JAL-2383 restore PID colour threshold from project; enable/disable

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3644b28..44a2318 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -66,6 +66,7 @@ import jalview.io.BioJsHTMLOutput;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.io.HtmlSvgOutput;
@@ -75,7 +76,6 @@ import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.io.JnetAnnotationMaker;
 import jalview.io.NewickFile;
-import jalview.io.StructureFile;
 import jalview.io.TCoffeeScoreFile;
 import jalview.jbgui.GAlignFrame;
 import jalview.schemes.Blosum62ColourScheme;
@@ -132,6 +132,8 @@ import java.awt.print.PageFormat;
 import java.awt.print.PrinterJob;
 import java.beans.PropertyChangeEvent;
 import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -147,7 +149,6 @@ import javax.swing.JInternalFrame;
 import javax.swing.JLayeredPane;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JRadioButtonMenuItem;
 import javax.swing.JScrollPane;
 import javax.swing.SwingUtilities;
@@ -859,7 +860,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     modifyConservation.setEnabled(!nucleotide);
     showGroupConservation.setEnabled(!nucleotide);
     rnahelicesColour.setEnabled(nucleotide);
+    nucleotideColour.setEnabled(nucleotide);
     purinePyrimidineColour.setEnabled(nucleotide);
+    RNAInteractionColour.setEnabled(nucleotide);
     showComplementMenuItem.setText(nucleotide ? MessageManager
             .getString("label.protein") : MessageManager
             .getString("label.nucleotide"));
@@ -891,7 +894,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     padGapsMenuitem.setSelected(av.isPadGaps());
     colourTextMenuItem.setSelected(av.isShowColourText());
     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
+    modifyPID.setEnabled(abovePIDThreshold.isSelected());
     conservationMenuItem.setSelected(av.getConservationSelected());
+    modifyConservation.setEnabled(conservationMenuItem.isSelected());
     seqLimits.setSelected(av.getShowJVSuffix());
     idRightAlign.setSelected(av.isRightAlignIds());
     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
@@ -1114,11 +1119,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void saveAs_actionPerformed(ActionEvent e)
   {
+    String format = currentFileFormat == null ? null : currentFileFormat
+            .getName();
     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
-            Cache.getProperty("LAST_DIRECTORY"),
-            // AppletFormatAdapter.WRITABLE_EXTENSIONS,
-            // AppletFormatAdapter.WRITABLE_FNAMES,
-            currentFileFormat.toString(), false);
+            Cache.getProperty("LAST_DIRECTORY"), format);
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager
@@ -1150,8 +1154,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       fileName = chooser.getSelectedFile().getPath();
 
-      Cache.setProperty("DEFAULT_FILE_FORMAT",
-              currentFileFormat.toString());
+      Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
 
       Cache.setProperty("LAST_DIRECTORY", fileName);
       saveAlignment(fileName, currentFileFormat);
@@ -1181,17 +1184,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
-      // {
-      // warningMessage("Cannot save file " + fileName + " using format "
-      // + format, "Alignment output format not supported");
-      // if (!Jalview.isHeadlessMode())
-      // {
-      // saveAs_actionPerformed(null);
-      // }
-      // return false;
-      // }
-
       AlignmentExportData exportData = getAlignmentForExport(format,
               viewport, null);
       if (exportData.getSettings().isCancelled())
@@ -1216,15 +1208,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         try
         {
-          java.io.PrintWriter out = new java.io.PrintWriter(
-                  new java.io.FileWriter(file));
+          PrintWriter out = new PrintWriter(new FileWriter(file));
 
           out.print(output);
           out.close();
           this.setTitle(file);
           statusBar.setText(MessageManager.formatMessage(
                   "label.successfully_saved_to_file_in_format",
-                  new Object[] { fileName, format }));
+                  new Object[] { fileName, format.getName() }));
         } catch (Exception ex)
         {
           success = false;
@@ -1269,8 +1260,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void outputText_actionPerformed(ActionEvent e)
   {
-
-    FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
+    FileFormatI fileFormat = FileFormats.getInstance().forName(
+            e.getActionCommand());
     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
             viewport, null);
     if (exportData.getSettings().isCancelled())
@@ -3509,12 +3500,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
    */
   @Override
-  protected void modifyPID_actionPerformed(ActionEvent e)
+  protected void modifyPID_actionPerformed()
   {
     if (viewport.getAbovePIDThreshold()
             && viewport.getGlobalColourScheme() != null)
@@ -3527,12 +3515,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
    */
   @Override
-  protected void modifyConservation_actionPerformed(ActionEvent e)
+  protected void modifyConservation_actionPerformed()
   {
     if (viewport.getConservationSelected()
             && viewport.getGlobalColourScheme() != null)
@@ -3544,41 +3529,45 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Action on selecting or deselecting (Colour) By Conservation
    */
   @Override
-  protected void conservationMenuItem_actionPerformed(ActionEvent e)
+  protected void conservationMenuItem_actionPerformed()
   {
-    viewport.setConservationSelected(conservationMenuItem.isSelected());
-
-    viewport.setAbovePIDThreshold(false);
-    abovePIDThreshold.setSelected(false);
+    boolean selected = conservationMenuItem.isSelected();
+    modifyConservation.setEnabled(selected);
+    viewport.setConservationSelected(selected);
 
     changeColour(viewport.getGlobalColourScheme());
-
-    modifyConservation_actionPerformed(null);
+    if (selected)
+    {
+      modifyConservation_actionPerformed();
+    }
+    else
+    {
+      SliderPanel.hideConservationSlider();
+    }
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Action on selecting or deselecting (Colour) Above PID Threshold
    */
   @Override
-  public void abovePIDThreshold_actionPerformed(ActionEvent e)
+  public void abovePIDThreshold_actionPerformed()
   {
-    viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
-
-    conservationMenuItem.setSelected(false);
-    viewport.setConservationSelected(false);
+    boolean selected = abovePIDThreshold.isSelected();
+    modifyPID.setEnabled(selected);
+    viewport.setAbovePIDThreshold(selected);
 
     changeColour(viewport.getGlobalColourScheme());
-
-    modifyPID_actionPerformed(null);
+    if (selected)
+    {
+      modifyPID_actionPerformed();
+    }
+    else
+    {
+      SliderPanel.hidePIDSlider();
+    }
   }
 
   /**
@@ -4899,13 +4888,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 type = null;
               }
-              if (type != null)
+              if (type != null && type.isStructureFile())
               {
-                if (FileFormat.PDB.equals(type) || FileFormat.MMCif.equals(type))
-                {
-                  filesmatched.add(new Object[] { file, protocol, mtch });
-                  continue;
-                }
+                filesmatched.add(new Object[] { file, protocol, mtch });
+                continue;
               }
             }
             // File wasn't named like one of the sequences or wasn't a PDB file.