/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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, 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 java.text.ParseException;\r
import java.util.*;\r
+import java.util.List;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
import javax.swing.event.*;\r
import javax.swing.table.*;\r
\r
-import org.biojava.dasobert.dasregistry.*;\r
+import org.biodas.jdas.dassources.Capabilities;\r
+import org.biodas.jdas.dassources.utils.DasCoordinateSystemCollector;\r
+import org.biodas.jdas.dassources.utils.DasTimeFormat;\r
+import org.biodas.jdas.schema.registrycoordinates.DASCOORDINATESYSTEM;\r
+import org.biodas.jdas.schema.sources.CAPABILITY;\r
+import org.biodas.jdas.schema.sources.COORDINATES;\r
+import org.biodas.jdas.schema.sources.MAINTAINER;\r
+import org.biodas.jdas.schema.sources.PROP;\r
+import org.biodas.jdas.schema.sources.SOURCE;\r
+import org.biodas.jdas.schema.sources.SOURCES;\r
+import org.biodas.jdas.schema.sources.VERSION;\r
+\r
import jalview.jbgui.*;\r
import jalview.util.*;\r
\r
-public class DasSourceBrowser\r
- extends GDasSourceBrowser implements Runnable, ListSelectionListener\r
+public class DasSourceBrowser extends GDasSourceBrowser implements\r
+ Runnable, ListSelectionListener\r
{\r
- static DasSource[] dasSources = null;\r
+ static org.biodas.jdas.schema.sources.SOURCE[] dasSources = null;\r
\r
- Hashtable localSources = null;\r
+ Hashtable<String, SOURCE> localSources = null;\r
\r
Vector selectedSources;\r
\r
- public static String DEFAULT_REGISTRY =\r
- "http://www.dasregistry.org/das1/sources/";\r
+ public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das1/sources/";\r
\r
/**\r
* true if thread is running and we are talking to DAS registry service\r
*/\r
public boolean loadingDasSources = false;\r
\r
- public DasSourceBrowser()\r
+ protected static String getDasRegistryURL()\r
{\r
String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
- DEFAULT_REGISTRY);\r
+ DEFAULT_REGISTRY);\r
\r
if (registry.indexOf("/registry/das1/sources/") > -1)\r
{\r
- jalview.bin.Cache.setProperty("DAS_REGISTRY_URL", DEFAULT_REGISTRY);\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
+ fs = featureSettings;\r
+ String registry = getDasRegistryURL();\r
\r
registryURL.setText(registry);\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
public void mouseClicked(MouseEvent evt)\r
{\r
if (evt.getClickCount() == 2\r
- || SwingUtilities.isRightMouseButton(evt))\r
+ || SwingUtilities.isRightMouseButton(evt))\r
{\r
editRemoveLocalSource(evt);\r
}\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
Object[][] data = new Object[dSize][2];\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][0] = dasSources[i].getTitle(); // what's equivalent of nickname\r
+ data[i][1] = new Boolean(selectedSources.contains(dasSources[i]\r
+ .getTitle()));\r
}\r
\r
refreshTableData(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
int dSize = dasSources.length;\r
for (int i = 0; i < dSize; i++)\r
{\r
- if (!dasSources[i].getNickname().equals(nickName))\r
+ if (!dasSources[i].getTitle().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
+ SOURCE ds = dasSources[i];\r
+ VERSION latest = getVersionFor(ds);\r
+ text.append("<font color=\"#0000FF\">Id:</font> "\r
+ + dasSources[i].getUri() + "<br>");\r
+ text.append("<font color=\"#0000FF\">Nickname:</font> "\r
+ + dasSources[i].getTitle() + "<br>");\r
