X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDasSourceBrowser.java;h=71efbd073ab55c0532b6a7fa5737416250c7e461;hb=e33b171845992fd21094ba754498f9ab3d29f110;hp=7f41d3cba535e49c22115dd2d28e447b5e68d564;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java index 7f41d3c..71efbd0 100755 --- a/src/jalview/gui/DasSourceBrowser.java +++ b/src/jalview/gui/DasSourceBrowser.java @@ -1,59 +1,66 @@ /* - * 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, J Engelhardt, LM Lui, 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; -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 +import jalview.jbgui.GDasSourceBrowser; +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 { - static DasSource[] dasSources = null; - - Hashtable localSources = null; - - Vector selectedSources; + DasSourceRegistryI sourceRegistry = null; - public static String DEFAULT_REGISTRY = - "http://www.dasregistry.org/das1/sources/"; + Vector selectedSources; - boolean loadingDasSources = false; - - public DasSourceBrowser() + public DasSourceBrowser(FeatureSettings featureSettings) { - 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; - } + fs = featureSettings; + // TODO DasSourceRegistryProvider API + sourceRegistry = jalview.bin.Cache.getDasSourceRegistry(); + String registry = sourceRegistry.getDasRegistryURL(); registryURL.setText(registry); @@ -66,7 +73,7 @@ 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() { @@ -86,22 +93,31 @@ public class DasSourceBrowser public void mouseClicked(MouseEvent evt) { if (evt.getClickCount() == 2 - || SwingUtilities.isRightMouseButton(evt)) + || SwingUtilities.isRightMouseButton(evt)) { editRemoveLocalSource(evt); } } }); - if (dasSources != null) + if (sourceRegistry.getSources() != null) { init(); } } + FeatureSettings fs = null; + + private boolean loadingDasSources; + + public DasSourceBrowser() + { + this(null); + } + public void paintComponent(java.awt.Graphics g) { - if (dasSources == null && !loadingDasSources) + if (sourceRegistry == null) { Thread worker = new Thread(this); worker.start(); @@ -110,17 +126,18 @@ public class DasSourceBrowser void init() { - int dSize = dasSources.length; + List sources = sourceRegistry.getSources(); + int dSize = sources.size(); 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())); + 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(dasSources); + setCapabilities(sourceRegistry); javax.swing.SwingUtilities.invokeLater(new Runnable() { @@ -149,64 +166,82 @@ 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; } - int dSize = dasSources.length; - for (int i = 0; i < dSize; i++) + int dSize = sourceRegistry.getSources().size(); + for (jalviewSourceI ds : sourceRegistry.getSources()) { - if (!dasSources[i].getNickname().equals(nickName)) + if (!ds.getTitle().equals(nickName)) { continue; } - DasSource ds = dasSources[i]; + VERSION latest = ds.getVersion(); + text.append("Id: " + ds.getUri() + + "
"); + text.append("Nickname: " + + ds.getTitle() + "
"); - text.append("Id: " + dasSources[i].getId() + - "
"); - text.append("Nickname: " + - dasSources[i].getNickname() + "
"); - text.append("URL: " + dasSources[i].getUrl() + - "
"); + text.append("URL: " + ds.getSourceURL() + "" + + "
"); + if (!ds.isLocal()) + { + if (ds.getDocHref() != null && ds.getDocHref().length() > 0) + { + text.append("Site: " + ds.getDocHref() + "" + + "
"); + } - text.append( - "Admin Email: " + dasSources[i].getAdminemail() + "" + - "
"); + text.append("Description: " + + ds.getDescription() + "
"); - text.append("Registered at: " + - dasSources[i].getRegisterDate() + - "
"); + text.append("Admin Email: " + ds.getEmail() + "" + "
"); - text.append("Last successful test: " + - dasSources[i].getLeaseDate() + - "
"); + 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: "); - for (int s = 0; s < dasSources[i].getLabels().length; s++) + boolean b = false; + for (PROP labl : latest.getPROP()) { - text.append(dasSources[i].getLabels()[s]); - if (s < dasSources[i].getLabels().length - 1) + if (labl.getName().equalsIgnoreCase("LABEL")) { - text.append(","); + if (b) + { + text.append(","); + } + text.append(" "); + + text.append(labl.getValue()); + b = true; } - text.append(" "); + ; } text.append("
"); text.append("Capabilities: "); - String[] scap = dasSources[i].getCapabilities(); + CAPABILITY[] scap = latest.getCAPABILITY().toArray(new CAPABILITY[0]); for (int j = 0; j < scap.length; j++) { - text.append(scap[j]); + text.append(scap[j].getType()); if (j < scap.length - 1) { text.append(", "); @@ -214,35 +249,25 @@ public class DasSourceBrowser } text.append("
"); - text.append("Coordinates: "); - DasCoordinateSystem[] dcs = ds.getCoordinateSystem(); - for (int j = 0; j < dcs.length; j++) + text.append("Coordinates:"); + int i=1; + for (COORDINATES dcs : latest.getCOORDINATES()) { - text.append("(" + dcs[j].getUniqueId() + ") " - + dcs[j].getCategory() + ", " + dcs[j].getName()); - if (dcs[j].getNCBITaxId() != 0) + text.append("
