/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.gui;\r
\r
-import jalview.jbgui.*;\r
-import javax.swing.table.AbstractTableModel;\r
-import javax.swing.event.*;\r
-import jalview.util.TableSorter;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
import java.util.*;\r
\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+import javax.swing.*;\r
+import javax.swing.event.*;\r
+import javax.swing.table.*;\r
\r
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;\r
-import org.biojava.dasobert.dasregistry.DasSource;\r
-import org.biojava.dasobert.dasregistry.Das1Source;\r
-import java.awt.BorderLayout;\r
+import org.biojava.dasobert.dasregistry.*;\r
+import jalview.jbgui.*;\r
+import jalview.util.*;\r
\r
-public class DasSourceBrowser extends GDasSourceBrowser\r
- implements Runnable, ListSelectionListener\r
+public class DasSourceBrowser extends GDasSourceBrowser implements\r
+ Runnable, ListSelectionListener\r
{\r
static DasSource[] dasSources = null;\r
\r
\r
Vector selectedSources;\r
\r
- String DEFAULT_REGISTRY = "http://das.sanger.ac.uk/registry/das1/sources/";\r
+ public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das1/sources/";\r
\r
- boolean loadingDasSources = false;\r
+ /**\r
+ * true if thread is running and we are talking to DAS registry service\r
+ */\r
+ public boolean loadingDasSources = false;\r
\r
+ protected static String getDasRegistryURL()\r
+ {\r
+ String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
+ DEFAULT_REGISTRY);\r
\r
- public DasSourceBrowser()\r
+ if (registry.indexOf("/registry/das1/sources/") > -1)\r
+ {\r
+ jalview.bin.Cache.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL,\r
+ DEFAULT_REGISTRY);\r
+ registry = DEFAULT_REGISTRY;\r
+ }\r
+ return registry;\r
+ }\r
+\r
+ public DasSourceBrowser(FeatureSettings featureSettings)\r
{\r
- registryURL.setText(jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
- DEFAULT_REGISTRY) );\r
+ fs = featureSettings;\r
+ String registry = getDasRegistryURL();\r
+\r
+ registryURL.setText(registry);\r
\r
setSelectedFromProperties();\r
\r
filter2.addListSelectionListener(this);\r
filter3.addListSelectionListener(this);\r
\r
- //Ask to be notified of selection changes.\r
+ // Ask to be notified of selection changes.\r
ListSelectionModel rowSM = table.getSelectionModel();\r
rowSM.addListSelectionListener(new ListSelectionListener()\r
{\r
});\r
\r
table.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ if (evt.getClickCount() == 2\r
+ || SwingUtilities.isRightMouseButton(evt))\r
{\r
- public void mouseClicked(MouseEvent evt)\r
- {\r
- if(evt.getClickCount()==2\r
- || SwingUtilities.isRightMouseButton(evt))\r
- editRemoveLocalSource(evt);\r
- }\r
- });\r
+ editRemoveLocalSource(evt);\r
+ }\r
+ }\r
+ });\r
\r
- if(dasSources!=null)\r
+ if (dasSources != null)\r
{\r
- init();\r
+ init();\r
}\r
}\r
\r
+ FeatureSettings fs = null;\r
+\r
+ public DasSourceBrowser()\r
+ {\r
+ this(null);\r
+ }\r
+\r
public void paintComponent(java.awt.Graphics g)\r
{\r
if (dasSources == null && !loadingDasSources)\r
for (int i = 0; i < dSize; i++)\r
{\r
data[i][0] = dasSources[i].getNickname();\r
- data[i][1] = new Boolean(selectedSources.contains(dasSources[i].\r
- getNickname()));\r
+ data[i][1] = new Boolean(selectedSources.contains(dasSources[i]\r
+ .getNickname()));\r
}\r
\r
refreshTableData(data);\r
setCapabilities(dasSources);\r
\r
javax.swing.SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- {\r
- TableSorter sorter = (TableSorter)table.getModel();\r
- sorter.setSortingStatus(1, TableSorter.DESCENDING);\r
- sorter.setSortingStatus(1, TableSorter.NOT_SORTED);\r
- }\r
- });\r
+ {\r
+ public void run()\r
+ {\r
+ TableSorter sorter = (TableSorter) table.getModel();\r
+ sorter.setSortingStatus(1, TableSorter.DESCENDING);\r
