import jalview.jbgui.GPreferences;
import jalview.jbgui.GSequenceLink;
import jalview.schemes.ColourSchemeProperty;
+import jalview.urls.UrlLinkTableModel;
+import jalview.urls.UrlProvider;
+import jalview.urls.UrlProviderI;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.sifts.SiftsSettings;
import java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Component;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.event.ActionEvent;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
-import java.util.StringTokenizer;
-import java.util.Vector;
import javax.help.HelpSetException;
import javax.swing.JColorChooser;
import javax.swing.JInternalFrame;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
+import javax.swing.ListSelectionModel;
+import javax.swing.RowFilter;
+import javax.swing.RowSorter;
+import javax.swing.SortOrder;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableColumn;
+import javax.swing.table.TableModel;
+import javax.swing.table.TableRowSorter;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
*/
- public static Vector<String> sequenceURLLinks;
+ public static UrlProviderI sequenceUrlLinks;
+
+ public static UrlLinkTableModel dataModel;
/**
* Holds name and link separated with | character. Sequence IDS and Sequences
public static List<String> groupURLLinks;
static
{
- String string = Cache
- .getDefault(
- "SEQUENCE_LINKS",
- "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
- sequenceURLLinks = new Vector<String>();
-
- try
- {
- StringTokenizer st = new StringTokenizer(string, "|");
- while (st.hasMoreElements())
- {
- String name = st.nextToken();
- String url = st.nextToken();
- // check for '|' within a regex
- int rxstart = url.indexOf("$SEQUENCE_ID$");
- while (rxstart == -1 && url.indexOf("/=$") == -1)
- {
- url = url + "|" + st.nextToken();
- }
- sequenceURLLinks.addElement(name + "|" + url);
- }
- } catch (Exception ex)
- {
- System.out.println(ex + "\nError parsing sequence links");
- }
- {
- // upgrade old SRS link
- int srsPos = sequenceURLLinks
- .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
- if (srsPos > -1)
- {
- sequenceURLLinks
- .setElementAt(
- "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
- srsPos);
- }
- }
+ String string = Cache.getDefault("SEQUENCE_LINKS",
+ UrlProviderI.DEFAULT_STRING);
+ sequenceUrlLinks = new UrlProvider(UrlProviderI.DEFAULT_LABEL, string);
+
+ List<String> colNames = new ArrayList<String>();
+ // colNames.add("ID");
+ // TODO KM add to properties file
+ colNames.add("URL");
+ colNames.add("In Menu");
+ colNames.add("Default");
+ dataModel = new UrlLinkTableModel(sequenceUrlLinks, colNames, "ID");
/**
* TODO: reformulate groupURL encoding so two or more can be stored in the
groupURLLinks = new ArrayList<String>();
}
- Vector<String> nameLinks, urlLinks;
-
JInternalFrame frame;
DasSourceBrowser dasSource;
private WsPreferences wsPrefs;
+ private OptionsParam promptEachTimeOpt = new OptionsParam(
+ MessageManager.getString("label.prompt_each_time"),
+ "Prompt each time");
+
+ private OptionsParam lineArtOpt = new OptionsParam(
+ MessageManager.getString("label.lineart"), "Lineart");
+
+ private OptionsParam textOpt = new OptionsParam(
+ MessageManager.getString("action.text"), "Text");
+
/**
* Creates a new Preferences object.