"+i+++". "); + text.append(dcs.getAuthority()+" : "+dcs.getSource()); + if (dcs.getTaxid() != null && dcs.getTaxid().trim().length() > 0) { - text.append(", " + dcs[j].getNCBITaxId()); + text.append(" [TaxId:" + dcs.getTaxid()+"]"); } - if (dcs[j].getOrganismName().length() > 0) + if (dcs.getVersion() != null + && dcs.getVersion().trim().length() > 0) { - text.append(", " + dcs[j].getOrganismName()); + { + text.append(" {v. " + dcs.getVersion()+"}"); + } } - - text.append("
"); + text.append(" ("+dcs.getUri() + ")"); } - - text.append("Description: " + - dasSources[i].getDescription() + "
"); - - if (dasSources[i].getHelperurl() != null - && dasSources[i].getHelperurl().length() > 0) - { - text.append("Go to site"); - } - text.append(""); break; @@ -266,45 +291,65 @@ public class DasSourceBrowser refresh.setVisible(false); progressBar.setVisible(true); progressBar.setIndeterminate(true); - - dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources(); - - appendLocalSources(); + setParentGuiEnabled(false); + // Refresh the source list. + sourceRegistry.refreshSources(); init(); + setParentGuiEnabled(true); loadingDasSources = false; } - public Vector getSelectedSources() + private void setParentGuiEnabled(boolean b) + { + if (fs != null) + { + fs.fetchDAS.setEnabled(b); + fs.saveDAS.setEnabled(b); + } + } + + public Vector getSelectedSources() { - Vector selected = new Vector(); - for (int r = 0; r < selectedSources.size(); r++) + // wait around if we're still loading. + while (sourceRegistry == null) { - for (int i = 0; i < dasSources.length; i++) + if (!loadingDasSources) { - if (dasSources[i].getNickname().equals( - selectedSources.elementAt(r))) + new Thread(this).start(); + try { - selected.addElement(dasSources[i]); - break; + Thread.sleep(5); + } catch (Exception e) + { + } + ; + while (loadingDasSources) + { + try + { + Thread.sleep(5); + } catch (Exception e) + { + } + ; } + ; } } - return selected; - } - - public DasSource[] getDASSource() - { - if (dasSources == null) + Vector selected = new Vector(); + for (String source : selectedSources) { - dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources(); - appendLocalSources(); + jalviewSourceI srce = sourceRegistry.getSource(source); + if (srce != null) + { + selected.addElement(srce); + } } - - return dasSources; + return selected; } public void refresh_actionPerformed(ActionEvent e) @@ -315,41 +360,39 @@ public class DasSourceBrowser worker.start(); } - private void setCapabilities(DasSource[] sources) + private void setCapabilities(DasSourceRegistryI sourceRegistry2) { - Vector authority = new Vector(); - Vector type = new Vector(); - Vector label = new Vector(); + 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"); - authority.addElement("Any"); - type.addElement("Any"); - label.addElement("Any"); - - for (int i = 0; i < sources.length; i++) + for (jalviewSourceI ds : sourceRegistry2.getSources()) { - DasSource ds = sources[i]; - - DasCoordinateSystem[] dcs = ds.getCoordinateSystem(); + VERSION latest = ds.getVersion(); - for (int j = 0; j < dcs.length; j++) + for (COORDINATES cs : latest.getCOORDINATES()) { - if (!type.contains(dcs[j].getCategory())) + if (!type.contains(cs.getSource())) { - type.addElement(dcs[j].getCategory()); + type.add(cs.getSource()); // source==category } - if (!authority.contains(dcs[j].getName())) + if (!authority.contains(cs.getAuthority())) { - authority.addElement(dcs[j].getName()); + authority.add(cs.getAuthority()); } } - String[] slabels = ds.getLabels(); - for (int s = 0; s < slabels.length; s++) + for (PROP slabel : latest.getPROP()) { - if (!label.contains(slabels[s])) + if (slabel.getName().equalsIgnoreCase("LABEL") + && !label.contains(slabel.getValue())) { - label.addElement(slabels[s]); + label.add(slabel.getValue()); } } @@ -358,6 +401,7 @@ public class DasSourceBrowser filter1.setListData(authority); filter2.setListData(type); filter3.setListData(label); + // filter4 taxIds javax.swing.SwingUtilities.invokeLater(new Runnable() { @@ -373,30 +417,34 @@ 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(); + 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("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) { @@ -408,62 +456,39 @@ public class DasSourceBrowser 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); + 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); - if (!newSource && !nickname.equals(nametf.getText())) + Object[][] data = new Object[size][2]; + DASTableModel dtm = (table != null) ? (DASTableModel) ((TableSorter) table + .getModel()).getTableModel() : null; + for (int i = 0; i < osize; i++) { - 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)) + String osrc = (dtm == null || i >= osize) ? null : (String) dtm + .getValueAt(i, 0); + if (!newSource && osrc != null + && dtm.getValueAt(i, 0).equals(nickname)) { - ( (DasSource) dasSources[i]).setNickname(local.getNickname()); - ( (DasSource) dasSources[i]).setUrl(local.getUrl()); - data[i][0] = local.getNickname(); + data[i][0] = local.getTitle(); 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][0] = osrc; + data[i][1] = new Boolean(selectedSources.contains(osrc)); } } - + // Always add a new source at the end if (newSource) { - data[size][0] = local.getNickname(); - data[size][1] = new Boolean(true); - selectedSources.add(local.getNickname()); + data[osize][0] = local.getTitle(); + data[osize][1] = new Boolean(true); + selectedSources.add(local.getTitle()); } - 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() @@ -471,12 +496,11 @@ public class DasSourceBrowser public void run() { scrollPane.getVerticalScrollBar().setValue( - scrollPane.getVerticalScrollBar().getMaximum() - ); + scrollPane.getVerticalScrollBar().getMaximum()); } }); - displayFullDetails(local.getNickname()); + displayFullDetails(local.getTitle()); } public void editRemoveLocalSource(MouseEvent evt) @@ -489,115 +513,66 @@ public class DasSourceBrowser String nickname = table.getValueAt(selectedRow, 0).toString(); - if (!localSources.containsKey(nickname)) + if (!sourceRegistry.getSource(nickname).isLocal()) { 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: + 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)) { - 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() - ); - } - }); - - 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()); + 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()); + } + }); - index++; + break; } - - dasSources = tmp; - - refreshTableData(data); } public void valueChanged(ListSelectionEvent evt) { - //Called when the MainTable selection changes + // Called when the MainTable selection changes if (evt.getValueIsAdjusting()) { return; @@ -606,63 +581,57 @@ public class DasSourceBrowser 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 + // 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) + { "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.getNickname()); - selected.add(new Boolean( - selectedSources.contains(ds.getNickname()))); + // 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.getCapabilities()) - || !selectedInList(filter3.getSelectedValues(), - ds.getLabels())) + if (!selectedInList(dummyFeatureList, ds.getCapabilityList(v)) + || !selectedInList(filter3.getSelectedValues(), + ds.getLabelsFor(v))) { continue; } - for (int j = 0; j < dcs.length; j++) + for (int j = 0; j < coords.size(); j++) { - if (selectedInList(filter1.getSelectedValues(), - new String[] - {dcs[j].getName()}) - && selectedInList(filter2.getSelectedValues(), - new String[] - {dcs[j].getCategory()})) + if (selectedInList(filter1.getSelectedValues(), new String[] + { coords.get(j).getAuthority() }) + && selectedInList(filter2.getSelectedValues(), new String[] + { coords.get(j).getSource() })) { - names.add(ds.getNickname()); - selected.add(new Boolean( - selectedSources.contains(ds.getNickname()))); + names.add(ds.getTitle()); + selected.add(new Boolean(selectedSources.contains(ds.getTitle()))); break; } } } - dSize = names.size(); + int dSize = names.size(); Object[][] data = new Object[dSize][2]; for (int d = 0; d < dSize; d++) { @@ -673,7 +642,7 @@ public class DasSourceBrowser refreshTableData(data); } - boolean selectedInList(Object[] selection, String[] items) + private boolean selectedInList(Object[] selection, String[] items) { for (int i = 0; i < selection.length; i++) { @@ -681,10 +650,15 @@ public class DasSourceBrowser { 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 (selection[i].equals(items[j])) + if (sel.equals(items[j])) { return true; } @@ -696,83 +670,55 @@ 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()) { 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); + 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("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()); - - 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()); - } + 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 + class DASTableModel extends AbstractTableModel { public DASTableModel(Object[][] data) @@ -781,8 +727,7 @@ public class DasSourceBrowser } private String[] columnNames = new String[] - { - "Nickname", "Use Source"}; + { "Nickname", "Use Source" }; private Object[][] data; @@ -807,10 +752,9 @@ 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) { @@ -818,20 +762,18 @@ 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) { @@ -839,7 +781,7 @@ 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) { @@ -852,4 +794,39 @@ 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 || 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); + } }