+ sorter.setSortingStatus(1, TableSorter.NOT_SORTED);\r
+ }\r
+ });\r
\r
progressBar.setIndeterminate(false);\r
progressBar.setVisible(false);\r
refresh.setVisible(true);\r
}\r
\r
-\r
public void refreshTableData(Object[][] data)\r
{\r
TableSorter sorter = new TableSorter(new DASTableModel(data));\r
{\r
\r
StringBuffer text = new StringBuffer(\r
- "<HTML><font size=\"2\" face=\"Verdana, Arial, Helvetica, sans-serif\">");\r
+ "<HTML><font size=\"2\" face=\"Verdana, Arial, Helvetica, sans-serif\">");\r
\r
if (nickName == null)\r
{\r
- fullDetails.setText(text +\r
- "Select a DAS service from the table"\r
- + " to read a full description here.</font></html>");\r
+ fullDetails.setText(text + "Select a DAS service from the table"\r
+ + " to read a full description here.</font></html>");\r
return;\r
}\r
\r
for (int i = 0; i < dSize; i++)\r
{\r
if (!dasSources[i].getNickname().equals(nickName))\r
+ {\r
continue;\r
+ }\r
\r
DasSource ds = dasSources[i];\r
\r
- text.append("<font color=\"#0000FF\">Id:</font> " + dasSources[i].getId() +\r
- "<br>");\r
- text.append("<font color=\"#0000FF\">Nickname:</font> " +\r
- dasSources[i].getNickname() + "<br>");\r
- text.append("<font color=\"#0000FF\">URL:</font> " + dasSources[i].getUrl() +\r
- "<br>");\r
+ text.append("<font color=\"#0000FF\">Id:</font> "\r
+ + dasSources[i].getId() + "<br>");\r
+ text.append("<font color=\"#0000FF\">Nickname:</font> "\r
+ + dasSources[i].getNickname() + "<br>");\r
+ text.append("<font color=\"#0000FF\">URL:</font> "\r
+ + dasSources[i].getUrl() + "<br>");\r
\r
text.append("<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"\r
- +dasSources[i].getAdminemail()\r
- +"\">"+dasSources[i].getAdminemail()+"</a>" +\r
- "<br>");\r
-\r
+ + dasSources[i].getAdminemail()\r
+ + "\">"\r
+ + dasSources[i].getAdminemail() + "</a>" + "<br>");\r
\r
- text.append("<font color=\"#0000FF\">Registered at:</font> " + dasSources[i].getRegisterDate() +\r
- "<br>");\r
+ text.append("<font color=\"#0000FF\">Registered at:</font> "\r
+ + dasSources[i].getRegisterDate() + "<br>");\r
\r
- text.append("<font color=\"#0000FF\">Last successful test:</font> " + dasSources[i].getLeaseDate() +\r
- "<br>");\r
+ text.append("<font color=\"#0000FF\">Last successful test:</font> "\r
+ + dasSources[i].getLeaseDate() + "<br>");\r
\r
text.append("<font color=\"#0000FF\">Labels:</font> ");\r
- for(int s=0; s<dasSources[i].getLabels().length; s++)\r
+ for (int s = 0; s < dasSources[i].getLabels().length; s++)\r
{\r
- text.append( dasSources[i].getLabels()[s]);\r
- if(s<dasSources[i].getLabels().length-1)\r
+ text.append(dasSources[i].getLabels()[s]);\r
+ if (s < dasSources[i].getLabels().length - 1)\r
+ {\r
text.append(",");\r
+ }\r
text.append(" ");\r
}\r
text.append("<br>");\r
\r
-\r
-\r
text.append("<font color=\"#0000FF\">Capabilities:</font> ");\r
String[] scap = dasSources[i].getCapabilities();\r
for (int j = 0; j < scap.length; j++)\r
{\r
text.append(scap[j]);\r
if (j < scap.length - 1)\r
+ {\r
text.append(", ");\r
+ }\r
}\r
text.append("<br>");\r
\r
for (int j = 0; j < dcs.length; j++)\r
{\r
text.append("(" + dcs[j].getUniqueId() + ") "\r
- + dcs[j].getCategory() + ", " + dcs[j].getName());\r
+ + dcs[j].getCategory() + ", " + dcs[j].getName());\r
if (dcs[j].getNCBITaxId() != 0)\r
+ {\r
text.append(", " + dcs[j].getNCBITaxId());\r
+ }\r
if (dcs[j].getOrganismName().length() > 0)\r
+ {\r
text.append(", " + dcs[j].getOrganismName());\r
+ }\r
\r
text.append("<br>");\r
}\r
\r
- text.append("<font color=\"#0000FF\">Description:</font> " +\r
- dasSources[i].getDescription() + "<br>");\r
-\r
+ text.append("<font color=\"#0000FF\">Description:</font> "\r
+ + dasSources[i].getDescription() + "<br>");\r
\r
- if (dasSources[i].getHelperurl()!=null\r
- && dasSources[i].getHelperurl().length() > 0)\r
+ if (dasSources[i].getHelperurl() != null\r
