X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDasSourceBrowser.java;h=c6235301db319ec1ba8855a8be70073796b0f0c7;hb=d4361e0bc5b31c5c659edef5ec825dbdb0615571;hp=e695d3d44d5524869019cd130130a62cdd14e1dc;hpb=dbbd8851fe0e30aa9606657b5f4eb41e0db21563;p=jalview.git diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java index e695d3d..c623530 100755 --- a/src/jalview/gui/DasSourceBrowser.java +++ b/src/jalview/gui/DasSourceBrowser.java @@ -1,20 +1,19 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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 . */ package jalview.gui; @@ -30,8 +29,8 @@ import org.biojava.dasobert.dasregistry.*; import jalview.jbgui.*; import jalview.util.*; -public class DasSourceBrowser - extends GDasSourceBrowser implements Runnable, ListSelectionListener +public class DasSourceBrowser extends GDasSourceBrowser implements + Runnable, ListSelectionListener { static DasSource[] dasSources = null; @@ -39,24 +38,31 @@ public class DasSourceBrowser Vector selectedSources; - public static String DEFAULT_REGISTRY = - "http://www.dasregistry.org/das1/sources/"; + public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das1/sources/"; /** * true if thread is running and we are talking to DAS registry service */ public boolean loadingDasSources = false; - public DasSourceBrowser() + protected static String getDasRegistryURL() { String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL", - DEFAULT_REGISTRY); + DEFAULT_REGISTRY); if (registry.indexOf("/registry/das1/sources/") > -1) { - jalview.bin.Cache.setProperty("DAS_REGISTRY_URL", DEFAULT_REGISTRY); + jalview.bin.Cache.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL, + DEFAULT_REGISTRY); registry = DEFAULT_REGISTRY; } + return registry; + } + + public DasSourceBrowser(FeatureSettings featureSettings) + { + fs = featureSettings; + String registry = getDasRegistryURL(); registryURL.setText(registry); @@ -69,7 +75,7 @@ public class DasSourceBrowser filter2.addListSelectionListener(this); filter3.addListSelectionListener(this); - //Ask to be notified of selection changes. + // Ask to be notified of selection changes. ListSelectionModel rowSM = table.getSelectionModel(); rowSM.addListSelectionListener(new ListSelectionListener() { @@ -89,7 +95,7 @@ public class DasSourceBrowser public void mouseClicked(MouseEvent evt) { if (evt.getClickCount() == 2 - || SwingUtilities.isRightMouseButton(evt)) + || SwingUtilities.isRightMouseButton(evt)) { editRemoveLocalSource(evt); } @@ -102,6 +108,13 @@ public class DasSourceBrowser } } + FeatureSettings fs = null; + + public DasSourceBrowser() + { + this(null); + } + public void paintComponent(java.awt.Graphics g) { if (dasSources == null && !loadingDasSources) @@ -118,8 +131,8 @@ public class DasSourceBrowser for (int i = 0; i < dSize; i++) { data[i][0] = dasSources[i].getNickname(); - data[i][1] = new Boolean(selectedSources.contains(dasSources[i]. - getNickname())); + data[i][1] = new Boolean(selectedSources.contains(dasSources[i] + .getNickname())); } refreshTableData(data); @@ -152,13 +165,12 @@ public class DasSourceBrowser { StringBuffer text = new StringBuffer( - ""); + ""); if (nickName == null) { - fullDetails.setText(text + - "Select a DAS service from the table" - + " to read a full description here."); + fullDetails.setText(text + "Select a DAS service from the table" + + " to read a full description here."); return; } @@ -172,26 +184,23 @@ public class DasSourceBrowser DasSource ds = dasSources[i]; - text.append("Id: " + dasSources[i].getId() + - "
"); - text.append("Nickname: " + - dasSources[i].getNickname() + "
"); - text.append("URL: " + dasSources[i].getUrl() + - "
"); + 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("Admin Email: " + + dasSources[i].getAdminemail() + "" + "
"); - text.append("Registered at: " + - dasSources[i].getRegisterDate() + - "
"); + text.append("Registered at: " + + dasSources[i].getRegisterDate() + "
"); - text.append("Last successful test: " + - dasSources[i].getLeaseDate() + - "
"); + text.append("Last successful test: " + + dasSources[i].getLeaseDate() + "
"); text.append("Labels: "); for (int s = 0; s < dasSources[i].getLabels().length; s++) @@ -222,7 +231,7 @@ public class DasSourceBrowser for (int j = 0; j < dcs.length; j++) { text.append("(" + dcs[j].getUniqueId() + ") " - + dcs[j].getCategory() + ", " + dcs[j].getName()); + + dcs[j].getCategory() + ", " + dcs[j].getName()); if (dcs[j].getNCBITaxId() != 0) { text.append(", " + dcs[j].getNCBITaxId()); @@ -235,15 +244,15 @@ public class DasSourceBrowser text.append("
"); } - text.append("Description: " + - dasSources[i].getDescription() + "
"); + text.append("Description: " + + dasSources[i].getDescription() + "