*/
/*
* Set Connections tab defaults
*/
- nameLinks = new Vector<String>();
- urlLinks = new Vector<String>();
- for (int i = 0; i < sequenceURLLinks.size(); i++)
+
+ // set up sorting
+ linkUrlTable.setModel(dataModel);
+ final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
+ linkUrlTable.getModel());
+ linkUrlTable.setRowSorter(sorter);
+ List<RowSorter.SortKey> sortKeys = new ArrayList<>();
+
+ sortKeys.add(new RowSorter.SortKey(3,
+ SortOrder.DESCENDING));
+ sortKeys.add(new RowSorter.SortKey(2, SortOrder.DESCENDING));
+ sortKeys.add(new RowSorter.SortKey(0, SortOrder.ASCENDING));
+
+ sorter.setSortKeys(sortKeys);
+ sorter.sort();
+
+ // set up filtering
+ ActionListener onReset;
+ onReset = new ActionListener()
{
- String link = sequenceURLLinks.elementAt(i).toString();
- nameLinks.addElement(link.substring(0, link.indexOf("|")));
- urlLinks.addElement(link.substring(link.indexOf("|") + 1));
- }
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterTB.setText("");
+ sorter.setRowFilter(RowFilter.regexFilter(""));
+ }
- updateLinkData();
+ };
+ doReset.addActionListener(onReset);
+
+ // filter to display only custom urls
+ final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
+ {
+ @Override
+ public boolean include(
+ Entry<? extends TableModel, ? extends Object> entry)
+ {
+ String id = entry.getStringValue(4);
+ return sequenceUrlLinks.isUserEntry(id);
+ }
+ };
+
+ final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
+ linkUrlTable.getModel());
+ customSorter.setRowFilter(customUrlFilter);
+
+ ActionListener onCustomOnly;
+ onCustomOnly = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterTB.setText("");
+ sorter.setRowFilter(customUrlFilter);
+ }
+ };
+ userOnly.addActionListener(onCustomOnly);
+
+ filterTB.getDocument().addDocumentListener(new DocumentListener()
+ {
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ sorter.setRowFilter(RowFilter.regexFilter("(?i)"
+ + filterTB.getText()));
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ sorter.setRowFilter(RowFilter.regexFilter("(?i)"
+ + filterTB.getText()));
+ }
+
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ sorter.setRowFilter(RowFilter.regexFilter("(?i)"
+ + filterTB.getText()));
+ }
+ });
+
+ // set up list selection functionality
+ linkUrlTable.getSelectionModel().addListSelectionListener(
+ new UrlListSelectionHandler());
+
+ // set up radio buttons
+ linkUrlTable.getColumn("Default").setCellRenderer(
+ new RadioButtonRenderer());
+ linkUrlTable.getColumn("Default")
+ .setCellEditor(new RadioButtonEditor());
+
+ // get boolean columns and resize those to min possible
+ for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
+ {
+ if (linkUrlTable.getModel().getColumnClass(column)
+ .equals(Boolean.class))
+ {
+ TableColumn tableColumn = linkUrlTable.getColumnModel().getColumn(
+ column);
+ int preferredWidth = tableColumn.getMinWidth();
+
+ TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
+ column);
+ Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
+ int cwidth = c.getPreferredSize().width
+ + linkUrlTable.getIntercellSpacing().width;
+ preferredWidth = Math.max(preferredWidth, cwidth);
+
+ tableColumn.setPreferredWidth(preferredWidth);
+ }
+ }
useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
+ useProxy_actionPerformed(); // make sure useProxy is correctly initialised
proxyServerTB.setEnabled(useProxy.isSelected());
proxyPortTB.setEnabled(useProxy.isSelected());
proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
/*
* Set Output tab defaults
*/
- epsRendering
-.addItem("Prompt each time");
- epsRendering.addItem(MessageManager.getString("label.lineart"));
- epsRendering.addItem(MessageManager.getString("action.text"));
- epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
- "Prompt each time"));
+ epsRendering.addItem(promptEachTimeOpt);
+ epsRendering.addItem(lineArtOpt);
+ epsRendering.addItem(textOpt);
+ String defaultEPS = Cache.getDefault("EPS_RENDERING",
+ "Prompt each time");
+ if (defaultEPS.equalsIgnoreCase("Text"))
+ {
+ epsRendering.setSelectedItem(textOpt);
+ }
+ else if (defaultEPS.equalsIgnoreCase("Lineart"))
+ {
+ epsRendering.setSelectedItem(lineArtOpt);
+ }
+ else
+ {
+ epsRendering.setSelectedItem(promptEachTimeOpt);
+ }
autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
userIdWidth.setEnabled(!autoIdWidth.isSelected());
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
/*
* Save Output settings
*/
- if (epsRendering.getSelectedItem().equals("Prompt each time"))
- {
- Cache.applicationProperties.remove("EPS_RENDERING");
- }
- else
- {
- Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
- .getSelectedItem().toString());
- }
+ Cache.applicationProperties.setProperty("EPS_RENDERING",