+ && dasSources[i].getHelperurl().length() > 0)\r
{\r
- text.append("<font color=\"#0000FF\"><a href=\"" +\r
- dasSources[i].getHelperurl()\r
- + "\">Go to site</a></font<br>");\r
+ text.append("<font color=\"#0000FF\"><a href=\""\r
+ + dasSources[i].getHelperurl()\r
+ + "\">Go to site</a></font<br>");\r
}\r
\r
text.append("</font></html>");\r
});\r
}\r
\r
-\r
public void run()\r
{\r
loadingDasSources = true;\r
refresh.setVisible(false);\r
progressBar.setVisible(true);\r
progressBar.setIndeterminate(true);\r
-\r
- dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();\r
-\r
- appendLocalSources();\r
+ setParentGuiEnabled(false);\r
+ // Refresh the source list.\r
+ dasSources = null;\r
+ getDASSource();\r
\r
init();\r
\r
+ setParentGuiEnabled(true);\r
loadingDasSources = false;\r
\r
}\r
\r
+ private void setParentGuiEnabled(boolean b)\r
+ {\r
+ if (fs != null)\r
+ {\r
+ fs.fetchDAS.setEnabled(b);\r
+ fs.saveDAS.setEnabled(b);\r
+ }\r
+ }\r
+\r
public Vector getSelectedSources()\r
{\r
- Vector selected = new Vector();\r
- for (int r = 0; r < selectedSources.size(); r++)\r
+ // wait around if we're still loading.\r
+ while (dasSources == null)\r
{\r
- for (int i = 0; i < dasSources.length; i++)\r
+ if (!loadingDasSources)\r
+ {\r
+ new Thread(this).start();\r
+ try\r
+ {\r
+ Thread.sleep(5);\r
+ } catch (Exception e)\r
+ {\r
+ }\r
+ ;\r
+ while (loadingDasSources)\r
{\r
- if (dasSources[i].getNickname().equals(\r
- selectedSources.elementAt(r)))\r
+ try\r
+ {\r
+ Thread.sleep(5);\r
+ } catch (Exception e)\r
{\r
- selected.addElement(dasSources[i]);\r
- break;\r
}\r
+ ;\r
}\r
+ ;\r
+ }\r
+ }\r
+\r
+ Vector selected = new Vector();\r
+ for (int r = 0; r < selectedSources.size(); r++)\r
+ {\r
+ for (int i = 0; i < dasSources.length; i++)\r
+ {\r
+ if (dasSources[i].getNickname()\r
+ .equals(selectedSources.elementAt(r)))\r
+ {\r
+ selected.addElement(dasSources[i]);\r
+ break;\r
+ }\r
+ }\r
}\r
\r
return selected;\r
}\r
\r
+ /**\r
+ * retrieve das sources from registry and add local source list\r
+ * \r
+ * @return\r
+ */\r
public DasSource[] getDASSource()\r
{\r
- if(dasSources==null)\r
+ if (dasSources == null)\r
{\r
- dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();\r
- appendLocalSources();\r
+ dasSources = jalview.ws.DasSequenceFeatureFetcher.getDASSources();\r
+ appendLocalSources();\r
}\r
\r
return dasSources;\r
for (int j = 0; j < dcs.length; j++)\r
{\r
if (!type.contains(dcs[j].getCategory()))\r
+ {\r
type.addElement(dcs[j].getCategory());\r
+ }\r
\r
if (!authority.contains(dcs[j].getName()))\r
+ {\r
authority.addElement(dcs[j].getName());\r
+ }\r
}\r
\r
String[] slabels = ds.getLabels();\r
public void amendLocal(boolean newSource)\r
{\r
String url = "http://localhost:8080/", nickname = "";\r
-\r
- if(!newSource)\r
+ boolean seqsrc = false;\r
+ if (!newSource)\r
{\r
int selectedRow = table.getSelectionModel().getMinSelectionIndex();\r
nickname = table.getValueAt(selectedRow, 0).toString();\r
- url = ((DasSource)localSources.get(nickname)).getUrl();\r
+ url = ((DasSource) localSources.get(nickname)).getUrl();\r
+ seqsrc = ((DasSource) localSources.get(nickname))\r
+ .hasCapability("sequence");\r
}\r
\r
JTextField nametf = new JTextField(nickname, 40);\r
JTextField urltf = new JTextField(url, 40);\r
-\r
+ JCheckBox seqs = new JCheckBox("Sequence Source");\r
+ seqs.setSelected(seqsrc);\r
JPanel panel = new JPanel(new BorderLayout());\r
JPanel pane12 = new JPanel(new BorderLayout());\r
pane12.add(new JLabel("Nickname: "), BorderLayout.CENTER);\r
pane12.add(nametf, BorderLayout.EAST);\r
panel.add(pane12, BorderLayout.NORTH);\r
pane12 = new JPanel(new BorderLayout());\r
- pane12.add(new JLabel("URL: "), BorderLayout.CENTER);\r
+ pane12.add(new JLabel("URL: "), BorderLayout.NORTH);\r
+ pane12.add(seqs, BorderLayout.SOUTH);\r