+ text.append("<font color=\"#0000FF\">URL:</font> " + latest.getUri()\r
+ + "<br>");\r
\r
- text.append(\r
- "<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"\r
- + dasSources[i].getAdminemail()\r
- + "\">" + dasSources[i].getAdminemail() + "</a>" +\r
- "<br>");\r
+ text.append("<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"\r
+ + ds.getMAINTAINER().getEmail()\r
+ + "\">"\r
+ + ds.getMAINTAINER().getEmail() + "</a>" + "<br>");\r
\r
- text.append("<font color=\"#0000FF\">Registered at:</font> " +\r
- dasSources[i].getRegisterDate() +\r
- "<br>");\r
+ text.append("<font color=\"#0000FF\">Registered at:</font> "\r
+ + latest.getCreated() + "<br>");\r
\r
- text.append("<font color=\"#0000FF\">Last successful test:</font> " +\r
- dasSources[i].getLeaseDate() +\r
- "<br>");\r
+ // TODO: Identify last successful test date\r
+ // text.append("<font color=\"#0000FF\">Last successful test:</font> "\r
+ // + latest.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
+ boolean b = false;\r
+ for (PROP labl : latest.getPROP())\r
{\r
- text.append(dasSources[i].getLabels()[s]);\r
- if (s < dasSources[i].getLabels().length - 1)\r
+ if (labl.getName().equalsIgnoreCase("LABEL"))\r
{\r
- text.append(",");\r
+ if (!b)\r
+ {\r
+ text.append(",");\r
+ }\r
+ text.append(" ");\r
+\r
+ text.append(labl.getValue());\r
+ b = true;\r
}\r
- text.append(" ");\r
+ ;\r
}\r
text.append("<br>");\r
\r
text.append("<font color=\"#0000FF\">Capabilities:</font> ");\r
- String[] scap = dasSources[i].getCapabilities();\r
+ CAPABILITY[] scap = latest.getCAPABILITY().toArray(new CAPABILITY[0]);\r
for (int j = 0; j < scap.length; j++)\r
{\r
text.append(scap[j]);\r
text.append("<br>");\r
\r
text.append("<font color=\"#0000FF\">Coordinates:</font> ");\r
- DasCoordinateSystem[] dcs = ds.getCoordinateSystem();\r
- for (int j = 0; j < dcs.length; j++)\r
+ for (COORDINATES dcs : latest.getCOORDINATES())\r
{\r
- text.append("(" + dcs[j].getUniqueId() + ") "\r
- + dcs[j].getCategory() + ", " + dcs[j].getName());\r
- if (dcs[j].getNCBITaxId() != 0)\r
+ text.append("(" + dcs.getUri() + ") "\r
+\r
+ + dcs.getSource() + ", " + dcs.getAuthority());\r
+ if (dcs.getTaxid() != null && dcs.getTaxid().trim().length() > 0)\r
{\r
- text.append(", " + dcs[j].getNCBITaxId());\r
+ text.append(", " + dcs.getTaxid());\r
}\r
- if (dcs[j].getOrganismName().length() > 0)\r
+ if (dcs.getVersion().trim().length() > 0)\r
{\r
- text.append(", " + dcs[j].getOrganismName());\r
- }\r
+ {\r
+ text.append(", " + dcs.getVersion());\r
+ }\r
\r
- text.append("<br>");\r
- }\r
+ text.append("<br>");\r
+ }\r
\r
- text.append("<font color=\"#0000FF\">Description:</font> " +\r
- dasSources[i].getDescription() + "<br>");\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
- {\r
- text.append("<font color=\"#0000FF\"><a href=\"" +\r
- dasSources[i].getHelperurl()\r
- + "\">Go to site</a></font<br>");\r
- }\r
+ if (dasSources[i].getDocHref() != null\r
+ && dasSources[i].getDocHref().length() > 0)\r
+ {\r
+ text.append("<font color=\"#0000FF\"><a href=\""\r
+ + dasSources[i].getDocHref()\r
+ + "\">Go to site</a></font<br>");\r
+ }\r
\r
- text.append("</font></html>");\r
+ text.append("</font></html>");\r
\r
- break;\r
+ break;\r
+ }\r
}\r
-\r
fullDetails.setText(text.toString());\r
javax.swing.SwingUtilities.invokeLater(new Runnable()\r
{\r
refresh.setVisible(false);\r
progressBar.setVisible(true);\r
