X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDasSourceBrowser.java;h=b1766721ca1efce2675a62a867a028ae1076c0a3;hb=af2dbf10bbcc54d9b9e4d398e9283b3c4a758e06;hp=e78d2d4c2b07391be4979dad26c35138d10f3d21;hpb=4123d7eb50c5959e29ddaf803af285d722d5a8a5;p=jalview.git
diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
old mode 100755
new mode 100644
index e78d2d4..b176672
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -1,810 +1,864 @@
-/*
- * 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
- */
-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.util.*;
-
-
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
-import org.biojava.dasobert.dasregistry.DasSource;
-import org.biojava.dasobert.dasregistry.Das1Source;
-import java.awt.BorderLayout;
-
-public class DasSourceBrowser extends GDasSourceBrowser
- implements Runnable, ListSelectionListener
-{
- static DasSource[] dasSources = null;
-
- Hashtable localSources = null;
-
- Vector selectedSources;
-
- String DEFAULT_REGISTRY = "http://das.sanger.ac.uk/registry/das1/sources/";
-
- boolean loadingDasSources = false;
-
-
- public DasSourceBrowser()
- {
- registryURL.setText(jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
- DEFAULT_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();
- }
- }
-
- 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].getNickname();
- data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
- getNickname()));
- }
-
- 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].getNickname().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() +
- "
");
-
- text.append("Admin Email: "+dasSources[i].getAdminemail()+"" +
- "
");
-
-
- text.append("Registered at: " + dasSources[i].getRegisterDate() +
- "
");
-
- text.append("Last successful test: " + dasSources[i].getLeaseDate() +
- "
");
-
- text.append("Labels: ");
- for(int s=0; s");
-
-
-
- text.append("Capabilities: ");
- String[] scap = dasSources[i].getCapabilities();
- 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("