/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
*/\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\r
+ extends GDasSourceBrowser implements Runnable, ListSelectionListener\r
{\r
static DasSource[] dasSources = null;\r
\r
\r
Vector selectedSources;\r
\r
- public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das1/sources/";\r
+ public static String DEFAULT_REGISTRY =\r
+ "http://www.dasregistry.org/das1/sources/";\r
\r
boolean loadingDasSources = false;\r
\r
-\r
public DasSourceBrowser()\r
{\r
String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
DEFAULT_REGISTRY);\r
\r
- if(registry.indexOf("/registry/das1/sources/")>-1)\r
+ if (registry.indexOf("/registry/das1/sources/") > -1)\r
{\r
jalview.bin.Cache.setProperty("DAS_REGISTRY_URL", DEFAULT_REGISTRY);\r
registry = DEFAULT_REGISTRY;\r
}\r
\r
- registryURL.setText( registry );\r
+ registryURL.setText(registry);\r
\r
setSelectedFromProperties();\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
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
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\">URL:</font> " + dasSources[i].getUrl() +\r
"<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
+ text.append(\r
+ "<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"\r
+ + dasSources[i].getAdminemail()\r
+ + "\">" + dasSources[i].getAdminemail() + "</a>" +\r
+ "<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() +\r
+ "<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() +\r
+ "<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
text.append("(" + dcs[j].getUniqueId() + ") "\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
text.append("<font color=\"#0000FF\">Description:</font> " +\r
dasSources[i].getDescription() + "<br>");\r
\r
-\r
- if (dasSources[i].getHelperurl()!=null\r
+ if (dasSources[i].getHelperurl() != null\r
&& dasSources[i].getHelperurl().length() > 0)\r
{\r
text.append("<font color=\"#0000FF\"><a href=\"" +\r
});\r
}\r
\r
-\r
public void run()\r
{\r
loadingDasSources = true;\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
+ for (int i = 0; i < dasSources.length; i++)\r
+ {\r
+ if (dasSources[i].getNickname().equals(\r
+ selectedSources.elementAt(r)))\r
{\r
- if (dasSources[i].getNickname().equals(\r
- selectedSources.elementAt(r)))\r
- {\r
- selected.addElement(dasSources[i]);\r
- break;\r
- }\r
+ selected.addElement(dasSources[i]);\r
+ break;\r
}\r
+ }\r
}\r
\r
return selected;\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.io.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
{\r
String url = "http://localhost:8080/", nickname = "";\r
\r
- if(!newSource)\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
}\r
\r
JTextField nametf = new JTextField(nickname, 40);\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
\r
- if (reply != JOptionPane.OK_OPTION )\r
- {\r
- return;\r
- }\r
-\r
- if(!urltf.getText().endsWith("/"))\r
- urltf.setText(urltf.getText()+"/");\r
-\r
- Das1Source local = new Das1Source();\r
-\r
- local.setUrl(urltf.getText());\r
- local.setNickname(nametf.getText());\r
+ if (reply != JOptionPane.OK_OPTION)\r
+ {\r
+ return;\r
+ }\r
\r
+ if (!urltf.getText().endsWith("/"))\r
+ {\r
+ urltf.setText(urltf.getText() + "/");\r
+ }\r
\r
- if(localSources==null)\r
- localSources = new Hashtable();\r
+ Das1Source local = new Das1Source();\r
\r
- localSources.put(local.getNickname(), local);\r
+ local.setUrl(urltf.getText());\r
+ local.setNickname(nametf.getText());\r
\r
- if(!newSource && !nickname.equals(nametf.getText()))\r
- {\r
- localSources.remove(nickname);\r
- }\r
+ if (localSources == null)\r
+ {\r
+ localSources = new Hashtable();\r
+ }\r
\r
- int size = dasSources.length;\r
- int adjust = newSource ? 1 : 0;\r
+ localSources.put(local.getNickname(), local);\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
+ if (!newSource && !nickname.equals(nametf.getText()))\r
+ {\r
+ localSources.remove(nickname);\r
+ }\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
+ int size = dasSources.length;\r
+ int adjust = newSource ? 1 : 0;\r
\r
- DasSource [] tmp = new DasSource[size+adjust];\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
- System.arraycopy(dasSources, 0, tmp, 0, size);\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
