Merge branch 'Jalview-BH/JAL-3048_dialogs' into Jalview-BH/JAL-3026

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2587866..aa0a1fe 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1118,6 +1118,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void saveAs_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 JalviewFileChooser - Save option
+
     String format = currentFileFormat == null ? null
             : currentFileFormat.getName();
     JalviewFileChooser chooser = JalviewFileChooser
@@ -1422,7 +1424,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void associatedData_actionPerformed(ActionEvent e)
   {
-    // Pick the tree file
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
@@ -3904,6 +3905,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 JalviewFileChooser
     // Pick the tree file
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
@@ -4550,7 +4552,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                  */
                 for (Object[] o : filesmatched)
                 {
-                  filesnotmatched.add((String) o[0]);
+                  filesnotmatched.add(o[0]);
                 }
               }
             }
@@ -5633,6 +5635,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void loadVcf_actionPerformed()
   {
+    // TODO: JAL-3048 - No VCF support in JsJalview
     JalviewFileChooser chooser = new JalviewFileChooser(
             Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 6fefbd0..35a463c 100644 (file)
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -135,6 +135,7 @@ public class AnnotationExporter extends JPanel
 
   private void toFile_actionPerformed()
   {
+    // TODO: JAL-3048 JalviewFileChooser - Save option
     JalviewFileChooser chooser = new JalviewFileChooser(
             Cache.getProperty("LAST_DIRECTORY"));
 

diff --git a/src/jalview/gui/CutAndPasteHtmlTransfer.java b/src/jalview/gui/CutAndPasteHtmlTransfer.java
index 2e51bce..03eb7d2 100644 (file)
--- a/src/jalview/gui/CutAndPasteHtmlTransfer.java
+++ b/src/jalview/gui/CutAndPasteHtmlTransfer.java
@@ -148,6 +148,8 @@ public class CutAndPasteHtmlTransfer extends GCutAndPasteHtmlTransfer
   @Override
   public void save_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 JalviewFileChooser - Save option
+
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 2a96daf..142dd75 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -135,6 +135,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
   @Override
   public void save_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 JalviewFileChooser - Save option
+
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 39098f2..06c3b36 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -63,7 +63,6 @@ import java.awt.datatransfer.ClipboardOwner;
 import java.awt.datatransfer.DataFlavor;
 import java.awt.datatransfer.Transferable;
 import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTarget;
 import java.awt.dnd.DropTargetDragEvent;
 import java.awt.dnd.DropTargetDropEvent;
 import java.awt.dnd.DropTargetEvent;
@@ -114,7 +113,6 @@ import javax.swing.JMenuItem;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.JProgressBar;
-import javax.swing.JTextArea;
 import javax.swing.KeyStroke;
 import javax.swing.SwingUtilities;
 import javax.swing.event.HyperlinkEvent;
@@ -423,45 +421,45 @@ public class Desktop extends jalview.jbgui.GDesktop
 
       checkURLLinks();
 
-    // Spawn a thread that shows the splashscreen
+      // Spawn a thread that shows the splashscreen
 
-    SwingUtilities.invokeLater(new Runnable()
-    {
-      @Override
-      public void run()
+      SwingUtilities.invokeLater(new Runnable()
       {
-        new SplashScreen();
-      }
-    });
+        @Override
+        public void run()
+        {
+          new SplashScreen();
+        }
+      });
 
-    // Thread off a new instance of the file chooser - this reduces the time it
-    // takes to open it later on.
-    new Thread(new Runnable()
-    {
-      @Override
-      public void run()
+      // Thread off a new instance of the file chooser - this reduces the time it
+      // takes to open it later on.
+      new Thread(new Runnable()
       {
-        Cache.log.debug("Filechooser init thread started.");
-        String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
-        JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
-                fileFormat);
-        Cache.log.debug("Filechooser init thread finished.");
-      }
-    }).start();
-    // Add the service change listener
-    changeSupport.addJalviewPropertyChangeListener("services",
-            new PropertyChangeListener()
-            {
-
-              @Override
-              public void propertyChange(PropertyChangeEvent evt)
+        @Override
+        public void run()
+        {
+          Cache.log.debug("Filechooser init thread started.");
+          String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+          JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
+                  fileFormat);
+          Cache.log.debug("Filechooser init thread finished.");
+        }
+      }).start();
+      // Add the service change listener
+      changeSupport.addJalviewPropertyChangeListener("services",
+              new PropertyChangeListener()
               {
-                Cache.log.debug("Firing service changed event for "
-                        + evt.getNewValue());
-                JalviewServicesChanged(evt);
-              }
 