progressBar.setIndeterminate(true);\r
+ setParentGuiEnabled(false);\r
// Refresh the source list.\r
- dasSources=null;\r
+ dasSources = null;\r
getDASSource();\r
- \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
+ // wait around if we're still loading.\r
+ while (dasSources == null)\r
+ {\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
+ try\r
+ {\r
+ Thread.sleep(5);\r
+ } catch (Exception e)\r
+ {\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().equals(\r
- selectedSources.elementAt(r)))\r
+ if (dasSources[i].getTitle().equals(selectedSources.elementAt(r)))\r
{\r
selected.addElement(dasSources[i]);\r
break;\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
+ public SOURCE[] getDASSource()\r
{\r
if (dasSources == null)\r
{\r
worker.start();\r
}\r
\r
- private void setCapabilities(DasSource[] sources)\r
+ private boolean isLaterThan(String ref, String newer)\r
+ {\r
+ Date refdate = null, newdate = null;\r
+ try\r
+ {\r
+ refdate = DasTimeFormat.fromDASString(ref);\r
+\r
+ } catch (ParseException x)\r
+ {\r
+ return false;\r
+ }\r
+ try\r
+ {\r
+ newdate = DasTimeFormat.fromDASString(newer);\r
+ } catch (ParseException e)\r
+ {\r
+ // TODO: handle exception\r
+ }\r
+ if (refdate != null)\r
+ {\r
+ if (newdate != null)\r
+ {\r
+ return refdate.before(newdate);\r
+ }\r
+ return false;\r
+ }\r
+ if (newdate != null)\r
+ {\r
+ return true;\r
+ }\r
+ // assume first instance of source is newest in list. - TODO: check if\r
+ // natural ordering of source versions is newest first or oldest first\r
+ return false;\r
+ }\r
+\r
+ private VERSION getVersionFor(SOURCE ds)\r
{\r
- Vector authority = new Vector();\r
- Vector type = new Vector();\r
- Vector label = new Vector();\r
+ VERSION latest = null;\r
+ for (VERSION v : ds.getVERSION())\r
+ {\r
+ if (latest == null\r
+ || isLaterThan(latest.getCreated(), v.getCreated()))\r
+ {\r
+ // TODO: das 1.6 - should just get the first version - ignore other\r
+ // versions since not specified how to construct URL from version's URI\r
+ // + source URI\r
+ latest = v;\r
+ }\r
+ }\r
+ return latest;\r
+ }\r
\r
- authority.addElement("Any");\r
- type.addElement("Any");\r
- label.addElement("Any");\r
+ private void setCapabilities(SOURCE[] sources)\r
+ {\r
+ Vector<String> authority = new Vector<String>();\r
+ Vector<String> type = new Vector<String>();\r
+ Vector<String> label = new Vector<String>();\r
+ Vector<String> taxIds = new Vector<String>();\r
+ authority.add("Any");\r
+ type.add("Any");\r
+ label.add("Any");\r
\r
for (int i = 0; i < sources.length; i++)\r
{\r
- DasSource ds = sources[i];\r
-\r
- DasCoordinateSystem[] dcs = ds.getCoordinateSystem();\r
+ SOURCE ds = sources[i];\r
+ VERSION latest = getVersionFor(ds);\r
\r
- for (int j = 0; j < dcs.length; j++)\r
+ for (COORDINATES cs : latest.getCOORDINATES())\r
{\r
- if (!type.contains(dcs[j].getCategory()))\r
+ if (!type.contains(cs.getSource()))\r
{\r
- type.addElement(dcs[j].getCategory());\r
+ type.add(cs.getSource()); // source==category\r
}\r
\r
- if (!authority.contains(dcs[j].getName()))\r
+ if (!authority.contains(cs.getAuthority()))\r
{\r
- authority.addElement(dcs[j].getName());\r
+ authority.add(cs.getAuthority());\r
}\r
}\r
\r
- String[] slabels = ds.getLabels();\r
- for (int s = 0; s < slabels.length; s++)\r
+ for (PROP slabel : latest.getPROP())\r
{\r
- if (!label.contains(slabels[s]))\r
+ if (slabel.getName().equalsIgnoreCase("LABEL")\r