"); if (dasSources[i].getHelperurl() != null - && dasSources[i].getHelperurl().length() > 0) + && dasSources[i].getHelperurl().length() > 0) { - text.append("Go to site"); + text.append("Go to site"); } text.append(""); @@ -269,25 +278,63 @@ public class DasSourceBrowser refresh.setVisible(false); progressBar.setVisible(true); progressBar.setIndeterminate(true); + setParentGuiEnabled(false); // Refresh the source list. - dasSources=null; + dasSources = null; getDASSource(); - + 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 (dasSources == 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 (int r = 0; r < selectedSources.size(); r++) { for (int i = 0; i < dasSources.length; i++) { - if (dasSources[i].getNickname().equals( - selectedSources.elementAt(r))) + if (dasSources[i].getNickname() + .equals(selectedSources.elementAt(r))) { selected.addElement(dasSources[i]); break; @@ -297,8 +344,10 @@ public class DasSourceBrowser return selected; } + /** * retrieve das sources from registry and add local source list + * * @return */ public DasSource[] getDASSource() @@ -378,30 +427,34 @@ public class DasSourceBrowser 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(); - url = ( (DasSource) localSources.get(nickname)).getUrl(); + url = ((DasSource) localSources.get(nickname)).getUrl(); + seqsrc = ((DasSource) localSources.get(nickname)) + .hasCapability("sequence"); } JTextField nametf = new JTextField(nickname, 40); JTextField urltf = new JTextField(url, 40); - + JCheckBox seqs = new JCheckBox("Sequence Source"); + seqs.setSelected(seqsrc); 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(new JLabel("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, "Enter Nickname & URL of Local DAS Source", - JOptionPane.OK_CANCEL_OPTION); + panel, "Enter Nickname & URL of Local DAS Source", + JOptionPane.OK_CANCEL_OPTION); if (reply != JOptionPane.OK_OPTION) { @@ -417,7 +470,11 @@ public class DasSourceBrowser local.setUrl(urltf.getText()); local.setNickname(nametf.getText()); - + if (seqs.isSelected()) + { + local.setCapabilities(new String[] + { "features", "sequence" }); + } if (localSources == null) { localSources = new Hashtable(); @@ -438,16 +495,16 @@ public class DasSourceBrowser { if (!newSource && dasSources[i].getNickname().equals(nickname)) { - ( (DasSource) dasSources[i]).setNickname(local.getNickname()); - ( (DasSource) dasSources[i]).setUrl(local.getUrl()); + ((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())); + data[i][1] = new Boolean(selectedSources.contains(dasSources[i] + .getNickname())); } } @@ -476,8 +533,7 @@ public class DasSourceBrowser public void run() { scrollPane.getVerticalScrollBar().setValue( - scrollPane.getVerticalScrollBar().getMaximum() - ); + scrollPane.getVerticalScrollBar().getMaximum()); } }); @@ -497,63 +553,58 @@ public class DasSourceBrowser 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); + "You can only edit or remove local DAS Sources!", + "Public DAS source - not editable", + JOptionPane.WARNING_MESSAGE); return; } Object[] options = - { - "Edit", "Remove", "Cancel"}; + { "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]); + "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++) + 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)) { - 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++; - } + continue; } - dasSources = tmp; - refreshTableData(data); - SwingUtilities.invokeLater(new Runnable() + else { - public void run() - { - scrollPane.getVerticalScrollBar().setValue( - scrollPane.getVerticalScrollBar().getMaximum() - ); - } - }); + 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; + break; } } @@ -563,7 +614,8 @@ public class DasSourceBrowser { return; } - + // note - we add all das sources to list so they can be filtered for the + // standard fetchDbRefs function int size = dasSources != null ? dasSources.length : 0; int lsize = localSources.size(); @@ -571,8 +623,8 @@ public class DasSourceBrowser for (int i = 0; i < size; i++) { data[i][0] = dasSources[i].getNickname(); - data[i][1] = new Boolean(selectedSources.contains(dasSources[i]. - getNickname())); + data[i][1] = new Boolean(selectedSources.contains(dasSources[i] + .getNickname())); } DasSource[] tmp = new DasSource[size + lsize]; @@ -590,7 +642,7 @@ public class DasSourceBrowser data[index][1] = new Boolean(false); tmp[index] = new Das1Source(); tmp[index].setNickname(key); - tmp[index].setUrl( ( (DasSource) localSources.get(key)).getUrl()); + tmp[index].setUrl(((DasSource) localSources.get(key)).getUrl()); index++; } @@ -602,7 +654,7 @@ public class DasSourceBrowser public void valueChanged(ListSelectionEvent evt) { - //Called when the MainTable selection changes + // Called when the MainTable selection changes if (evt.getValueIsAdjusting()) { return; @@ -617,12 +669,11 @@ public class DasSourceBrowser 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 + // 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"}; + { "features" }; for (int i = 0; i < dSize; i++) { @@ -630,38 +681,35 @@ public class DasSourceBrowser DasCoordinateSystem[] dcs = ds.getCoordinateSystem(); if (dcs.length == 0 && ds.getCapabilities().length == 0 - && filter1.getSelectedIndex() == 0 - && filter2.getSelectedIndex() == 0 - && filter3.getSelectedIndex() == 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 + // 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()))); + selected.add(new Boolean(selectedSources.contains(ds.getNickname()))); continue; } if (!selectedInList(dummyFeatureList, ds.getCapabilities()) - || !selectedInList(filter3.getSelectedValues(), - ds.getLabels())) + || !