X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;fp=src%2Fjalview%2Fgui%2FPreferences.java;h=cf80a6d955fafe1d9c33da03085430ea424ebe2b;hb=9eabd6dffd6d19b2826b887a5def80351b9bceed;hp=d32ff46212da0dbe2eb8a4a8643e4e16811197da;hpb=9debcac658224e1a84ddff4c4fd9f696e812913f;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index d32ff46..cf80a6d 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -20,11 +20,6 @@
  */
 package jalview.gui;
 
-import static jalview.util.UrlConstants.DB_ACCESSION;
-import static jalview.util.UrlConstants.EMBLEBI_STRING;
-import static jalview.util.UrlConstants.SEQUENCE_ID;
-import static jalview.util.UrlConstants.SRS_STRING;
-
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.bin.Cache;
 import jalview.gui.Help.HelpId;
@@ -37,12 +32,18 @@ import jalview.jbgui.GSequenceLink;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
+import jalview.urls.UrlLinkTableModel;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.desktop.DesktopUrlProviderFactory;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.util.UrlConstants;
 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;
@@ -51,14 +52,24 @@ import java.awt.event.MouseEvent;
 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.JFileChooser;
 import javax.swing.JInternalFrame;
 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;
 
@@ -104,7 +115,9 @@ public class Preferences extends GPreferences
    * 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
@@ -117,40 +130,23 @@ public class Preferences extends GPreferences
   public static List<String> groupURLLinks;
   static
   {
-    String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING);
-    sequenceURLLinks = new Vector<String>();
-
-    try
+    // get links selected to be in the menu (SEQUENCE_LINKS)
+    // and links entered by the user but not selected (STORED_LINKS)
+    String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
+    String notInMenuString = Cache.getDefault("STORED_LINKS", "");
+    String defaultUrl = Cache.getDefault("DEFAULT_URL",
+            UrlConstants.DEFAULT_LABEL);
+
+    // if both links lists are empty, add the DEFAULT_URL link
+    // otherwise we assume the default link is in one of the lists
+    if (inMenuString.isEmpty() && notInMenuString.isEmpty())
     {
-      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("$" + DB_ACCESSION + "$");
-        if (rxstart == -1)
-        {
-          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_STRING);
-      if (srsPos > -1)
-      {
-        sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
-      }
+      inMenuString = UrlConstants.DEFAULT_STRING;
     }
+    UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
+            inMenuString, notInMenuString);
+    sequenceUrlLinks = factory.createUrlProvider();
+    dataModel = new UrlLinkTableModel(sequenceUrlLinks);
 
     /**
      * TODO: reformulate groupURL encoding so two or more can be stored in the
@@ -160,8 +156,6 @@ public class Preferences extends GPreferences
     groupURLLinks = new ArrayList<String>();
   }
 
-  Vector<String> nameLinks, urlLinks;
-
   JInternalFrame frame;
 
   DasSourceBrowser dasSource;
@@ -349,20 +343,128 @@ public class Preferences extends GPreferences
     /*
      * 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<>();
+
+    UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
+    sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
+            SortOrder.DESCENDING));
+    sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
+            SortOrder.DESCENDING));
+    sortKeys.add(new RowSorter.SortKey(m.getNameColumn(),
+            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(""));
+      }
+
+    };
+    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)
+      {
+        return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
+      }
+    };
+
+    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()
+    {
+      String caseInsensitiveFlag = "(?i)";
 
-    updateLinkData();
+      @Override
+      public void changedUpdate(DocumentEvent e)
+      {
+        sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
+                + filterTB.getText()));
+      }
+
+      @Override
+      public void removeUpdate(DocumentEvent e)
+      {
+        sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
+                + filterTB.getText()));
+      }
+
+      @Override
+      public void insertUpdate(DocumentEvent e)
+      {
+        sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
+                + filterTB.getText()));
+      }
+    });
+
+    // set up list selection functionality
+    linkUrlTable.getSelectionModel().addListSelectionListener(
+            new UrlListSelectionHandler());
+
+    // set up radio buttons
+    int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
+            .getPrimaryColumn();
+    String onClickName = linkUrlTable.getColumnName(onClickCol);
+    linkUrlTable.getColumn(onClickName).setCellRenderer(
+               new RadioButtonRenderer());
+    linkUrlTable.getColumn(onClickName)
+            .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));
-    proxyServerTB.setEnabled(useProxy.isSelected());
-    proxyPortTB.setEnabled(useProxy.isSelected());
+    useProxy_actionPerformed(); // make sure useProxy is correctly initialised
     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 
@@ -554,28 +656,32 @@ public class Preferences extends GPreferences
 
     jalview.util.BrowserLauncher.resetBrowser();
 
