type.contains(dcs[j].getCategory())) type.addElement(dcs[j].getCategory()); if (!authority.contains(dcs[j].getName())) authority.addElement(dcs[j].getName()); } String[] slabels = ds.getLabels(); for (int s = 0; s < slabels.length; s++) { if (!label.contains(slabels[s])) { label.addElement(slabels[s]); } } } filter1.setListData(authority); filter2.setListData(type); filter3.setListData(label); javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { filter1.setSelectedIndex(0); filter2.setSelectedIndex(0); filter3.setSelectedIndex(0); } }); } public void amendLocal(boolean newSource) { String url = "http://localhost:8080/", nickname = ""; if(!newSource) { int selectedRow = table.getSelectionModel().getMinSelectionIndex(); nickname = table.getValueAt(selectedRow, 0).toString(); url = ((DasSource)localSources.get(nickname)).getUrl(); } JTextField nametf = new JTextField(nickname, 40); JTextField urltf = new JTextField(url, 40); JPanel panel = new JPanel(new BorderLayout()); JPanel pane12 = new JPanel(new BorderLayout()); pane12.add(new JLabel("Nickname: "), BorderLayout.CENTER); pane12.add(nametf, BorderLayout.EAST); panel.add(pane12, BorderLayout.NORTH); pane12 = new JPanel(new BorderLayout()); pane12.add(new JLabel("URL: "), BorderLayout.CENTER); pane12.add(urltf, BorderLayout.EAST); panel.add(pane12, BorderLayout.SOUTH); int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, panel, "Enter Nickname & URL of Local DAS Source", JOptionPane.OK_CANCEL_OPTION); if (reply != JOptionPane.OK_OPTION ) { return; } if(!urltf.getText().endsWith("/")) urltf.setText(urltf.getText()+"/"); Das1Source local = new Das1Source(); local.setUrl(urltf.getText()); local.setNickname(nametf.getText()); if(localSources==null) localSources = new Hashtable(); localSources.put(local.getNickname(), local); if(!newSource && !nickname.equals(nametf.getText())) { localSources.remove(nickname); } int size = dasSources.length; int adjust = newSource ? 1 : 0; Object[][] data = new Object[size+adjust][2]; for (int i = 0; i < size; i++) { if(!newSource && dasSources[i].getNickname().equals(nickname)) { ((DasSource)dasSources[i]).setNickname(local.getNickname()); ((DasSource)dasSources[i]).setUrl(local.getUrl()); data[i][0] = local.getNickname(); data[i][1] = new Boolean(true); } else { data[i][0] = dasSources[i].getNickname(); data[i][1] = new Boolean(selectedSources.contains(dasSources[i]. getNickname())); } } if(newSource) { data[size][0] = local.getNickname(); data[size][1] = new Boolean(true); selectedSources.add(local.getNickname()); } DasSource [] tmp = new DasSource[size+adjust]; System.arraycopy(dasSources, 0, tmp, 0, size); if(newSource) tmp[size] = local; dasSources = tmp; refreshTableData(data); SwingUtilities.invokeLater(new Runnable() { public void run() { scrollPane.getVerticalScrollBar().setValue( scrollPane.getVerticalScrollBar().getMaximum() ); } }); displayFullDetails(local.getNickname()); } public void editRemoveLocalSource(MouseEvent evt) { int selectedRow = table.getSelectionModel().getMinSelectionIndex(); if(selectedRow==-1) return; String nickname = table.getValueAt(selectedRow, 0).toString(); if (!localSources.containsKey(nickname)) { JOptionPane.showInternalMessageDialog(Desktop.desktop, "You can only edit or remove local DAS Sources!", "Public DAS source - not editable", JOptionPane.WARNING_MESSAGE); return; } Object[] options = {"Edit", "Remove", "Cancel"}; int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop, "Do you want to edit or remove "+nickname+"?", "Edit / Remove Local DAS Source", JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, options, options[2]); switch(choice) { case 0: amendLocal(false); break; case 1: localSources.remove(nickname); selectedSources.remove(nickname); Object[][] data = new Object[dasSources.length-1][2]; DasSource [] tmp = new DasSource[dasSources.length-1]; int index = 0; for (int i = 0; i < dasSources.length; i++) { if (dasSources[i].getNickname().equals(nickname)) { continue; } else { tmp[index] = dasSources[i]; data[index][0] = dasSources[i].getNickname(); data[index][1] = new Boolean(selectedSources.contains(dasSources[i]. getNickname())); index++; } } dasSources = tmp; refreshTableData(data); SwingUtilities.invokeLater(new Runnable() { public void run() { scrollPane.getVerticalScrollBar().setValue( scrollPane.getVerticalScrollBar().getMaximum() ); } }); break; } } void appendLocalSources() { if(localSources==null) return; int size = dasSources!=null ? dasSources.length : 0; int lsize = localSources.size(); Object[][] data = new Object[size+lsize][2]; for (int i = 0; i < size; i++) { data[i][0] = dasSources[i].getNickname(); data[i][1] = new Boolean(selectedSources.contains(dasSources[i]. getNickname())); } DasSource [] tmp = new DasSource[size+lsize]; if(dasSources!=null) System.arraycopy(dasSources, 0, tmp, 0, size); Enumeration en = localSources.keys(); int index = size; while(en.hasMoreElements()) { String key = en.nextElement().toString(); data[index][0] = key; data[index][1] = new Boolean(false); tmp[index] = new Das1Source(); tmp[index].setNickname(key); tmp[index].setUrl( ((DasSource)localSources.get(key)).getUrl() ); index++; } dasSources = tmp; refreshTableData(data); } public void valueChanged(ListSelectionEvent evt) { //Called when the MainTable selection changes if (evt.getValueIsAdjusting()) { return; } displayFullDetails(null); // Filter the displayed data sources int dSize = dasSources.length; ArrayList names = new ArrayList(); ArrayList selected = new ArrayList(); DasSource ds; //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"}; // capabilities.get for (int i = 0; i < dSize; i++) { ds = dasSources[i]; if (!selectedInList(dummyFeatureList, ds.getCapabilities()) || !selectedInList(filter3.getSelectedValues(), ds.getLabels())) { continue; } DasCoordinateSystem[] dcs = ds.getCoordinateSystem(); for (int j = 0; j < dcs.length; j++) { if (selectedInList(dummyFeatureList,ds.getCapabilities()) && selectedInList(filter1.getSelectedValues(), new String[] {dcs[j].getName()}) && selectedInList(filter2.getSelectedValues(), new String[] {dcs[j].getCategory()})) { names.add(ds.getNickname()); selected.add(new Boolean( selectedSources.contains(ds.getNickname()))); break; } } } 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); } boolean selectedInList(Object [] selection, String[] items) { for (int i = 0; i < selection.length; i++) { if (selection[i].equals("Any")) return true; for (int j = 0; j < items.length; j++) { if (selection[i].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()); } String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE"); if(local!=null) { if(localSources == null) localSources = new Hashtable(); st = new StringTokenizer(local, "\t"); while(st.hasMoreTokens()) { String token = st.nextToken(); int bar = token.indexOf("|"); Das1Source source = new Das1Source(); source.setUrl(token.substring(bar + 1)); source.setNickname(token.substring(0, bar)); localSources.put(source.getNickname(), source); } } } public void saveProperties(Properties properties) { properties.setProperty("DAS_REGISTRY_URL", registryURL.getText()); StringBuffer sb = new StringBuffer(); for(int r=0; r