JAL-2316 Changes following review.

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 1c40ea1..c5bff31 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -24,6 +24,7 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.bin.Cache;
 import jalview.gui.Help.HelpId;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.FileFormatI;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.GPreferences;
@@ -54,7 +55,6 @@ import javax.help.HelpSetException;
 import javax.swing.JColorChooser;
 import javax.swing.JFileChooser;
 import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.ListSelectionModel;
 import javax.swing.RowFilter;
@@ -346,7 +346,7 @@ public class Preferences extends GPreferences
     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 
     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
-    sortKeys.add(new RowSorter.SortKey(m.getDefaultColumn(),
+    sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
             SortOrder.DESCENDING));
     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
             SortOrder.DESCENDING));
@@ -377,9 +377,7 @@ public class Preferences extends GPreferences
       public boolean include(
               Entry<? extends TableModel, ? extends Object> entry)
       {
-        int col = ((UrlLinkTableModel) entry.getModel()).getIdColumn();
-        String id = entry.getStringValue(col);
-        return sequenceUrlLinks.isUserEntry(id);
+        return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
       }
     };
 
@@ -431,7 +429,7 @@ public class Preferences extends GPreferences
 
     // set up radio buttons
     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
-            .getDefaultColumn();
+            .getPrimaryColumn();
     String onClickName = linkUrlTable.getColumnName(onClickCol);
     linkUrlTable.getColumn(onClickName).setCellRenderer(
                new RadioButtonRenderer());
@@ -678,7 +676,7 @@ public class Preferences extends GPreferences
     }
 
     Cache.applicationProperties.setProperty("DEFAULT_URL",
-            sequenceUrlLinks.getDefaultUrlId());
+            sequenceUrlLinks.getPrimaryUrlId());
 
     Cache.applicationProperties.setProperty("USE_PROXY",
             Boolean.toString(useProxy.isSelected()));
@@ -796,12 +794,9 @@ public class Preferences extends GPreferences
   @Override
   public void startupFileTextfield_mouseClicked()
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
-                "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-                "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
-                "PIR", "BLC", "Jalview" },
-            jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+    String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+    JalviewFileChooser chooser = JalviewFileChooser.forRead(
+            Cache.getProperty("LAST_DIRECTORY"), fileFormat);
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager
             .getString("label.select_startup_file"));
@@ -810,8 +805,12 @@ public class Preferences extends GPreferences
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      jalview.bin.Cache.applicationProperties.setProperty(
-              "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
+      FileFormatI format = chooser.getSelectedFormat();
+      if (format != null)
+      {
+        Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
+                format.toString());
+      }
       startupFileTextfield.setText(chooser.getSelectedFile()
               .getAbsolutePath());
     }
@@ -863,15 +862,24 @@ public class Preferences extends GPreferences
     boolean valid = false;
     while (!valid)
     {
-      if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
               MessageManager.getString("label.new_sequence_url_link"),
-              JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
+              JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
       {
         if (link.checkValid())
         {
-          ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
-                  link.getName(), link.getURL());
-          valid = true;
+          if (((UrlLinkTableModel) linkUrlTable.getModel())
+                  .isUniqueName(link.getName()))
+          {
+            ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
+                    link.getName(), link.getURL());
+            valid = true;
+          }
+          else
+          {
+            link.notifyDuplicate();
+            continue;
+          }
         }
       }
       else
@@ -900,15 +908,24 @@ public class Preferences extends GPreferences
     boolean valid = false;
     while (!valid)
     {
-      if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
               MessageManager.getString("label.edit_sequence_url_link"),
-              JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
+              JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
       {
         if (link.checkValid())
         {
-          linkUrlTable.setValueAt(link.getName(), index, 0);
-          linkUrlTable.setValueAt(link.getURL(), index, 1);
-          valid = true;
+          if (((UrlLinkTableModel) linkUrlTable.getModel())
+                  .isUniqueName(link.getName()))
+          {
+            linkUrlTable.setValueAt(link.getName(), index, 0);
+            linkUrlTable.setValueAt(link.getURL(), index, 1);
+            valid = true;
+          }
+          else
+          {
+            link.notifyDuplicate();
+            continue;
+          }
         }
       }
       else
@@ -1017,10 +1034,10 @@ public class Preferences extends GPreferences
       }
     } catch (NumberFormatException x)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .getString("warn.user_defined_width_requirements"),
               MessageManager.getString("label.invalid_id_column_width"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
       userIdWidth.setText("");
     }
   }
@@ -1043,10 +1060,10 @@ public class Preferences extends GPreferences
       File f = new File(chimeraPath.getText());
       if (!f.canExecute())
       {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.getString("label.invalid_chimera_path"),
                 MessageManager.getString("label.invalid_name"),
-                JOptionPane.ERROR_MESSAGE);
+                JvOptionPane.ERROR_MESSAGE);
         return false;
       }
     }
@@ -1082,13 +1099,13 @@ public class Preferences extends GPreferences
     if (!found)
     {
       String[] options = { "OK", "Help" };
-      int showHelp = JOptionPane.showInternalOptionDialog(
+      int showHelp = JvOptionPane.showInternalOptionDialog(
               Desktop.desktop,
               JvSwingUtils.wrapTooltip(true,
                       MessageManager.getString("label.chimera_missing")),
-              "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
+              "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
               null, options, options[0]);
-      if (showHelp == JOptionPane.NO_OPTION)
+      if (showHelp == JvOptionPane.NO_OPTION)
       {
         try
         {
@@ -1174,29 +1191,25 @@ public class Preferences extends GPreferences
       }
       int modelIndex = linkUrlTable.convertRowIndexToModel(index);
 
-      // determine if the new selection is a custom url or not
-      int col = ((UrlLinkTableModel) linkUrlTable.getModel())
-              .getNameColumn();
-      if (!sequenceUrlLinks.isUserEntry((String) linkUrlTable.getModel()
-              .getValueAt(modelIndex, col)))
+      // enable/disable edit and delete link buttons
+      if (((UrlLinkTableModel) linkUrlTable.getModel())
+              .isRowDeletable(modelIndex))
       {
-        // entry is not a user-defined url and so should not be edited
-        // disable edit and delete buttons
-        deleteLink.setEnabled(false);
-        editLink.setEnabled(false);
+        deleteLink.setEnabled(true);
       }
       else
       {
-        deleteLink.setEnabled(true);
-        editLink.setEnabled(true);
+        deleteLink.setEnabled(false);
       }
 
-      // BUT if it's the default url, don't allow deletion
-      col = ((UrlLinkTableModel) linkUrlTable.getModel())
-              .getDefaultColumn();
-      if ((boolean) linkUrlTable.getValueAt(index, col))
+      if (((UrlLinkTableModel) linkUrlTable.getModel())
+              .isRowEditable(modelIndex))
       {
-        deleteLink.setEnabled(false);
+        editLink.setEnabled(true);
+      }
+      else
+      {
+        editLink.setEnabled(false);
       }
     }
 }