X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDasSourceBrowser.java;h=c0fefd1df7be7227b55a7cb3a04dd44a8a7d85df;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=d6c0247e51fb0ed7a13f302642e6a46dd3149a0a;hpb=40ecea964afaaf404465d75873ec915b901117a3;p=jalview.git diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java old mode 100755 new mode 100644 index d6c0247..c0fefd1 --- a/src/jalview/gui/DasSourceBrowser.java +++ b/src/jalview/gui/DasSourceBrowser.java @@ -1,855 +1,844 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 java.util.*; - -import java.awt.*; -import java.awt.event.*; -import javax.swing.*; -import javax.swing.event.*; -import javax.swing.table.*; - -import org.biojava.dasobert.dasregistry.*; -import jalview.jbgui.*; -import jalview.util.*; - -public class DasSourceBrowser - extends GDasSourceBrowser implements Runnable, ListSelectionListener -{ - static DasSource[] dasSources = null; - - Hashtable localSources = null; - - Vector selectedSources; - - public static String DEFAULT_REGISTRY = - "http://www.dasregistry.org/das1/sources/"; - - boolean loadingDasSources = false; - - public DasSourceBrowser() - { - String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL", - DEFAULT_REGISTRY); - - if (registry.indexOf("/registry/das1/sources/") > -1) - { - jalview.bin.Cache.setProperty("DAS_REGISTRY_URL", DEFAULT_REGISTRY); - registry = DEFAULT_REGISTRY; - } - - 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() - { - 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() - { - public void mouseClicked(MouseEvent evt) - { - if (evt.getClickCount() == 2 - || SwingUtilities.isRightMouseButton(evt)) - { - editRemoveLocalSource(evt); - } - } - }); - - if (dasSources != null) - { - init(); - } - } - - public void paintComponent(java.awt.Graphics g) - { - if (dasSources == null && !loadingDasSources) - { - Thread worker = new Thread(this); - worker.start(); - } - } - - 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 < dasSources[i].getLabels().length; s++) - { - text.append(dasSources[i].getLabels()[s]); - if (s < dasSources[i].getLabels().length - 1) - { - text.append(","); - } - text.append(" "); - } - text.append("
"); - - 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() - { - loadingDasSources = true; - - addLocal.setVisible(false); - refresh.setVisible(false); - progressBar.setVisible(true); - progressBar.setIndeterminate(true); - - dasSources = jalview.ws.DasSequenceFeatureFetcher.getDASSources(); - - appendLocalSources(); - - init(); - - loadingDasSources = false; - - } - - 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.ws.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"}; - - for (int i = 0; i < dSize; i++) - { - ds = dasSources[i]; - DasCoordinateSystem[] dcs = ds.getCoordinateSystem(); - - if (dcs.length == 0 && ds.getCapabilities().length == 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.getNickname()); - selected.add(new Boolean( - selectedSources.contains(ds.getNickname()))); - continue; - } - - if (!selectedInList(dummyFeatureList, ds.getCapabilities()) - || !selectedInList(filter3.getSelectedValues(), - ds.getLabels())) - { - continue; - } - - for (int j = 0; j < dcs.length; j++) - { - if (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 reset_actionPerformed(ActionEvent e) - { - registryURL.setText(DEFAULT_REGISTRY); - } - - public void saveProperties(Properties properties) - { - if (registryURL.getText() == null || registryURL.getText().length() < 1) - { - properties.remove("DAS_REGISTRY_URL"); - } - else - { - properties.setProperty("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("DAS_ACTIVE_SOURCE", sb.toString()); - - if (localSources != null) - { - sb = new StringBuffer(); - Enumeration en = localSources.keys(); - while (en.hasMoreElements()) - { - String token = en.nextElement().toString(); - sb.append(token + "|" - + ( (DasSource) localSources.get(token)).getUrl() - + "\t"); - } - - properties.setProperty("DAS_LOCAL_SOURCE", sb.toString()); - } - - } - - class DASTableModel - extends AbstractTableModel - { - - public DASTableModel(Object[][] data) - { - this.data = data; - } - - private String[] columnNames = new String[] - { - "Nickname", "Use Source"}; - - private Object[][] data; - - public int getColumnCount() - { - return columnNames.length; - } - - public int getRowCount() - { - return data.length; - } - - public String getColumnName(int col) - { - return columnNames[col]; - } - - 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. - */ - public Class getColumnClass(int c) - { - return getValueAt(0, c).getClass(); - } - - /* - * Don't need to implement this method unless your table's - * editable. - */ - 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. - */ - 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); - } - } - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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 . + * 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 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() + { + 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() + { + public void mouseClicked(MouseEvent evt) + { + if (evt.getClickCount() == 2 + || SwingUtilities.isRightMouseButton(evt)) + { + editRemoveLocalSource(evt); + } + } + }); + + if (sourceRegistry.getSources() != null) + { + init(); + } + } + + FeatureSettings fs = null; + + private boolean loadingDasSources; + + public DasSourceBrowser() + { + this(null); + } + + public void paintComponent(java.awt.Graphics g) + { + if (sourceRegistry == null) + { + Thread worker = new Thread(this); + worker.start(); + } + } + + void init() + { + List 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() + { + 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 + + 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("Id: " + ds.getUri() + + "
"); + text.append("Nickname: " + + ds.getTitle() + "
"); + + text.append("URL: " + ds.getSourceURL() + "" + + "
"); + if (!ds.isLocal()) + { + if (ds.getDocHref() != null && ds.getDocHref().length() > 0) + { + text.append("Site: " + ds.getDocHref() + "" + + "
"); + } + + text.append("Description: " + + ds.getDescription() + "
"); + + text.append("Admin Email: " + ds.getEmail() + "" + "
"); + + text.append("Registered at: " + + latest.getCreated() + "
"); + + // TODO: Identify last successful test date + // text.append("Last successful test: " + // + latest.dasSources[i].getLeaseDate() + "
"); + } + else + { + text.append("Source was added manually.
"); + } + text.append("Labels: "); + 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("
"); + + text.append("Capabilities: "); + 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("
"); + + text.append("Coordinates:"); + int i = 1; + for (COORDINATES dcs : latest.getCOORDINATES()) + { + text.append("
" + 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(" (" + dcs.getUri() + + ")"); + } + text.append(""); + + break; + } + + fullDetails.setText(text.toString()); + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + fullDetailsScrollpane.getVerticalScrollBar().setValue(0); + } + }); + } + + 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 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 selected = new Vector(); + for (String source : selectedSources) + { + jalviewSourceI srce = sourceRegistry.getSource(source); + if (srce != null) + { + selected.addElement(srce); + } + } + return selected; + } + + public void refresh_actionPerformed(ActionEvent e) + { + saveProperties(jalview.bin.Cache.applicationProperties); + + Thread worker = new Thread(this); + worker.start(); + } + + private void setCapabilities(DasSourceRegistryI sourceRegistry2) + { + Vector authority = new Vector(); + Vector type = new Vector(); + Vector label = new Vector(); + Vector taxIds = new Vector(); + 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() + { + public void run() + { + filter1.setSelectedIndex(0); + filter2.setSelectedIndex(0); + filter3.setSelectedIndex(0); + } + }); + } + + 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 = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + panel, + MessageManager.getString("label.enter_local_das_source"), + JOptionPane.OK_CANCEL_OPTION); + + if (reply != JOptionPane.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() + { + 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()) + { + JOptionPane + .showInternalMessageDialog( + Desktop.desktop, + MessageManager + .getString("label.you_can_only_edit_or_remove_local_das_sources"), + MessageManager.getString("label.public_das_source"), + 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: + 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() + { + public void run() + { + scrollPane.getVerticalScrollBar().setValue( + scrollPane.getVerticalScrollBar().getMaximum()); + } + }); + + break; + } + } + + 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 srcs = sourceRegistry.getSources(); + for (jalviewSourceI ds : srcs) + { + + VERSION v = ds.getVersion(); + List 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()); + } + } + + 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; + + public int getColumnCount() + { + return columnNames.length; + } + + public int getRowCount() + { + return data.length; + } + + public String getColumnName(int col) + { + return columnNames[col]; + } + + 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. + */ + public Class getColumnClass(int c) + { + return getValueAt(0, c).getClass(); + } + + /* + * Don't need to implement this method unless your table's editable. + */ + 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. + */ + 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() + { + 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); + } +}