-            });
+                @Override
+                public void propertyChange(PropertyChangeEvent evt)
+                {
+                  Cache.log.debug("Firing service changed event for "
+                          + evt.getNewValue());
+                  JalviewServicesChanged(evt);
+                }
+
+              });
 
     } // end BH 2018 ignore
 
@@ -1613,6 +1611,8 @@ public class Desktop extends jalview.jbgui.GDesktop
   @Override
   public void saveState_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 not needed for Jalview-JS
+
     JalviewFileChooser chooser = new JalviewFileChooser("jvp",
             "Jalview Project");
 
@@ -1686,6 +1686,8 @@ public class Desktop extends jalview.jbgui.GDesktop
   @Override
   public void loadState_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 not needed for Jalview-JS
+
     JalviewFileChooser chooser = new JalviewFileChooser(
             Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "jvp", "jar" },
@@ -1993,6 +1995,8 @@ public class Desktop extends jalview.jbgui.GDesktop
   @Override
   public void vamsasImport_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 not needed for Jalview-JS
+
     if (v_client == null)
     {
       // Load and try to start a session.
@@ -2269,6 +2273,8 @@ public class Desktop extends jalview.jbgui.GDesktop
   @Override
   public void vamsasSave_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 not needed for Jalview-JS
+
     if (v_client != null)
     {
       // TODO: VAMSAS DOCUMENT EXTENSION is VDJ

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 78c1cac..75e8ec9 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -846,6 +846,9 @@ public class FeatureSettings extends JPanel
    */
   void load()
   {
+    // TODO: JAL-3048 relies on Castor XML parsing: not needed for JS-jalview core
+    // functionalty
+
     JalviewFileChooser chooser = new JalviewFileChooser("fc",
             SEQUENCE_FEATURE_COLOURS);
     chooser.setFileView(new JalviewFileView());
@@ -928,6 +931,7 @@ public class FeatureSettings extends JPanel
    */
   void save()
   {
+    // TODO: JAL-3048 not needed for Jalview-JS - save colours
     JalviewFileChooser chooser = new JalviewFileChooser("fc",
             SEQUENCE_FEATURE_COLOURS);
     chooser.setFileView(new JalviewFileView());

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 7d02fac..019b29e 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -833,6 +833,7 @@ public class Preferences extends GPreferences
   @Override
   public void startupFileTextfield_mouseClicked()
   {
+    // TODO: JAL-3048 not needed for Jalview-JS
     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
     JalviewFileChooser chooser = JalviewFileChooser
             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
@@ -1006,17 +1007,22 @@ public class Preferences extends GPreferences
   @Override
   public void defaultBrowser_mouseClicked(MouseEvent e)
   {
-    JFileChooser chooser = new JFileChooser(".");
-    chooser.setDialogTitle(
-            MessageManager.getString("label.select_default_browser"));
+    // TODO: JAL-3048 not needed for j2s
+    /*
+     * @j2sNative
+     */
+    {
+      JFileChooser chooser = new JFileChooser(".");
+      chooser.setDialogTitle(
+              MessageManager.getString("label.select_default_browser"));
 
-    int value = chooser.showOpenDialog(this);
+      int value = chooser.showOpenDialog(this);
 
-    if (value == JFileChooser.APPROVE_OPTION)
-    {
-      defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+      if (value == JFileChooser.APPROVE_OPTION)
+      {
+        defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+      }
     }
-
   }
 
   /*

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index e18d6af..97ff404 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -565,6 +565,8 @@ public class StructureChooser extends GStructureChooser
   @Override
   protected void pdbFromFile_actionPerformed()
   {
+    // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and StructureChooser
+    // works
     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new jalview.io.JalviewFileView());

