JAL-1760 JAL-1641 Serialisation of Hidden Seqs and Cols in JSON output. Added ability...

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index c068728..9fbe2be 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -121,7 +121,7 @@ action.save_as_default = Save as default
 action.save_as = Save as
 action.save = Save
 action.cancel_fetch = Cancel Fetch
-action.save_omit_hidden_columns = Save / Omit Hidden Columns
+action.save_omit_hidden_columns = Save / Omit Hidden Regions
 action.change_font = Change Font
 action.change_font_tree_panel = Change Font (Tree Panel)
 action.colour = Colour
@@ -361,7 +361,7 @@ label.example = Example
 label.example_param = Example: {0}
 label.select_file_format_before_saving = You must select a file format before saving!
 label.file_format_not_specified = File format not specified
-label.alignment_contains_hidden_columns = The Alignment contains hidden columns.\nDo you want to save only the visible alignment?
+label.alignment_contains_hidden_columns = The Alignment contains hidden regions (hidden sequences/columns).\nDo you want to save only the visible alignment?
 label.couldnt_save_file = Couldn't save file: {0}
 label.error_saving_file = Error Saving File
 label.remove_from_default_list = Remove from default list?

diff --git a/src/jalview/api/AlignViewControllerGuiI.java b/src/jalview/api/AlignViewControllerGuiI.java
index f768451..b08a0aa 100644 (file)
--- a/src/jalview/api/AlignViewControllerGuiI.java
+++ b/src/jalview/api/AlignViewControllerGuiI.java
@@ -20,6 +20,8 @@
  */
 package jalview.api;
 
+import java.util.List;
+
 import jalview.commands.CommandI;
 import jalview.schemes.ColourSchemeI;
 
@@ -47,4 +49,8 @@ public interface AlignViewControllerGuiI
   void setMenusForViewport();
   
   void changeColour(ColourSchemeI cs);
+
+  void hideColumns(List<int[]> colsToHide);
+
+  void syncHiddenSequences();
 }

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 478aa09..ee64dda 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -20,6 +20,40 @@
  */
 package jalview.appletgui;
 
+import java.awt.BorderLayout;
+import java.awt.Canvas;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.IOException;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.AlignViewControllerGuiI;
@@ -71,40 +105,6 @@ import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
-import java.awt.BorderLayout;
-import java.awt.Canvas;
-import java.awt.CheckboxMenuItem;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Frame;
-import java.awt.Graphics;
-import java.awt.Label;
-import java.awt.Menu;
-import java.awt.MenuBar;
-import java.awt.MenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
-import java.awt.event.FocusListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.IOException;
-import java.net.URL;
-import java.net.URLEncoder;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
 public class AlignFrame extends EmbmenuFrame implements ActionListener,
         ItemListener, KeyListener, AlignViewControllerGuiI
 {
@@ -4183,7 +4183,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public void setShowSeqFeatures(boolean b)
   {
     // showSeqFeatures.setSelected(b);
-    viewport.setShowSequenceFeatures(b);
+    // viewport.setShowSequenceFeatures(b);
 
   }
 
@@ -4193,4 +4193,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // setMenusFromViewport(viewport);
 
   }
+
+  @Override
+  public void hideColumns(List<int[]> colsToHide)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void syncHiddenSequences()
+  {
+    // TODO Auto-generated method stub
+
+  }
 }

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e184db7..00a042d 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -225,8 +225,7 @@ public class Jalview
       desktop.checkForNews();
     }
 
-    BioJsHTMLOutput bjs = new BioJsHTMLOutput(null, null);
-    bjs.updateBioJS();
+    BioJsHTMLOutput.updateBioJS();
 
     String file = null, protocol = null, format = null, data = null;
     jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 929e56e..dcc5f26 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -272,8 +272,13 @@ public class HiddenSequences
         index++;
       }
     }
+    Alignment fAlignmt = new Alignment(seq);
+    fAlignmt.annotations = alignment.getAlignmentAnnotation();
+    fAlignmt.alignmentProperties = alignment.getProperties();
+    fAlignmt.groups = alignment.getGroups();
+    fAlignmt.hasRNAStructure = alignment.hasRNAStructure();
 
