JAL-1705 (new preference option to) hide introns when fetching genomic

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 1b274a8..8b33deb 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -30,6 +30,7 @@ import jalview.jbgui.GPreferences;
 import jalview.jbgui.GSequenceLink;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
+import jalview.ws.sifts.SiftsSettings;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -87,6 +88,8 @@ public class Preferences extends GPreferences
 
   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
 
+  public static final String HIDE_INTRONS = "HIDE_INTRONS";
+
   private static final int MIN_FONT_SIZE = 1;
 
   private static final int MAX_FONT_SIZE = 30;
@@ -174,11 +177,11 @@ public class Preferences extends GPreferences
     dasTab.add(dasSource, BorderLayout.CENTER);
     wsPrefs = new WsPreferences();
     wsTab.add(wsPrefs, BorderLayout.CENTER);
-    int width = 500, height = 450;
+    int width = 500, height = 470;
     if (new jalview.util.Platform().isAMac())
     {
       width = 570;
-      height = 480;
+      height = 500;
     }
 
     Desktop.addInternalFrame(frame,
@@ -240,6 +243,7 @@ public class Preferences extends GPreferences
     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 
     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
+    hideIntrons.setSelected(Cache.getDefault(HIDE_INTRONS, true));
 
     gapSymbolCB.addItem("-");
     gapSymbolCB.addItem(".");
@@ -263,8 +267,7 @@ public class Preferences extends GPreferences
 
     sortAutocalc.addItem("Autocalculated first");
     sortAutocalc.addItem("Autocalculated last");
-    final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE,
-            true);
+    final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
             : sortAutocalc.getItemAt(1));
     startupCheckbox
@@ -298,8 +301,7 @@ public class Preferences extends GPreferences
     structFromPdb.setSelected(structSelected);
     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
     useRnaView.setEnabled(structSelected);
-    addSecondaryStructure
-            .setSelected(Cache.getDefault(ADD_SS_ANN, false));
+    addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
     addSecondaryStructure.setEnabled(structSelected);
     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
     addTempFactor.setEnabled(structSelected);
@@ -315,6 +317,18 @@ public class Preferences extends GPreferences
       }
     });
 
+    if (Cache.getDefault("MAP_WITH_SIFTS", false))
+    {
+      siftsMapping.setSelected(true);
+    }
+    else
+    {
+      nwMapping.setSelected(true);
+    }
+
+    SiftsSettings
+            .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+
     /*
      * Set Connections tab defaults
      */
@@ -353,8 +367,8 @@ public class Preferences extends GPreferences
     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
             "Prompt each time"));
     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
-    userIdWidth.setEnabled(autoIdWidth.isSelected());
-    userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
+    userIdWidth.setEnabled(!autoIdWidth.isSelected());
+    userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
     userIdWidth.setText(wi == null ? "" : wi.toString());
     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
@@ -386,6 +400,7 @@ public class Preferences extends GPreferences
    * 
    * @param e
    */
+  @Override
   public void ok_actionPerformed(ActionEvent e)
   {
     if (!validateSettings())
@@ -446,6 +461,8 @@ public class Preferences extends GPreferences
 
     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
             Boolean.toString(wrap.isSelected()));
+    Cache.applicationProperties.setProperty(HIDE_INTRONS,
+            Boolean.toString(hideIntrons.isSelected()));
 
     Cache.applicationProperties.setProperty("STARTUP_FILE",
             startupFileTextfield.getText());
@@ -465,8 +482,8 @@ public class Preferences extends GPreferences
     }
 
     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
-    Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
-            Boolean.valueOf(showAutocalcFirst).toString());
+    Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
+            .valueOf(showAutocalcFirst).toString());
 
     /*
      * Save Colours settings
@@ -494,6 +511,9 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
             .getSelectedItem().toString());
     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
+    Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
+            Boolean.toString(siftsMapping.isSelected()));
+    SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 
     /*
      * Save Output settings
@@ -645,20 +665,22 @@ public class Preferences extends GPreferences
     return validateChimeraPath();
 
   }
+
   /**
    * DOCUMENT ME!
    */
+  @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("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"));
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.select_startup_file"));
 
     int value = chooser.showOpenDialog(this);
 
@@ -677,6 +699,7 @@ public class Preferences extends GPreferences
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void cancel_actionPerformed(ActionEvent e)
   {
     try
@@ -695,6 +718,7 @@ public class Preferences extends GPreferences
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void annotations_actionPerformed(ActionEvent e)
   {
     conservation.setEnabled(annotations.isSelected());
@@ -708,6 +732,7 @@ public class Preferences extends GPreferences
             && (identity.isSelected() || showGroupConsensus.isSelected()));
   }
 
+  @Override
   public void newLink_actionPerformed(ActionEvent e)
   {
 
@@ -734,6 +759,7 @@ public class Preferences extends GPreferences
     }
   }
 
+  @Override
   public void editLink_actionPerformed(ActionEvent e)
   {
     GSequenceLink link = new GSequenceLink();
@@ -775,6 +801,7 @@ public class Preferences extends GPreferences
     }
   }
 
+  @Override
   public void deleteLink_actionPerformed(ActionEvent e)
   {
     int index = linkNameList.getSelectedIndex();
@@ -797,10 +824,12 @@ public class Preferences extends GPreferences
     linkURLList.setListData(urlLinks);
   }
 
+  @Override
   public void defaultBrowser_mouseClicked(MouseEvent e)
   {
     JFileChooser chooser = new JFileChooser(".");
-    chooser.setDialogTitle(MessageManager.getString("label.select_default_browser"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.select_default_browser"));
 
     int value = chooser.showOpenDialog(this);
 
@@ -818,6 +847,7 @@ public class Preferences extends GPreferences
    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
    * .ActionEvent)
    */
+  @Override
   protected void showunconserved_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub
@@ -833,7 +863,8 @@ public class Preferences extends GPreferences
   public void minColour_actionPerformed(JPanel panel)
   {
     Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
+            MessageManager.getString("label.select_colour_minimum_value"),
+            minColour.getBackground());
     if (col != null)
     {
       panel.setBackground(col);
@@ -845,7 +876,8 @@ public class Preferences extends GPreferences
   public void maxColour_actionPerformed(JPanel panel)
   {
     Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
+            MessageManager.getString("label.select_colour_maximum_value"),
+            maxColour.getBackground());
     if (col != null)
     {
       panel.setBackground(col);
@@ -870,12 +902,10 @@ public class Preferences extends GPreferences
       }
     } catch (NumberFormatException x)
     {
-      JOptionPane
-              .showInternalMessageDialog(
-                      Desktop.desktop,
-                      MessageManager.getString("warn.user_defined_width_requirements"),
-                      MessageManager.getString("label.invalid_id_column_width"),
-                      JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+              .getString("warn.user_defined_width_requirements"),
+              MessageManager.getString("label.invalid_id_column_width"),
+              JOptionPane.WARNING_MESSAGE);
       userIdWidth.setText("");
     }
   }
@@ -936,14 +966,13 @@ public class Preferences extends GPreferences
     }
     if (!found)
     {
-      String[] options =
-      { "OK", "Help" };
+      String[] options = { "OK", "Help" };
       int showHelp = JOptionPane.showInternalOptionDialog(
               Desktop.desktop,
               JvSwingUtils.wrapTooltip(true,
                       MessageManager.getString("label.chimera_missing")),
-              "", JOptionPane.YES_NO_OPTION,
-              JOptionPane.WARNING_MESSAGE, null, options, options[0]);
+              "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
+              null, options, options[0]);
       if (showHelp == JOptionPane.NO_OPTION)
       {
         try