- if(newSource)\r
- tmp[size] = local;\r
+ DasSource[] tmp = new DasSource[size + adjust];\r
\r
- dasSources = tmp;\r
+ System.arraycopy(dasSources, 0, tmp, 0, size);\r
\r
- refreshTableData(data);\r
+ if (newSource)\r
+ {\r
+ tmp[size] = local;\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
+ dasSources = tmp;\r
\r
- displayFullDetails(local.getNickname());\r
- }\r
+ refreshTableData(data);\r
\r
- public void editRemoveLocalSource(MouseEvent evt)\r
+ SwingUtilities.invokeLater(new Runnable()\r
{\r
- int selectedRow = table.getSelectionModel().getMinSelectionIndex();\r
- if(selectedRow==-1)\r
- return;\r
-\r
- String nickname = table.getValueAt(selectedRow, 0).toString();\r
-\r
- if (!localSources.containsKey(nickname))\r
+ public void run()\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
+ scrollPane.getVerticalScrollBar().setValue(\r
+ scrollPane.getVerticalScrollBar().getMaximum()\r
+ );\r
}\r
+ });\r
\r
+ displayFullDetails(local.getNickname());\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
+ public void editRemoveLocalSource(MouseEvent evt)\r
+ {\r
+ int selectedRow = table.getSelectionModel().getMinSelectionIndex();\r
+ if (selectedRow == -1)\r
+ {\r
+ return;\r
+ }\r
\r
- switch(choice)\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
+ String nickname = table.getValueAt(selectedRow, 0).toString();\r
+\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
+ return;\r
+ }\r
+\r
+ Object[] options =\r
+ {\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
+\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
+ if (dasSources[i].getNickname().equals(nickname))\r
+ {\r
+ continue;\r
+ }\r
+ else\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
+ 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
- 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
+ }\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
\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
+ return;\r
+ }\r
\r
- int size = dasSources!=null ? dasSources.length : 0;\r
- int lsize = localSources.size();\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
+ 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
- DasSource [] tmp = new DasSource[size+lsize];\r
- if(dasSources!=null)\r
- System.arraycopy(dasSources, 0, tmp, 0, size);\r
+ DasSource[] tmp = new DasSource[size + lsize];\r
+ if (dasSources != null)\r
+ {\r
+ System.arraycopy(dasSources, 0, tmp, 0, size);\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
-\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
+ 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
//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
+ Object[] dummyFeatureList = new Object[]\r
+ {\r
+ "features"};\r
\r
for (int i = 0; i < dSize; i++)\r
{\r
//IS ADDED FROM THE REGISTRY\r
names.add(ds.getNickname());\r
selected.add(new Boolean(\r
- selectedSources.contains(ds.getNickname())));\r
+ 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
+ if (selectedInList(filter1.getSelectedValues(),\r
new String[]\r
{dcs[j].getName()})\r
&& selectedInList(filter2.getSelectedValues(),\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", "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
+ {\r
+ localSources = new Hashtable();\r
+ }\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
}\r
\r
public void reset_actionPerformed(ActionEvent e)\r
public void saveProperties(Properties properties)\r
{\r
if (registryURL.getText() == null || registryURL.getText().length() < 1)\r
+ {\r
properties.remove("DAS_REGISTRY_URL");\r
+ }\r
else\r
+ {\r
properties.setProperty("DAS_REGISTRY_URL", 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("DAS_ACTIVE_SOURCE", 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
+ + ( (DasSource) localSources.get(token)).getUrl()\r
+ + "\t");\r
}\r
\r
properties.setProperty("DAS_LOCAL_SOURCE", sb.toString());\r
this.data = data;\r
}\r
\r
- private String[] columnNames = new String[] {"Nickname", "Use Source"};\r
+ private String[] columnNames = new String[]\r
+ {\r
+ "Nickname", "Use Source"};\r
\r
private Object[][] data;\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
-\r
git://source.jalview.org / jalview.git / blobdiff