pane12.add(urltf, BorderLayout.EAST);\r
panel.add(pane12, BorderLayout.SOUTH);\r
\r
-\r
int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
- panel, "Enter Nickname & URL of Local DAS Source",\r
- JOptionPane.OK_CANCEL_OPTION);\r
+ panel, "Enter Nickname & URL of Local DAS Source",\r
+ JOptionPane.OK_CANCEL_OPTION);\r
\r
- if (reply != JOptionPane.OK_OPTION )\r
- {\r
- return;\r
- }\r
+ if (reply != JOptionPane.OK_OPTION)\r
+ {\r
+ return;\r
+ }\r
\r
- if(!urltf.getText().endsWith("/"))\r
- urltf.setText(urltf.getText()+"/");\r
+ if (!urltf.getText().endsWith("/"))\r
+ {\r
+ urltf.setText(urltf.getText() + "/");\r
+ }\r
\r
- Das1Source local = new Das1Source();\r
+ Das1Source local = new Das1Source();\r
\r
- local.setUrl(urltf.getText());\r
- local.setNickname(nametf.getText());\r
+ local.setUrl(urltf.getText());\r
+ local.setNickname(nametf.getText());\r
+ if (seqs.isSelected())\r
+ {\r
+ local.setCapabilities(new String[]\r
+ { "features", "sequence" });\r
+ }\r
+ if (localSources == null)\r
+ {\r
+ localSources = new Hashtable();\r
+ }\r
\r
+ localSources.put(local.getNickname(), local);\r
\r
- if(localSources==null)\r
- localSources = new Hashtable();\r
+ if (!newSource && !nickname.equals(nametf.getText()))\r
+ {\r
+ localSources.remove(nickname);\r
+ }\r
\r
- localSources.put(local.getNickname(), local);\r
+ int size = dasSources.length;\r
+ int adjust = newSource ? 1 : 0;\r
\r
- if(!newSource && !nickname.equals(nametf.getText()))\r
- {\r
- localSources.remove(nickname);\r
- }\r
+ Object[][] data = new Object[size + adjust][2];\r
+ for (int i = 0; i < size; i++)\r
+ {\r
+ if (!newSource && dasSources[i].getNickname().equals(nickname))\r
+ {\r
+ ((DasSource) dasSources[i]).setNickname(local.getNickname());\r
+ ((DasSource) dasSources[i]).setUrl(local.getUrl());\r
+ data[i][0] = local.getNickname();\r
+ data[i][1] = new Boolean(true);\r
+ }\r
+ else\r
+ {\r
+ data[i][0] = dasSources[i].getNickname();\r
+ data[i][1] = new Boolean(selectedSources.contains(dasSources[i]\r
+ .getNickname()));\r
+ }\r
+ }\r
\r
- int size = dasSources.length;\r
- int adjust = newSource ? 1 : 0;\r
+ if (newSource)\r
+ {\r
+ data[size][0] = local.getNickname();\r
+ data[size][1] = new Boolean(true);\r
+ selectedSources.add(local.getNickname());\r
+ }\r
\r
- Object[][] data = new Object[size+adjust][2];\r
- for (int i = 0; i < size; i++)\r
- {\r
- if(!newSource && dasSources[i].getNickname().equals(nickname))\r
- {\r
- ((DasSource)dasSources[i]).setNickname(local.getNickname());\r
- ((DasSource)dasSources[i]).setUrl(local.getUrl());\r
- data[i][0] = local.getNickname();\r
- data[i][1] = new Boolean(true);\r
- }\r
- else\r
- {\r
- data[i][0] = dasSources[i].getNickname();\r
- data[i][1] = new Boolean(selectedSources.contains(dasSources[i].\r
- getNickname()));\r
- }\r
- }\r
+ DasSource[] tmp = new DasSource[size + adjust];\r
\r
- if(newSource)\r
- {\r
- data[size][0] = local.getNickname();\r
- data[size][1] = new Boolean(true);\r
- selectedSources.add(local.getNickname());\r
- }\r
+ System.arraycopy(dasSources, 0, tmp, 0, size);\r
\r
- DasSource [] tmp = new DasSource[size+adjust];\r
+ if (newSource)\r
+ {\r
+ tmp[size] = local;\r
+ }\r
\r
- System.arraycopy(dasSources, 0, tmp, 0, size);\r
+ dasSources = tmp;\r
\r
- if(newSource)\r
- tmp[size] = local;\r
+ refreshTableData(data);\r
\r
- dasSources = tmp;\r
+ SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ scrollPane.getVerticalScrollBar().setValue(\r
+ scrollPane.getVerticalScrollBar().getMaximum());\r
+ }\r
+ });\r
\r
- refreshTableData(data);\r
+ displayFullDetails(local.getNickname());\r
+ }\r
\r
- SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- {\r
- scrollPane.getVerticalScrollBar().setValue(\r
- scrollPane.getVerticalScrollBar().getMaximum()\r
- );\r
- }\r
- });\r