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()})) + 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()))); + selected.add(new Boolean(selectedSources.contains(ds + .getNickname()))); break; } } @@ -701,7 +749,8 @@ public class DasSourceBrowser void setSelectedFromProperties() { - String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot"); + String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", + "uniprot"); StringTokenizer st = new StringTokenizer(active, "\t"); selectedSources = new Vector(); while (st.hasMoreTokens()) @@ -709,24 +758,17 @@ public class DasSourceBrowser selectedSources.addElement(st.nextToken()); } - String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE"); - if (local != null) + Vector _localSources = jalview.bin.Cache.getLocalDasSources(); + if (_localSources != null) { if (localSources == null) { localSources = new Hashtable(); } - - st = new StringTokenizer(local, "\t"); - while (st.hasMoreTokens()) + Enumeration sources = _localSources.elements(); + while (sources.hasMoreElements()) { - String token = st.nextToken(); - int bar = token.indexOf("|"); - Das1Source source = new Das1Source(); - - source.setUrl(token.substring(bar + 1)); - source.setNickname(token.substring(0, bar)); - + Das1Source source = (Das1Source) sources.nextElement(); localSources.put(source.getNickname(), source); } } @@ -737,27 +779,34 @@ public class DasSourceBrowser registryURL.setText(DEFAULT_REGISTRY); } + /** + * 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("DAS_REGISTRY_URL"); + properties.remove(jalview.bin.Cache.DAS_REGISTRY_URL); } else { - properties.setProperty("DAS_REGISTRY_URL", registryURL.getText()); + 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()) + if (((Boolean) table.getValueAt(r, 1)).booleanValue()) { sb.append(table.getValueAt(r, 0) + "\t"); } } - properties.setProperty("DAS_ACTIVE_SOURCE", sb.toString()); + properties.setProperty(jalview.bin.Cache.DAS_ACTIVE_SOURCE, + sb.toString()); if (localSources != null) { @@ -766,18 +815,20 @@ public class DasSourceBrowser while (en.hasMoreElements()) { String token = en.nextElement().toString(); - sb.append(token + "|" - + ( (DasSource) localSources.get(token)).getUrl() - + "\t"); + sb.append(token + + "|" + + (((DasSource) localSources.get(token)) + .hasCapability("sequence") ? "sequence:" : "") + + ((DasSource) localSources.get(token)).getUrl() + "\t"); } - properties.setProperty("DAS_LOCAL_SOURCE", sb.toString()); + properties.setProperty(jalview.bin.Cache.DAS_LOCAL_SOURCE, + sb.toString()); } } - class DASTableModel - extends AbstractTableModel + class DASTableModel extends AbstractTableModel { public DASTableModel(Object[][] data) @@ -786,8 +837,7 @@ public class DasSourceBrowser } private String[] columnNames = new String[] - { - "Nickname", "Use Source"}; + { "Nickname", "Use Source" }; private Object[][] data; @@ -812,10 +862,9 @@ public class DasSourceBrowser } /* - * 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. + * 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) { @@ -823,20 +872,18 @@ public class DasSourceBrowser } /* - * Don't need to implement this method unless your table's - * editable. + * 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. + // 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. + * Don't need to implement this method unless your table's data can change. */ public void setValueAt(Object value, int row, int col) { @@ -844,7 +891,7 @@ public class DasSourceBrowser fireTableCellUpdated(row, col); String name = getValueAt(row, 0).toString(); - boolean selected = ( (Boolean) value).booleanValue(); + boolean selected = ((Boolean) value).booleanValue(); if (selectedSources.contains(name) && !selected) { @@ -857,4 +904,59 @@ public class DasSourceBrowser } } } + + 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 || dasSources == null) + { + try + { + Thread.sleep(10); + } catch (Exception e) + { + } + ; + } + } + + public Vector resolveSourceNicknames(Vector sources) + { + + Vector resolved = new Vector(); + if (sources != null) + { + for (int i = 0; i < dasSources.length; i++) + { + if (sources.contains(dasSources[i].getNickname())) + { + if (!resolved.contains(dasSources[i])) + { + resolved.addElement(dasSources[i]); + } + } + } + } + return resolved; + } + + /** + * disable or enable the buttons on the source browser + * + * @param b + */ + public void setGuiEnabled(boolean b) + { + refresh.setEnabled(b); + addLocal.setEnabled(b); + } }