+ && !label.contains(slabel.getValue()))\r
{\r
- label.addElement(slabels[s]);\r
+ label.add(slabel.getValue());\r
}\r
}\r
\r
filter1.setListData(authority);\r
filter2.setListData(type);\r
filter3.setListData(label);\r
+ // filter4 taxIds\r
\r
javax.swing.SwingUtilities.invokeLater(new Runnable()\r
{\r
public void amendLocal(boolean newSource)\r
{\r
String url = "http://localhost:8080/", nickname = "";\r
-\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 = ((SOURCE) localSources.get(nickname)).getUri();\r
+ seqsrc = ((SOURCE) localSources.get(nickname)).getVERSION().get(0)\r
+ .getCAPABILITY().contains(Capabilities.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
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
urltf.setText(urltf.getText() + "/");\r
}\r
\r
- Das1Source local = new Das1Source();\r
-\r
- local.setUrl(urltf.getText());\r
- local.setNickname(nametf.getText());\r
-\r
+ SOURCE local = createLocalSource(urltf.getText(), nametf.getText(), seqs.isSelected(), true);\r
+ \r
if (localSources == null)\r
{\r
localSources = new Hashtable();\r
}\r
\r
- localSources.put(local.getNickname(), local);\r
+ localSources.put(local.getTitle(), local);\r
\r
if (!newSource && !nickname.equals(nametf.getText()))\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
+ if (!newSource && dasSources[i].getTitle().equals(nickname))\r
{\r
- ( (DasSource) dasSources[i]).setNickname(local.getNickname());\r
- ( (DasSource) dasSources[i]).setUrl(local.getUrl());\r
- data[i][0] = local.getNickname();\r
+ dasSources[i] = local;\r
+ data[i][0] = local.getTitle();\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
+ data[i][0] = dasSources[i].getTitle();\r
+ data[i][1] = new Boolean(selectedSources.contains(dasSources[i]\r
+ .getTitle()));\r
}\r
}\r
\r
if (newSource)\r
{\r
- data[size][0] = local.getNickname();\r
+ data[size][0] = local.getTitle();\r
data[size][1] = new Boolean(true);\r
- selectedSources.add(local.getNickname());\r
+ selectedSources.add(local.getTitle());\r
}\r
\r
- DasSource[] tmp = new DasSource[size + adjust];\r
+ SOURCE[] tmp = new SOURCE[size + adjust];\r
\r
System.arraycopy(dasSources, 0, tmp, 0, size);\r
\r
public void run()\r
{\r
scrollPane.getVerticalScrollBar().setValue(\r
- scrollPane.getVerticalScrollBar().getMaximum()\r
- );\r
+ scrollPane.getVerticalScrollBar().getMaximum());\r
}\r
});\r
\r
- displayFullDetails(local.getNickname());\r
+ displayFullDetails(local.getTitle());\r
+ }\r
+\r
+ private SOURCE createLocalSource(String url, String name,\r
+ boolean sequence, boolean features)\r
+ {\r
+ SOURCE local = new SOURCE();\r
+\r
+ local.setUri(url);\r
+ local.setTitle(name);\r
+ local.setVERSION(new ArrayList<VERSION>());\r
+ VERSION v = new VERSION();\r
+ List<CAPABILITY> cp = new ArrayList<CAPABILITY>();\r
+ if (sequence)\r
+ {\r
+/* Could try and synthesize a coordinate system for the source if needbe\r
+ * COORDINATES coord = new COORDINATES();\r
+ coord.setAuthority("NCBI");\r
+ coord.setSource("Chromosome");\r
+ coord.setTaxid("9606");\r
+ coord.setVersion("35");\r
+ version.getCOORDINATES().add(coord);*/\r
+ CAPABILITY cap=new CAPABILITY();\r
+ cap.setType("das1:"+Capabilities.SEQUENCE.getName());\r
+ cp.add(cap);\r
+ }\r
+ if (features)\r
+ {\r
+ CAPABILITY cap = new CAPABILITY();\r
+ cap.setType("das1:"+Capabilities.FEATURES.getName());\r
+ cp.add(cap);\r
+ }\r
+ \r
+ v.getCAPABILITY().addAll(cp);\r