+ public void editRemoveLocalSource(MouseEvent evt)\r
+ {\r
+ int selectedRow = table.getSelectionModel().getMinSelectionIndex();\r
+ if (selectedRow == -1)\r
+ {\r
+ return;\r
+ }\r
\r
- displayFullDetails(local.getNickname());\r
- }\r
+ String nickname = table.getValueAt(selectedRow, 0).toString();\r
\r
- public void editRemoveLocalSource(MouseEvent evt)\r
+ if (!localSources.containsKey(nickname))\r
{\r
- int selectedRow = table.getSelectionModel().getMinSelectionIndex();\r
- if(selectedRow==-1)\r
- return;\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "You can only edit or remove local DAS Sources!",\r
+ "Public DAS source - not editable",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ return;\r
+ }\r
\r
- String nickname = table.getValueAt(selectedRow, 0).toString();\r
+ Object[] options =\r
+ { "Edit", "Remove", "Cancel" };\r
+ int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,\r
+ "Do you want to edit or remove " + nickname + "?",\r
+ "Edit / Remove Local DAS Source",\r
+ JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE,\r
+ null, options, options[2]);\r
\r
- if (!localSources.containsKey(nickname))\r
+ switch (choice)\r
+ {\r
+ case 0:\r
+ amendLocal(false);\r
+ break;\r
+ case 1:\r
+ localSources.remove(nickname);\r
+ selectedSources.remove(nickname);\r
+ Object[][] data = new Object[dasSources.length - 1][2];\r
+ DasSource[] tmp = new DasSource[dasSources.length - 1];\r
+ int index = 0;\r
+ for (int i = 0; i < dasSources.length; i++)\r
{\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "You can only edit or remove local DAS Sources!",\r
- "Public DAS source - not editable",\r
- JOptionPane.WARNING_MESSAGE);\r
- return;\r
+ if (dasSources[i].getNickname().equals(nickname))\r
+ {\r
+ continue;\r
+ }\r
+ else\r
+ {\r
+ tmp[index] = dasSources[i];\r
+ data[index][0] = dasSources[i].getNickname();\r
+ data[index][1] = new Boolean(\r
+ selectedSources.contains(dasSources[i].getNickname()));\r
+ index++;\r
+ }\r
}\r
-\r
-\r
- Object[] options = {"Edit", "Remove", "Cancel"};\r
- int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,\r
- "Do you want to edit or remove "+nickname+"?",\r
- "Edit / Remove Local DAS Source",\r
- JOptionPane.YES_NO_CANCEL_OPTION,\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- options,\r
- options[2]);\r
-\r
- switch(choice)\r
+ dasSources = tmp;\r
+ refreshTableData(data);\r
+ SwingUtilities.invokeLater(new Runnable()\r
{\r
- case 0: amendLocal(false); break;\r
- case 1:\r
- localSources.remove(nickname);\r
- selectedSources.remove(nickname);\r
- Object[][] data = new Object[dasSources.length-1][2];\r
- DasSource [] tmp = new DasSource[dasSources.length-1];\r
- int index = 0;\r
- for (int i = 0; i < dasSources.length; i++)\r
- {\r
- if (dasSources[i].getNickname().equals(nickname))\r
- {\r
- continue;\r
- }\r
- else\r
- {\r
- tmp[index] = dasSources[i];\r
- data[index][0] = dasSources[i].getNickname();\r
- data[index][1] = new Boolean(selectedSources.contains(dasSources[i].\r
- getNickname()));\r
- index++;\r
- }\r
- }\r
- dasSources = tmp;\r
- refreshTableData(data);\r
- SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- {\r
- scrollPane.getVerticalScrollBar().setValue(\r
- scrollPane.getVerticalScrollBar().getMaximum()\r
- );\r
- }\r
- });\r
+ public void run()\r
+ {\r
+ scrollPane.getVerticalScrollBar().setValue(\r
+ scrollPane.getVerticalScrollBar().getMaximum());\r
+ }\r
+ });\r
\r
- break;\r
- }\r
+ break;\r
}\r
+ }\r
\r
- void appendLocalSources()\r
+ void appendLocalSources()\r
+ {\r
+ if (localSources == null)\r
{\r
- if(localSources==null)\r
- return;\r
-\r
- int size = dasSources!=null ? dasSources.length : 0;\r
- int lsize = localSources.size();\r
-\r
- Object[][] data = new Object[size+lsize][2];\r
- for (int i = 0; i < size; i++)\r
- {\r
