X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FDasSourceBrowser.java;h=c0fefd1df7be7227b55a7cb3a04dd44a8a7d85df;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=2f257afd52875e85fb3263a51d8b61a6e8cbfe5e;hpb=90d7e508abaf1010078fce1fec804b70179caad5;p=jalview.git
diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
old mode 100755
new mode 100644
index 2f257af..c0fefd1
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -1,1043 +1,844 @@
-/*
- * 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 java.security.interfaces.DSAKey;
-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.DasTimeFormat;
-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.jbgui.*;
-import jalview.util.*;
-
-public class DasSourceBrowser extends GDasSourceBrowser implements
- Runnable, ListSelectionListener
-{
- static org.biodas.jdas.schema.sources.SOURCE[] dasSources = null;
-
- Hashtable localSources = null;
-
- Vector selectedSources;
-
- 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()
- {
- 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();
-
- 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();
- }
- }
-
- 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();
- }
- }
-
- void init()
- {
- int dSize = dasSources.length;
- Object[][] data = new Object[dSize][2];
- for (int i = 0; i < dSize; i++)
- {
- 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);
- }
- });
-
- 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].getTitle().equals(nickName))
- {
- continue;
- }
-
- 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: "
- + ds.getMAINTAINER().getEmail() + "" + "
");
-
- text.append("Registered at: "
- + latest.getCreated() + "
");
-
- // TODO: Identify last successful test date
-// text.append("Last successful test: "
-// + latest.dasSources[i].getLeaseDate() + "
");
-
- text.append("Labels: ");
- for (int s = 0; s < latest.getPROP().length; s++)
- {
- text.append(dasSources[i].getLabels()[s]);
- if (s < dasSources[i].getLabels().length - 1)
- {
- text.append(",");
- }
- text.append(" ");
- }
- 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]);
- 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("