+ local.getVERSION().add(v);\r
+\r
+ return local;\r
}\r
\r
public void editRemoveLocalSource(MouseEvent evt)\r
if (!localSources.containsKey(nickname))\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
+ "You can only edit or remove local DAS Sources!",\r
+ "Public DAS source - not editable",\r
+ JOptionPane.WARNING_MESSAGE);\r
return;\r
}\r
\r
Object[] options =\r
- {\r
- "Edit", "Remove", "Cancel"};\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,\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,\r
- options,\r
- options[2]);\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
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
+ 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
+ SOURCE[] tmp = new SOURCE[dasSources.length - 1];\r
+ int index = 0;\r
+ for (int i = 0; i < dasSources.length; i++)\r
+ {\r
+ if (dasSources[i].getTitle().equals(nickname))\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
+ continue;\r
}\r
- dasSources = tmp;\r
- refreshTableData(data);\r
- SwingUtilities.invokeLater(new Runnable()\r
+ else\r
{\r
- public void run()\r
- {\r
- scrollPane.getVerticalScrollBar().setValue(\r
- scrollPane.getVerticalScrollBar().getMaximum()\r
- );\r
- }\r
- });\r
+ tmp[index] = dasSources[i];\r
+ data[index][0] = dasSources[i].getTitle();\r
+ data[index][1] = new Boolean(\r
+ selectedSources.contains(dasSources[i].getTitle()));\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
- break;\r
+ break;\r
}\r
}\r
\r
{\r
return;\r
}\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
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
+ data[i][0] = dasSources[i].getTitle();\r
+ data[i][1] = new Boolean(selectedSources.contains(dasSources[i]\r
+ .getTitle()));\r
}\r
\r
- DasSource[] tmp = new DasSource[size + lsize];\r
+ SOURCE[] tmp = new SOURCE[size + lsize];\r
if (dasSources != null)\r
{\r
System.arraycopy(dasSources, 0, tmp, 0, size);\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
+ tmp[index] = createLocalSource(localSources.get(key).getUri(), key, false, true);\r
\r
index++;\r
}\r
\r
public void valueChanged(ListSelectionEvent evt)\r
{\r
- //Called when the MainTable selection changes\r
+ // Called when the MainTable selection changes\r
if (evt.getValueIsAdjusting())\r
{\r
return;\r
\r
ArrayList names = new ArrayList();\r
ArrayList selected = new ArrayList();\r
- DasSource ds;\r
+ SOURCE 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
+ // 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
- {\r
- "features"};\r
+ { "features" };\r
\r
for (int i = 0; i < dSize; i++)\r
{\r
ds = dasSources[i];\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
- {\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
+ VERSION v=getVersionFor(ds);\r
+ List<COORDINATES> coords = v.getCOORDINATES();\r
+ if ((coords==null || coords.size()==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
+ names.add(ds.getTitle());\r
+ selected.add(new Boolean(selectedSources.contains(ds.getTitle())));\r
continue;\r
}\r
\r
- if (!selectedInList(dummyFeatureList, ds.getCapabilities())\r
- || !selectedInList(filter3.getSelectedValues(),\r
- ds.getLabels()))\r
+ if (!selectedInList(dummyFeatureList, getCapabilityKeys(v))\r
+ || !selectedInList(filter3.getSelectedValues(),\r
+ getLabelsFor(v)))\r
{\r
continue;\r
}\r
\r
- for (int j = 0; j < dcs.length; j++)\r
+ for (int j = 0; j <coords.size(); 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