- data[i][0] = dasSources[i].getNickname();\r
- data[i][1] = new Boolean(selectedSources.contains(dasSources[i].\r
- getNickname()));\r
- }\r
+ return;\r
+ }\r
+ // note - we add all das sources to list so they can be filtered for the\r
+ // standard fetchDbRefs function\r
+ int size = dasSources != null ? dasSources.length : 0;\r
+ int lsize = localSources.size();\r
\r
- DasSource [] tmp = new DasSource[size+lsize];\r
- if(dasSources!=null)\r
- System.arraycopy(dasSources, 0, tmp, 0, size);\r
+ Object[][] data = new Object[size + lsize][2];\r
+ for (int i = 0; i < size; i++)\r
+ {\r
+ data[i][0] = dasSources[i].getNickname();\r
+ data[i][1] = new Boolean(selectedSources.contains(dasSources[i]\r
+ .getNickname()));\r
+ }\r
\r
- Enumeration en = localSources.keys();\r
- int index = size;\r
- while(en.hasMoreElements())\r
- {\r
- String key = en.nextElement().toString();\r
- data[index][0] = key;\r
- data[index][1] = new Boolean(false);\r
- tmp[index] = new Das1Source();\r
- tmp[index].setNickname(key);\r
- tmp[index].setUrl( ((DasSource)localSources.get(key)).getUrl() );\r
+ DasSource[] tmp = new DasSource[size + lsize];\r
+ if (dasSources != null)\r
+ {\r
+ System.arraycopy(dasSources, 0, tmp, 0, size);\r
+ }\r
\r
- index++;\r
- }\r
+ Enumeration en = localSources.keys();\r
+ int index = size;\r
+ while (en.hasMoreElements())\r
+ {\r
+ String key = en.nextElement().toString();\r
+ data[index][0] = key;\r
+ data[index][1] = new Boolean(false);\r
+ tmp[index] = new Das1Source();\r
+ tmp[index].setNickname(key);\r
+ tmp[index].setUrl(((DasSource) localSources.get(key)).getUrl());\r
+\r
+ index++;\r
+ }\r
\r
- dasSources = tmp;\r
+ dasSources = tmp;\r
\r
- refreshTableData(data);\r
+ refreshTableData(data);\r
}\r
\r
public void valueChanged(ListSelectionEvent evt)\r
{\r
- //Called when the MainTable selection changes\r
- if (evt.getValueIsAdjusting() )\r
+ // Called when the MainTable selection changes\r
+ if (evt.getValueIsAdjusting())\r
{\r
return;\r
}\r
\r
-\r
displayFullDetails(null);\r
\r
// Filter the displayed data sources\r
int dSize = dasSources.length;\r
\r
-\r
ArrayList names = new ArrayList();\r
ArrayList selected = new ArrayList();\r
DasSource ds;\r
\r
- //The features filter is not visible, but we must still\r
- //filter the das source list here.\r
- //July 2006 - only 6 sources fo not serve features\r
- Object [] dummyFeatureList = new Object[]{"features"};\r
+ // The features filter is not visible, but we must still\r
+ // filter the das source list here.\r
+ // July 2006 - only 6 sources fo not serve features\r
+ Object[] dummyFeatureList = new Object[]\r
+ { "features" };\r
\r
for (int i = 0; i < dSize; i++)\r
{\r
DasCoordinateSystem[] dcs = ds.getCoordinateSystem();\r
\r
if (dcs.length == 0 && ds.getCapabilities().length == 0\r
- && filter1.getSelectedIndex() == 0\r
- && filter2.getSelectedIndex() == 0\r
- && filter3.getSelectedIndex() == 0)\r
+ && filter1.getSelectedIndex() == 0\r
+ && filter2.getSelectedIndex() == 0\r
+ && filter3.getSelectedIndex() == 0)\r
{\r
- //THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT\r
- //HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT\r
- //IS ADDED FROM THE REGISTRY\r
+ // THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT\r
+ // HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT\r
+ // IS ADDED FROM THE REGISTRY\r
names.add(ds.getNickname());\r
- selected.add(new Boolean(\r
- selectedSources.contains(ds.getNickname())));\r
+ selected.add(new Boolean(selectedSources.contains(ds.getNickname())));\r
continue;\r
}\r
\r
-\r
if (!selectedInList(dummyFeatureList, ds.getCapabilities())\r
- || !selectedInList(filter3.getSelectedValues(),\r
- ds.getLabels()))\r
+ || !selectedInList(filter3.getSelectedValues(),\r
+ ds.getLabels()))\r
{\r
continue;\r
}\r
\r
for (int j = 0; j < dcs.length; j++)\r