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 72b0bcc..9ed08b8 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -876,6 +876,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   @Override
   public void pdbFile_actionPerformed(ActionEvent actionEvent)
   {
+    // TODO: JAL-3048 not needed for Jalview-JS - save PDB file
     JalviewFileChooser chooser = new JalviewFileChooser(
             Cache.getProperty("LAST_DIRECTORY"));
 

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 2727db1..5795a9f 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -390,6 +390,7 @@ public class TreePanel extends GTreePanel
   @Override
   public void saveAsNewick_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 save newick file for Jalview-JS
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
@@ -696,6 +697,7 @@ public class TreePanel extends GTreePanel
 
     try
     {
+      // TODO: JAL-3048 not needed for Jalview-JS - Requires EpsGraphics2D dependency
       JalviewFileChooser chooser = new JalviewFileChooser(
               ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
       chooser.setFileView(new JalviewFileView());
@@ -739,6 +741,7 @@ public class TreePanel extends GTreePanel
   @Override
   public void pngTree_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 image export supported in JalviewJS ?
     int width = treeCanvas.getWidth();
     int height = treeCanvas.getHeight();
 

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 3290500..89ddf87 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -633,7 +633,7 @@ public class UserDefinedColours extends GUserDefinedColours
   {
     upperCaseButtons = new ArrayList<>();
     lowerCaseButtons = new ArrayList<>();
-
+    // TODO: JAL-3048 requires Castor dependency for Jalview-JS
     JalviewFileChooser chooser = new JalviewFileChooser("jc",
             "Jalview User Colours");
     chooser.setFileView(new JalviewFileView());
@@ -754,6 +754,8 @@ public class UserDefinedColours extends GUserDefinedColours
         return false;
       }
     }
+    // TODO: JAL-3048 saveas, also requires Castor dependency for Jalview-JS
+
     JalviewFileChooser chooser = new JalviewFileChooser("jc",
             "Jalview User Colours");
 

diff --git a/src/jalview/gui/WsParamSetManager.java b/src/jalview/gui/WsParamSetManager.java
index d91775c..a826503 100644 (file)
--- a/src/jalview/gui/WsParamSetManager.java
+++ b/src/jalview/gui/WsParamSetManager.java
@@ -180,6 +180,8 @@ public class WsParamSetManager implements ParamManager
     }
     if (filename == null)
     {
+      // TODO: JAL-3048 webservice - not required for Jalview-JS
+
       JalviewFileChooser chooser = new JalviewFileChooser("wsparams",
               "Web Service Parameter File");
       chooser.setFileView(new JalviewFileView());

diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index bebfd28..bf8c431 100644 (file)
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -228,6 +228,8 @@ public abstract class HTMLOutput implements Runnable
               pSessionId);
     }
 
+    // TODO: JAL-3048 generate html rendered view (requires SvgGraphics and/or
+    // Jalview HTML rendering system- probably not required for Jalview-JS)
     JalviewFileChooser jvFileChooser = new JalviewFileChooser("html",
             "HTML files");
     jvFileChooser.setFileView(new JalviewFileView());

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 1cf482d..a64030b 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1722,7 +1722,13 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(exportAnnotations);
     fileMenu.add(loadTreeMenuItem);
     fileMenu.add(associatedData);
-    fileMenu.add(loadVcf);
+    /*
+     * No VCF import in Jalview-JS
+     * @j2sNative
+     */
+    {
+      fileMenu.add(loadVcf);
+    }
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
 

diff --git a/src/jalview/util/ImageMaker.java b/src/jalview/util/ImageMaker.java
index 7840261..3398fea 100755 (executable)
--- a/src/jalview/util/ImageMaker.java
+++ b/src/jalview/util/ImageMaker.java
@@ -123,6 +123,8 @@ public class ImageMaker
     this.headless = headless;
     if (file == null)
     {
+      // TODO: JAL-3048 export SVG/EPS/PNG- not required for Jalview-JS
+
       setProgressMessage(MessageManager.formatMessage(
               "status.waiting_for_user_to_select_output_file", type.name));
       JalviewFileChooser chooser;