+ ((OptionsParam) epsRendering.getSelectedItem()).getCode());
/*
* Save Connections settings
jalview.util.BrowserLauncher.resetBrowser();
- if (nameLinks.size() > 0)
+ // save user-defined and selected links
+ String links = linkUrlTable.getModel().toString();
+ if (links.isEmpty())
{
- StringBuffer links = new StringBuffer();
- sequenceURLLinks = new Vector<String>();
- for (int i = 0; i < nameLinks.size(); i++)
- {
- sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
- + urlLinks.elementAt(i));
- links.append(sequenceURLLinks.elementAt(i).toString());
- links.append("|");
- }
- // remove last "|"
- links.setLength(links.length() - 1);
- Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
- links.toString());
+ Cache.applicationProperties.remove("SEQUENCE_LINKS");
}
else
{
- Cache.applicationProperties.remove("SEQUENCE_LINKS");
+ Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
+ links.toString());
}
Cache.applicationProperties.setProperty("USE_PROXY",
{
if (link.checkValid())
{
- nameLinks.addElement(link.getName());
- urlLinks.addElement(link.getURL());
- updateLinkData();
+ ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
+ link.getName(), link.getURL());
valid = true;
}
}
{
GSequenceLink link = new GSequenceLink();
- int index = linkNameList.getSelectedIndex();
+ int index = linkUrlTable.getSelectedRow();
if (index == -1)
{
+ // no row was selected
JOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.no_link_selected"),
MessageManager.getString("label.no_link_selected"),
return;
}
- link.setName(nameLinks.elementAt(index).toString());
- link.setURL(urlLinks.elementAt(index).toString());
+ link.setName(linkUrlTable.getValueAt(index, 0).toString());
+ link.setURL(linkUrlTable.getValueAt(index, 1).toString());
boolean valid = false;
while (!valid)
{
if (link.checkValid())
{
- nameLinks.setElementAt(link.getName(), index);
- urlLinks.setElementAt(link.getURL(), index);
- updateLinkData();
+
+ linkUrlTable.setValueAt(link.getName(), index, 0);
+ linkUrlTable.setValueAt(link.getURL(), index, 1);
valid = true;
}
}
-
else
{
break;
@Override
public void deleteLink_actionPerformed(ActionEvent e)
{
- int index = linkNameList.getSelectedIndex();
+ int index = linkUrlTable.getSelectedRow();
+ int modelIndex = -1;
if (index == -1)
{
+ // no row is selected
JOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.no_link_selected"),
MessageManager.getString("label.no_link_selected"),
JOptionPane.WARNING_MESSAGE);
return;
}
- nameLinks.removeElementAt(index);
- urlLinks.removeElementAt(index);
- updateLinkData();
- }
+ else
+ {
+ modelIndex = linkUrlTable.convertRowIndexToModel(index);
+ }
- void updateLinkData()
- {
- linkNameList.setListData(nameLinks);
- linkURLList.setListData(urlLinks);
+ // make sure we use the model index to delete, and not the table index
+ ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
}
+
@Override
public void defaultBrowser_mouseClicked(MouseEvent e)
{
}
}
+ public class OptionsParam
+ {
+ private String name;
+
+ private String code;
+
+ public OptionsParam(String name, String code)
+ {
+ this.name = name;
+ this.code = code;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+
+ public String getCode()
+ {
+ return code;
+ }
+
+ public void setCode(String code)
+ {
+ this.code = code;
+ }
+
+ @Override
+ public String toString()
+ {
+ return name;
+ }
+
+ @Override
+ public boolean equals(Object that)
+ {
+ if (!(that instanceof OptionsParam))
+ {
+ return false;
+ }
+ return this.code.equalsIgnoreCase(((OptionsParam) that).code);
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return name.hashCode() + code.hashCode();
+ }
+ }
+
+ private class UrlListSelectionHandler implements ListSelectionListener
+ {
+
+ @Override
+ public void valueChanged(ListSelectionEvent e)
+ {
+ ListSelectionModel lsm = (ListSelectionModel) e.getSource();
+
+ int index = lsm.getMinSelectionIndex();
+ if (index == -1)
+ {
+ // no selection, so disable delete/edit buttons
+ editLink.setEnabled(false);
+ deleteLink.setEnabled(false);
+ return;
+ }
+ int modelIndex = linkUrlTable.convertRowIndexToModel(index);
+
+ // determine if the new selection is a custom url or not
+ if (!sequenceUrlLinks.isUserEntry((String) linkUrlTable
+.getModel()
+ .getValueAt(modelIndex, 4))) // KM TODO do this better
+ {
+ // entry is not a user-defined url and so should not be edited
+ // disable edit and delete buttons
+ deleteLink.setEnabled(false);
+ editLink.setEnabled(false);
+ }
+ else
+ {
+ deleteLink.setEnabled(true);
+ editLink.setEnabled(true);
+ }
+
+ // BUT it's the default url, don't allow deletion
+ if ((boolean) linkUrlTable.getValueAt(index, 3))
+ {
+ deleteLink.setEnabled(false);
+ }
+ }
+}
}
git://source.jalview.org / jalview.git / blobdiff