JAL-3253-applet adds NOMENUBAR, NOSTATUS, NOCALCULATION, SHOWOVERVIEW

adds "overview" name for overview panel.

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index adfb8ca..062dbf8 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -882,7 +882,7 @@ public class AlignFrame extends EmbmenuFrame implements AlignFrameI,
     }
     else if (source == autoCalculate)
     {
-      viewport.autoCalculateConsensus = autoCalculate.getState();
+      viewport.setAutoCalculateConsensusAndConservation(autoCalculate.getState());
     }
     else if (source == sortByTree)
     {

diff --git a/src/jalview/bin/ArgsParser.java b/src/jalview/bin/ArgsParser.java
index 45ea206..91c8838 100644 (file)
--- a/src/jalview/bin/ArgsParser.java
+++ b/src/jalview/bin/ArgsParser.java
@@ -35,6 +35,17 @@ import java.util.Vector;
 public class ArgsParser
 {
 
+  // BH 2019 - new
+
+  public static final String NOCALCULATION = "nocalculation";
+
+  public static final String NOMENUBAR = "nomenubar";
+
+  public static final String NOSTATUS = "nostatus";
+
+  public static final String SHOWOVERVIEW = "showoverview";
+
+  //
   public static final String ANNOTATIONS = "annotations";
 
   public static final String COLOUR = "colour";

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index bb2038e..d9de469 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -146,6 +146,24 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
   protected JSFunctionExec jsFunctionExec;
 
+  private boolean noCalculation, noMenuBar, noStatus;
+
+  public boolean getStartCalculations()
+  {
+    return !noCalculation;
+  }
+
+  public boolean getAllowMenuBar()
+  {
+    return !noMenuBar;
+  }
+
+  public boolean getShowStatus()
+  {
+    return !noStatus;
+  }
+
+
   public static AlignFrame getCurrentAlignFrame()
   {
     return getInstance().currentAlignFrame;
@@ -255,26 +273,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     getInstance().doMain(args);
   }
 
-  /**
-   * Allow an outside entity to initiate the second half of argument parsing
-   * (only).
-   * 
-   * @param args
-   * @return null is good
-   */
-  @Override
-  public Object parseArguments(String[] args)
-  {
-
-    try
-    {
-      ArgsParser aparser = new ArgsParser(args);
-      return parseArguments(aparser, false);
-    } catch (Throwable t)
-    {
-      return t;
-    }
-  }
 
   private static void logClass(String name)
   {
@@ -553,6 +551,33 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     parseArguments(aparser, true);
   }
 
+  /**
+   * Allow an outside entity to initiate the second half of argument parsing
+   * (only).
+   * 
+   * @param args
+   * @return null is good
+   */
+  @Override
+  public Object parseArguments(String[] args)
+  {
+
+    try
+    {
+      ArgsParser aparser = new ArgsParser(args);
+      return parseArguments(aparser, false);
+    } catch (Throwable t)
+    {
+      return t;
+    }
+  }
+
+  /**
+   * 
+   * @param aparser
+   * @param isStartup
+   * @return
+   */
   private Object parseArguments(ArgsParser aparser, boolean isStartup)
   {
     boolean isJS = Platform.isJS();
@@ -569,7 +594,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     String fileFormat = (isJavaAppletTag
             ? aparser.getAppletValue("format", null)
             : null);
-
     FileFormatI format = null;
     DataSourceType protocol = null;
 
@@ -597,8 +621,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       }
     }
 
+    String data;
+
     if (file != null)
     {
+
       if (!headless)
       {
         desktop.setProgressBar(
@@ -645,6 +672,32 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         // TODO ?
       }
 