+ { coords.get(j).getAuthority() })\r
+ && selectedInList(filter2.getSelectedValues(), new String[]\r
+ { coords.get(j).getSource()}))\r
{\r
- names.add(ds.getNickname());\r
- selected.add(new Boolean(\r
- selectedSources.contains(ds.getNickname())));\r
+ names.add(ds.getTitle());\r
+ selected.add(new Boolean(selectedSources.contains(ds.getTitle())));\r
break;\r
}\r
}\r
refreshTableData(data);\r
}\r
\r
+ private String[] getLabelsFor(VERSION v)\r
+ {\r
+ ArrayList<String> labels=new ArrayList<String>();\r
+ for (PROP p: v.getPROP())\r
+ {\r
+ if (p.getName().equalsIgnoreCase("LABEL"))\r
+ {\r
+ labels.add(p.getValue());\r
+ }\r
+ }\r
+ return labels.toArray(new String[0]);\r
+ }\r
+\r
+ private String[] getCapabilityKeys(VERSION v)\r
+ {\r
+\r
+ ArrayList<String> labels=new ArrayList<String>();\r
+ for (CAPABILITY p: v.getCAPABILITY())\r
+ {\r
+ // TODO: work out what to do with namespace prefix \r
+ // does SEQUENCE == das1:SEQUENCE and das2:SEQUENCE ?\r
+ // for moment, just show all capabilities...\r
+ if (p.getType().startsWith("das1:"))\r
+ {\r
+ labels.add(p.getType());\r
+ }\r
+ }\r
+ return labels.toArray(new String[0]);\r
+ }\r
+\r
boolean selectedInList(Object[] selection, String[] items)\r
{\r
for (int i = 0; i < selection.length; i++)\r
\r
void setSelectedFromProperties()\r
{\r
- String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");\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
selectedSources.addElement(st.nextToken());\r
}\r
\r
- String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");\r
- if (local != null)\r
+ Vector _localSources = jalview.bin.Cache.getLocalDasSources();\r
+ if (_localSources != null)\r
{\r
if (localSources == null)\r
{\r
- localSources = new Hashtable();\r
+ localSources = new Hashtable<String, SOURCE>();\r
}\r
-\r
- st = new StringTokenizer(local, "\t");\r
- while (st.hasMoreTokens())\r
+ Enumeration sources = _localSources.elements();\r
+ while (sources.hasMoreElements())\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
+ SOURCE source = (SOURCE) sources.nextElement();\r
+ localSources.put(source.getTitle(), source);\r
}\r
}\r
}\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
{\r
- properties.remove("DAS_REGISTRY_URL");\r
+ properties.remove(jalview.bin.Cache.DAS_REGISTRY_URL);\r
}\r
else\r
{\r
- properties.setProperty("DAS_REGISTRY_URL", registryURL.getText());\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
{\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
}\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
{\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
+ + (selectedInList(getCapabilityKeys(getVersionFor(localSources.get(token))),\r
+ new String[] { "das1:"+Capabilities.SEQUENCE.getName()}) ? "sequence:" : "")\r
+ + getVersionFor(localSources.get(token)).getUri() + "\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
}\r
\r
private String[] columnNames = new String[]\r
- {\r
- "Nickname", "Use Source"};\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
fireTableCellUpdated(row, col);\r
\r
String name = getValueAt(row, 0).toString();\r
- boolean selected = ( (Boolean) value).booleanValue();\r
+ boolean selected = ((Boolean) value).booleanValue();\r
\r
if (selectedSources.contains(name) && !selected)\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].getTitle()))\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