X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDasSourceBrowser.java;fp=src%2Fjalview%2Fgui%2FDasSourceBrowser.java;h=0000000000000000000000000000000000000000;hb=95d7a34b009144b172d60bbb5827df2fbb43524e;hp=8570ac38dc44f1f015ab660042380a98c16561f7;hpb=1c52130ad032d77caac874c3a8be23a399a3ec93;p=jalview.git diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java deleted file mode 100644 index 8570ac3..0000000 --- a/src/jalview/gui/DasSourceBrowser.java +++ /dev/null @@ -1,864 +0,0 @@ -/* - * 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 . - * 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() - { - @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 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( - ""); - - 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() - { - @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 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; - } - - @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 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() - { - @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 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()); - } - } - - @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); - } -}