{\r
- if ( selectedInList(filter1.getSelectedValues(),\r
- new String[]\r
- {dcs[j].getName()})\r
- && selectedInList(filter2.getSelectedValues(),\r
- new String[]\r
- {dcs[j].getCategory()}))\r
+ if (selectedInList(filter1.getSelectedValues(), new String[]\r
+ { dcs[j].getName() })\r
+ && selectedInList(filter2.getSelectedValues(), new String[]\r
+ { dcs[j].getCategory() }))\r
{\r
names.add(ds.getNickname());\r
- selected.add(new Boolean(\r
- selectedSources.contains(ds.getNickname())));\r
+ selected.add(new Boolean(selectedSources.contains(ds\r
+ .getNickname())));\r
break;\r
}\r
}\r
refreshTableData(data);\r
}\r
\r
- boolean selectedInList(Object [] selection, String[] items)\r
+ boolean selectedInList(Object[] selection, String[] items)\r
{\r
for (int i = 0; i < selection.length; i++)\r
{\r
- if (selection[i].equals("Any") )\r
+ if (selection[i].equals("Any"))\r
+ {\r
return true;\r
+ }\r
\r
for (int j = 0; j < items.length; j++)\r
{\r
if (selection[i].equals(items[j]))\r
+ {\r
return true;\r
+ }\r
}\r
}\r
\r
\r
void setSelectedFromProperties()\r
{\r
- String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");\r
- StringTokenizer st = new StringTokenizer(active, "\t");\r
- selectedSources = new Vector();\r
- while(st.hasMoreTokens())\r
- {\r
- selectedSources.addElement(st.nextToken());\r
- }\r
-\r
- String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");\r
- if(local!=null)\r
- {\r
- if(localSources == null)\r
- localSources = new Hashtable();\r
-\r
- st = new StringTokenizer(local, "\t");\r
- while(st.hasMoreTokens())\r
- {\r
- String token = st.nextToken();\r
- int bar = token.indexOf("|");\r
- Das1Source source = new Das1Source();\r
-\r
- source.setUrl(token.substring(bar + 1));\r
- source.setNickname(token.substring(0, bar));\r
-\r
- localSources.put(source.getNickname(), source);\r
- }\r
- }\r
+ String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",\r
+ "uniprot");\r
+ StringTokenizer st = new StringTokenizer(active, "\t");\r
+ selectedSources = new Vector();\r
+ while (st.hasMoreTokens())\r
+ {\r
+ selectedSources.addElement(st.nextToken());\r
+ }\r
+\r
+ Vector _localSources = jalview.bin.Cache.getLocalDasSources();\r
+ if (_localSources != null)\r
+ {\r
+ if (localSources == null)\r
+ {\r
+ localSources = new Hashtable();\r
+ }\r
+ Enumeration sources = _localSources.elements();\r
+ while (sources.hasMoreElements())\r
+ {\r
+ Das1Source source = (Das1Source) sources.nextElement();\r
+ localSources.put(source.getNickname(), source);\r
+ }\r
+ }\r
}\r
\r
public void reset_actionPerformed(ActionEvent e)\r
registryURL.setText(DEFAULT_REGISTRY);\r
}\r
\r
+ /**\r
+ * set the DAS source settings in the given jalview properties.\r
+ * \r
+ * @param properties\r
+ */\r
public void saveProperties(Properties properties)\r
{\r
if (registryURL.getText() == null || registryURL.getText().length() < 1)\r
- properties.remove("DAS_REGISTRY_URL");\r
+ {\r
+ properties.remove(jalview.bin.Cache.DAS_REGISTRY_URL);\r
+ }\r
else\r
- properties.setProperty("DAS_REGISTRY_URL", registryURL.getText());\r
+ {\r
+ properties.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL,\r
+ registryURL.getText());\r
+ }\r
\r
StringBuffer sb = new StringBuffer();\r
- for(int r=0; r<table.getModel().getRowCount(); r++)\r
+ for (int r = 0; r < table.getModel().getRowCount(); r++)\r
{\r
- if( ((Boolean)table.getValueAt(r,1)).booleanValue())\r
+ if (((Boolean) table.getValueAt(r, 1)).booleanValue())\r
{\r
- sb.append(table.getValueAt(r,0)+"\t");\r
+ sb.append(table.getValueAt(r, 0) + "\t");\r
}\r
}\r
\r
- properties.setProperty("DAS_ACTIVE_SOURCE", sb.toString() );\r
+ properties.setProperty(jalview.bin.Cache.DAS_ACTIVE_SOURCE,\r
+ sb.toString());\r
\r
- if(localSources!=null)\r
+ if (localSources != null)\r
{\r
sb = new StringBuffer();\r