+      if (aparser.contains(ArgsParser.SHOWOVERVIEW))
+      {
+        jalview.bin.Cache.setPropertyNoSave(Preferences.SHOW_OVERVIEW,
+                "true");
+
+        System.out.println("CMD [showoverview] executed successfully!");
+      }
+
+      if (aparser.contains(ArgsParser.NOMENUBAR))
+      {
+        noMenuBar = true;
+        System.out.println("CMD [nomenu] executed successfully!");
+      }
+
+      if (aparser.contains(ArgsParser.NOSTATUS))
+      {
+        noStatus = true;
+        System.out.println("CMD [nostatus] executed successfully!");
+      }
+
+      if (aparser.contains(ArgsParser.NOCALCULATION))
+      {
+        noCalculation = true;
+        System.out.println("CMD [nocalculation] executed successfully!");
+      }
+
       AlignFrame af = new FileLoader(!headless).loadFileWaitTillLoaded(file,
               protocol, format);
       if (af == null)
@@ -686,7 +739,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
         // TODO: file2 How to implement file2 for the applet spit screen?
 
-        String data = aparser.getValue(ArgsParser.COLOUR, true);
+        data = aparser.getValue(ArgsParser.COLOUR, true);
         if (data != null)
         {
           data.replaceAll("%20", " ");
@@ -2005,4 +2058,5 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
   }
 
+
 }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3b53f18..d87f0f0 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -353,6 +353,8 @@ public class AlignFrame extends GAlignFrame
     if (!Jalview.isHeadlessMode())
     {
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+      statusPanel.setVisible(Jalview.getInstance().getShowStatus());
+      alignFrameMenuBar.setVisible(Jalview.getInstance().getAllowMenuBar());
     }
 
     avc = new jalview.controller.AlignViewController(this, viewport,
@@ -793,9 +795,12 @@ public class AlignFrame extends GAlignFrame
       {
         ap.av.getAlignment().padGaps();
       }
-      ap.av.updateConservation(ap);
-      ap.av.updateConsensus(ap);
-      ap.av.updateStrucConsensus(ap);
+      if (Jalview.getInstance().getStartCalculations())
+      {
+        ap.av.updateConservation(ap);
+        ap.av.updateConsensus(ap);
+        ap.av.updateStrucConsensus(ap);
+      }
     }
   }
 
@@ -945,7 +950,7 @@ public class AlignFrame extends GAlignFrame
     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
-    autoCalculate.setSelected(av.autoCalculateConsensus);
+    autoCalculate.setSelected(av.getAutoCalculateConsensusAndConservation());
     sortByTree.setSelected(av.sortByTree);
     listenToViewSelections.setSelected(av.followSelection);
 
@@ -3374,7 +3379,7 @@ public class AlignFrame extends GAlignFrame
     Desktop.addInternalFrame(frame, MessageManager
             .formatMessage("label.overview_params", new Object[]
             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
-            true, true);
+            true, true, "overview");
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(
@@ -3654,8 +3659,8 @@ public class AlignFrame extends GAlignFrame
   @Override
   public void autoCalculate_actionPerformed(ActionEvent e)
   {
-    viewport.autoCalculateConsensus = autoCalculate.isSelected();
-    if (viewport.autoCalculateConsensus)
+    viewport.setAutoCalculateConsensusAndConservation(autoCalculate.isSelected());
+    if (viewport.getAutoCalculateConsensusAndConservation())
     {
       viewport.firePropertyChange("alignment", null,
               viewport.getAlignment().getSequences());

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7c3dca0..eb9c180 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -214,7 +214,7 @@ public class AlignViewport extends AlignmentViewport
 
     setRightAlignIds(Cache.getDefault(Preferences.RIGHT_ALIGN_IDS, false));
     setCentreColumnLabels(Cache.getDefault(Preferences.CENTRE_COLUMN_LABELS, false));
-    autoCalculateConsensus = Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true);
+    autoCalculateConsensusAndConservation = Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true);
 
     setPadGaps(Cache.getDefault(Preferences.PAD_GAPS, true));
     setShowNPFeats(Cache.getDefault(Preferences.SHOW_NPFEATS_TOOLTIP, true));

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 2a972e3..957fb96 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -864,7 +864,7 @@ public class Desktop extends GDesktop
           final JInternalFrame frame, String title, int w, int h,
           boolean resizable)
   {
-    addInternalFrame(frame, title, true, w, h, resizable, false);
+    addInternalFrame(frame, title, true, w, h, resizable, false, null);
   }
 
   /**
@@ -887,15 +887,51 @@ public class Desktop extends GDesktop
    *          Do not set the default minimum size for frame
    */
   public static synchronized void addInternalFrame(
+          JInternalFrame frame, String title, boolean makeVisible, int w,
+          int h, boolean resizable, boolean ignoreMinSize)
+  {
+    addInternalFrame(frame, title, makeVisible, w, h, resizable,
+            ignoreMinSize, null);
+  }
+
+  /**
+   * Add an internal frame to the Jalview desktop
+   * 
+   * @param frame
+   *          Frame to show
+   * @param title
+   *          Visible Title
+   * @param makeVisible
+   *          When true, display frame immediately, otherwise, caller must call
+   *          setVisible themselves.
+   * @param w
+   *          width
+   * @param h
+   *          height
+   * @param resizable
+   *          Allow resize
+   * @param ignoreMinSize
+   *          Do not set the default minimum size for frame
+   * @param name
+   *          for HTML div embedding
+   */
+  public static synchronized void addInternalFrame(
           final JInternalFrame frame, String title, boolean makeVisible,
-          int w, int h, boolean resizable, boolean ignoreMinSize)
+          int w, int h, boolean resizable, boolean ignoreMinSize,
+          String name)
   {
 
+
     // TODO: allow callers to determine X and Y position of frame (eg. via
     // bounds object).
     // TODO: consider fixing method to update entries in the window submenu with
     // the current window title
 
+    if (name != null)
+    {
+      frame.setName(Jalview.getAppID(name));
+    }
+
     frame.setTitle(title);
     if (frame.getWidth() < 1 || frame.getHeight() < 1)
     {

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 536f767..4116c3b 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -605,10 +605,30 @@ public abstract class AlignmentViewport
 
   protected ColumnSelection colSel = new ColumnSelection();
 
-  public boolean autoCalculateConsensus = true;
+  protected boolean autoCalculateConsensusAndConservation = true;
+
+  public boolean getAutoCalculateConsensusAndConservation()
+  { // BH 2019.07.24
+    return autoCalculateConsensusAndConservation;
+  }
+
+  public void setAutoCalculateConsensusAndConservation(boolean b)
+  {
+    autoCalculateConsensusAndConservation = b;
+  }
 
   protected boolean autoCalculateStrucConsensus = true;
 
+  public boolean getAutoCalculateStrucConsensus()
+  { // BH 2019.07.24
+    return autoCalculateStrucConsensus;
+  }
+
+  public void setAutoCalculateStrucConsensus(boolean b)
+  {
+    autoCalculateStrucConsensus = b;
+  }
+
   protected boolean ignoreGapsInConsensusCalculation = false;
 
   protected ResidueShaderI residueShading = new ResidueShader();
@@ -824,7 +844,7 @@ public abstract class AlignmentViewport
     // see note in mantis : issue number 8585
     if (alignment.isNucleotide()
             || (conservation == null && quality == null)
-            || !autoCalculateConsensus)
+            || !autoCalculateConsensusAndConservation)
     {
       return;
     }
@@ -842,7 +862,7 @@ public abstract class AlignmentViewport
   public void updateConsensus(final AlignmentViewPanel ap)
   {
     // see note in mantis : issue number 8585
-    if (consensus == null || !autoCalculateConsensus)
+    if (consensus == null || !autoCalculateConsensusAndConservation)
     {
       return;
     }
@@ -1859,11 +1879,11 @@ public abstract class AlignmentViewport
     {
       alignment.padGaps();
     }
-    if (autoCalculateConsensus)
+    if (autoCalculateConsensusAndConservation)
     {
       updateConsensus(ap);
     }
-    if (hconsensus != null && autoCalculateConsensus)
+    if (hconsensus != null && autoCalculateConsensusAndConservation)
     {
       updateConservation(ap);
     }