-    if (nameLinks.size() > 0)
+    // save user-defined and selected links
+    String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
+    if (menuLinks.isEmpty())
+    {
+      Cache.applicationProperties.remove("SEQUENCE_LINKS");
+    }
+    else
     {
-      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());
+              menuLinks.toString());
+    }
+
+    String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
+    if (nonMenuLinks.isEmpty())
+    {
+      Cache.applicationProperties.remove("STORED_LINKS");
     }
     else
     {
-      Cache.applicationProperties.remove("SEQUENCE_LINKS");
-      sequenceURLLinks.clear();
+      Cache.applicationProperties.setProperty("STORED_LINKS",
+              nonMenuLinks.toString());
     }
 
+    Cache.applicationProperties.setProperty("DEFAULT_URL",
+            sequenceUrlLinks.getPrimaryUrlId());
+
     Cache.applicationProperties.setProperty("USE_PROXY",
             Boolean.toString(useProxy.isSelected()));
 
@@ -756,7 +862,6 @@ public class Preferences extends GPreferences
   @Override
   public void newLink_actionPerformed(ActionEvent e)
   {
-
     GSequenceLink link = new GSequenceLink();
     boolean valid = false;
     while (!valid)
@@ -767,10 +872,18 @@ public class Preferences extends GPreferences
       {
         if (link.checkValid())
         {
-          nameLinks.addElement(link.getName());
-          urlLinks.addElement(link.getURL());
-          updateLinkData();
-          valid = true;
+          if (((UrlLinkTableModel) linkUrlTable.getModel())
+                  .isUniqueName(link.getName()))
+          {
+            ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
+                    link.getName(), link.getURL());
+            valid = true;
+          }
+          else
+          {
+            link.notifyDuplicate();
+            continue;
+          }
         }
       }
       else
@@ -785,36 +898,46 @@ public class Preferences extends GPreferences
   {
     GSequenceLink link = new GSequenceLink();
 
-    int index = linkNameList.getSelectedIndex();
+    int index = linkUrlTable.getSelectedRow();
     if (index == -1)
     {
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-              MessageManager.getString("label.no_link_selected"),
-              MessageManager.getString("label.no_link_selected"),
-              JvOptionPane.WARNING_MESSAGE);
+      // button no longer enabled if row is not selected
+      Cache.log.debug("Edit with no row selected in linkUrlTable");
       return;
     }
 
-    link.setName(nameLinks.elementAt(index).toString());
-    link.setURL(urlLinks.elementAt(index).toString());
+    int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
+            .getNameColumn();
+    int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
+            .getUrlColumn();
+    String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
+    link.setName(oldName);
+    link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 
     boolean valid = false;
     while (!valid)
     {
-
       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
-              MessageManager.getString("label.new_sequence_url_link"),
+              MessageManager.getString("label.edit_sequence_url_link"),
               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
       {
         if (link.checkValid())
         {
-          nameLinks.setElementAt(link.getName(), index);
-          urlLinks.setElementAt(link.getURL(), index);
-          updateLinkData();
-          valid = true;
+          if ((oldName.equals(link.getName()))
+                  || (((UrlLinkTableModel) linkUrlTable.getModel())
+                          .isUniqueName(link.getName())))
+          {
+            linkUrlTable.setValueAt(link.getName(), index, nameCol);
+            linkUrlTable.setValueAt(link.getURL(), index, urlCol);
+            valid = true;
+          }
+          else
+          {
+            link.notifyDuplicate();
+            continue;
+          }
         }
       }
-
       else
       {
         break;
@@ -825,26 +948,24 @@ public class Preferences extends GPreferences
   @Override
   public void deleteLink_actionPerformed(ActionEvent e)
   {
-    int index = linkNameList.getSelectedIndex();
+    int index = linkUrlTable.getSelectedRow();
+    int modelIndex = -1;
     if (index == -1)
     {
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-              MessageManager.getString("label.no_link_selected"),
-              MessageManager.getString("label.no_link_selected"),
-              JvOptionPane.WARNING_MESSAGE);
+      // button no longer enabled if row is not selected
+      Cache.log.debug("Delete with no row selected in linkUrlTable");
       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)
   {
@@ -1061,4 +1182,45 @@ public class Preferences extends GPreferences
       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);
+
+      // enable/disable edit and delete link buttons
+      if (((UrlLinkTableModel) linkUrlTable.getModel())
+              .isRowDeletable(modelIndex))
+      {
+        deleteLink.setEnabled(true);
+      }
+      else
+      {
+        deleteLink.setEnabled(false);
+      }
+
+      if (((UrlLinkTableModel) linkUrlTable.getModel())
+              .isRowEditable(modelIndex))
+      {
+        editLink.setEnabled(true);
+      }
+      else
+      {
+        editLink.setEnabled(false);
+      }
+    }
+}
 }