Enumeration en = localSources.keys();\r
- while(en.hasMoreElements())\r
+ while (en.hasMoreElements())\r
{\r
String token = en.nextElement().toString();\r
- sb.append(token+"|"\r
- + ((DasSource)localSources.get(token)).getUrl()\r
- +"\t");\r
+ sb.append(token\r
+ + "|"\r
+ + (((DasSource) localSources.get(token))\r
+ .hasCapability("sequence") ? "sequence:" : "")\r
+ + ((DasSource) localSources.get(token)).getUrl() + "\t");\r
}\r
\r
- properties.setProperty("DAS_LOCAL_SOURCE", sb.toString());\r
+ properties.setProperty(jalview.bin.Cache.DAS_LOCAL_SOURCE,\r
+ sb.toString());\r
}\r
\r
}\r
\r
- class DASTableModel\r
- extends AbstractTableModel\r
+ class DASTableModel extends AbstractTableModel\r
{\r
\r
public DASTableModel(Object[][] data)\r
this.data = data;\r
}\r
\r
- private String[] columnNames = new String[] {"Nickname", "Use Source"};\r
+ private String[] columnNames = new String[]\r
+ { "Nickname", "Use Source" };\r
\r
private Object[][] data;\r
\r
}\r
\r
/*\r
- * JTable uses this method to determine the default renderer/\r
- * editor for each cell. If we didn't implement this method,\r
- * then the last column would contain text ("true"/"false"),\r
- * rather than a check box.\r
+ * JTable uses this method to determine the default renderer/ editor for\r
+ * each cell. If we didn't implement this method, then the last column would\r
+ * contain text ("true"/"false"), rather than a check box.\r
*/\r
public Class getColumnClass(int c)\r
{\r
}\r
\r
/*\r
- * Don't need to implement this method unless your table's\r
- * editable.\r
+ * Don't need to implement this method unless your table's editable.\r
*/\r
public boolean isCellEditable(int row, int col)\r
{\r
- //Note that the data/cell address is constant,\r
- //no matter where the cell appears onscreen.\r
+ // Note that the data/cell address is constant,\r
+ // no matter where the cell appears onscreen.\r
return col == 1;\r
\r
}\r
\r
/*\r
- * Don't need to implement this method unless your table's\r
- * data can change.\r
+ * Don't need to implement this method unless your table's data can change.\r
*/\r
public void setValueAt(Object value, int row, int col)\r
{\r
data[row][col] = value;\r
fireTableCellUpdated(row, col);\r
\r
- String name = getValueAt(row,0).toString();\r
- boolean selected = ((Boolean)value).booleanValue();\r
+ String name = getValueAt(row, 0).toString();\r
+ boolean selected = ((Boolean) value).booleanValue();\r
\r
- if(selectedSources.contains(name) && !selected)\r
+ if (selectedSources.contains(name) && !selected)\r
+ {\r
selectedSources.remove(name);\r
+ }\r
\r
- if(!selectedSources.contains(name) && selected)\r
+ if (!selectedSources.contains(name) && selected)\r
+ {\r
selectedSources.add(name);\r
+ }\r
}\r
}\r
-}\r
\r
+ public void initDasSources()\r
+ {\r
\r
+ Thread thr = new Thread(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ // this actually initialises the das source list\r
+ paintComponent(null); // yuk\r
+ }\r
+ });\r
+ thr.start();\r
+ while (loadingDasSources || dasSources == null)\r
+ {\r
+ try\r
+ {\r
+ Thread.sleep(10);\r
+ } catch (Exception e)\r
+ {\r
+ }\r
+ ;\r
+ }\r
+ }\r
+\r
+ public Vector resolveSourceNicknames(Vector sources)\r
+ {\r
+\r
+ Vector resolved = new Vector();\r
+ if (sources != null)\r
+ {\r
+ for (int i = 0; i < dasSources.length; i++)\r
+ {\r
+ if (sources.contains(dasSources[i].getNickname()))\r
+ {\r
+ if (!resolved.contains(dasSources[i]))\r
+ {\r
+ resolved.addElement(dasSources[i]);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ return resolved;\r
+ }\r
+\r
+ /**\r
+ * disable or enable the buttons on the source browser\r
+ * \r
+ * @param b\r
+ */\r
+ public void setGuiEnabled(boolean b)\r
+ {\r
+ refresh.setEnabled(b);\r
+ addLocal.setEnabled(b);\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff