X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDasSourceBrowser.java;h=faf47122677230eca04c79d6616da79df3f9f72c;hb=1d4bc65204bdb63740d3692f13633c463d5c08fd;hp=bdb3b572ff7d28c0c8b03342a68a95f38bca13f5;hpb=8f759d39bf8d95e5657eccda618b65ad31171fcf;p=jalview.git
diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index bdb3b57..faf4712 100755
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -1,50 +1,83 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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;
-import jalview.jbgui.*;
-import javax.swing.table.AbstractTableModel;
-import javax.swing.event.*;
-import jalview.util.TableSorter;
-import java.awt.event.*;
-import javax.swing.*;
+import java.text.ParseException;
import java.util.*;
+import java.util.List;
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+import javax.swing.table.*;
+
+import org.biodas.jdas.dassources.Capabilities;
+import org.biodas.jdas.dassources.utils.DasCoordinateSystemCollector;
+import org.biodas.jdas.dassources.utils.DasTimeFormat;
+import org.biodas.jdas.schema.registrycoordinates.DASCOORDINATESYSTEM;
+import org.biodas.jdas.schema.sources.CAPABILITY;
+import org.biodas.jdas.schema.sources.COORDINATES;
+import org.biodas.jdas.schema.sources.MAINTAINER;
+import org.biodas.jdas.schema.sources.PROP;
+import org.biodas.jdas.schema.sources.SOURCE;
+import org.biodas.jdas.schema.sources.SOURCES;
+import org.biodas.jdas.schema.sources.VERSION;
-import jalview.biojava.dasobert.dasregistry.DasCoordinateSystem;
-import jalview.biojava.dasobert.dasregistry.DasSource;
-import jalview.biojava.dasobert.dasregistry.Das1Source;
-import java.awt.BorderLayout;
+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;
+ static org.biodas.jdas.schema.sources.SOURCE[] dasSources = null;
- Hashtable localSources = null;
+ Hashtable localSources = null;
Vector selectedSources;
- public DasSourceBrowser()
+ 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;
+
+ protected static String getDasRegistryURL()
{
- registryURL.setText(jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
- "http://das.sanger.ac.uk/registry/das1/sources/") );
+ String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
+ DEFAULT_REGISTRY);
+
+ if (registry.indexOf("/registry/das1/sources/") > -1)
+ {
+ 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);
setSelectedFromProperties();
@@ -55,16 +88,12 @@ public class DasSourceBrowser extends GDasSourceBrowser
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()
{
public void valueChanged(ListSelectionEvent e)
{
- //Ignore extra messages.
- if (e.getValueIsAdjusting())
- return;
-
ListSelectionModel lsm = (ListSelectionModel) e.getSource();
if (!lsm.isSelectionEmpty())
{
@@ -75,24 +104,37 @@ public class DasSourceBrowser extends GDasSourceBrowser
});
table.addMouseListener(new MouseAdapter()
+ {
+ public void mouseClicked(MouseEvent evt)
+ {
+ if (evt.getClickCount() == 2
+ || SwingUtilities.isRightMouseButton(evt))
{
- public void mouseClicked(MouseEvent evt)
- {
- if(evt.getClickCount()==2
- || SwingUtilities.isRightMouseButton(evt))
- editRemoveLocalSource(evt);
- }
- });
+ editRemoveLocalSource(evt);
+ }
+ }
+ });
- if(dasSources==null)
+ if (dasSources != null)
{
- Thread worker = new Thread(this);
- worker.start();
+ init();
+ }
+ }
+
+ FeatureSettings fs = null;
+
+ public DasSourceBrowser()
+ {
+ this(null);
+ }
+
+ public void paintComponent(java.awt.Graphics g)
+ {
+ if (dasSources == null && !loadingDasSources)
+ {
+ Thread worker = new Thread(this);
+ worker.start();
}
- else
- {
- init();
- }
}
void init()
@@ -101,23 +143,23 @@ public class DasSourceBrowser extends GDasSourceBrowser
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] = dasSources[i].getTitle(); // what's equivalent of nickname
+ data[i][1] = new Boolean(selectedSources.contains(dasSources[i]
+ .getTitle()));
}
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);
- }
- });
+ {
+ 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);
@@ -125,7 +167,6 @@ public class DasSourceBrowser extends GDasSourceBrowser
refresh.setVisible(true);
}
-
public void refreshTableData(Object[][] data)
{
TableSorter sorter = new TableSorter(new DASTableModel(data));
@@ -137,96 +178,110 @@ public class DasSourceBrowser extends GDasSourceBrowser
{
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++)
{
- if (!dasSources[i].getNickname().equals(nickName))
+ if (!dasSources[i].getTitle().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() +
- "
");
+ SOURCE ds = dasSources[i];
+ VERSION latest = getVersionFor(ds);
+ text.append("Id: "
+ + dasSources[i].getUri() + "
");
+ text.append("Nickname: "
+ + dasSources[i].getTitle() + "
");
+ text.append("URL: " + latest.getUri()
+ + "
");
text.append("Admin Email: "+dasSources[i].getAdminemail()+"" +
- "
");
+ + ds.getMAINTAINER().getEmail()
+ + "\">"
+ + ds.getMAINTAINER().getEmail() + "" + "
");
+ text.append("Registered at: "
+ + latest.getCreated() + "
");
- text.append("Registered at: " + dasSources[i].getRegisterDate() +
- "
");
-
- text.append("Last successful test: " + dasSources[i].getLeaseDate() +
- "
");
+ // TODO: Identify last successful test date
+ // text.append("Last successful test: "
+ // + latest.dasSources[i].getLeaseDate() + "
");
text.append("Labels: ");
- for(int s=0; s");
-
-
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]);
if (j < scap.length - 1)
+ {
text.append(", ");
+ }
}
text.append("
");
text.append("Coordinates: ");
- DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
- for (int j = 0; j < dcs.length; j++)
+ for (COORDINATES dcs : latest.getCOORDINATES())
{
- 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("(" + dcs.getUri() + ") "
- text.append("
");
- }
+ + dcs.getSource() + ", " + dcs.getAuthority());
+ if (dcs.getTaxid() != null && dcs.getTaxid().trim().length() > 0)
+ {
+ text.append(", " + dcs.getTaxid());
+ }
+ if (dcs.getVersion().trim().length() > 0)
+ {
+ {
+ text.append(", " + dcs.getVersion());
+ }
- text.append("Description: " +
- dasSources[i].getDescription() + "
");
+ text.append("
");
+ }
+ text.append("Description: "
+ + dasSources[i].getDescription() + "
");
- if (dasSources[i].getHelperurl()!=null
- && dasSources[i].getHelperurl().length() > 0)
- {
- text.append("Go to site");
- }
+ if (dasSources[i].getDocHref() != null
+ && dasSources[i].getDocHref().length() > 0)
+ {
+ text.append("Go to site");
+ }
- text.append("