-    return new Alignment(seq);
+    return fAlignmt;
   }
 
   public boolean isHidden(SequenceI seq)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index cab1ac7..9f328ee 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -59,6 +59,8 @@ public class Sequence implements SequenceI
 
   RNA rna;
 
+  private boolean hidden;
+
   /**
    * This annotation is displayed below the alignment but the positions are tied
    * to the residues of this sequence
@@ -1283,4 +1285,16 @@ public class Sequence implements SequenceI
     return result;
   }
 
+  @Override
+  public boolean isHidden()
+  {
+    return this.hidden;
+  }
+
+  @Override
+  public void setHidden(Boolean hidden)
+  {
+    this.hidden = hidden;
+  }
+
 }

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 38ae372..bd193fb 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -419,4 +419,17 @@ public interface SequenceI
    */
   public List<int[]> getInsertions();
 
+  /**
+   * 
+   * @return returns true if the sequence is hidden
+   */
+  public boolean isHidden();
+
+  /**
+   * 
+   * @param hidden
+   *          visibility status of the sequence
+   */
+  public void setHidden(Boolean hidden);
+
 }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 553ddd2..ad2bbc3 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -20,6 +20,52 @@
  */
 package jalview.gui;
 
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+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;
+
 import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
@@ -51,6 +97,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SeqCigar;
 import jalview.datamodel.Sequence;
@@ -97,52 +144,6 @@ import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Set;
-import java.util.Vector;
-
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JEditorPane;
-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;
-
 /**
  * DOCUMENT ME!
  * 
@@ -1120,32 +1121,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         return false;
       }
 
-      String[] omitHidden = null;
-
-      if (viewport.hasHiddenColumns())
-      {
-        int reply = JOptionPane
-                .showInternalConfirmDialog(
-                        Desktop.desktop,
-                        MessageManager
-                                .getString("label.alignment_contains_hidden_columns"),
-                        MessageManager
-                                .getString("action.save_omit_hidden_columns"),
-                        JOptionPane.YES_NO_OPTION,
-                        JOptionPane.QUESTION_MESSAGE);
-
-        if (reply == JOptionPane.YES_OPTION)
-        {
-          omitHidden = viewport.getViewAsString(false);
-        }
-      }
-      FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
-      viewport.setFeatureRenderer(fr);
+      ExportData exportData = getAlignmentForExport();
       FormatAdapter f = new FormatAdapter(viewport);
       String output = f.formatSequences(format,
-              viewport.getAlignment(), // class cast exceptions will
+              exportData.getAlignment(), // class cast exceptions will
               // occur in the distant future
-              omitHidden, f.getCacheSuffixDefault(format),
+              exportData.getOmitHidden(), f.getCacheSuffixDefault(format),
               viewport.getColumnSelection());
 
       if (output == null)
@@ -1186,6 +1167,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return success;
   }
 
+
   private void warningMessage(String warning, String title)
   {
     if (new jalview.util.Platform().isHeadless())
@@ -1210,10 +1192,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void outputText_actionPerformed(ActionEvent e)
   {
+
+    ExportData exportData = getAlignmentForExport();
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    cap.setForInput(null);
+
+    try
+    {
+      cap.setText(new FormatAdapter(viewport).formatSequences(
+              e.getActionCommand(),
+ exportData.getAlignment(),
+              exportData.getOmitHidden(),
+              viewport.getColumnSelection()));
+      Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+              "label.alignment_output_command", new Object[]
+              { e.getActionCommand() }), 600, 500);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
+      cap.dispose();
+    }
+
+  }
+
+  public ExportData getAlignmentForExport()
+  {
+    AlignmentI alignmentToExport = null;
     String[] omitHidden = null;
     FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
     viewport.setFeatureRenderer(fr);
-    if (viewport.hasHiddenColumns())
+    HiddenSequences hiddenSeqs = viewport.getAlignment()
+            .getHiddenSequences();
+    if (viewport.hasHiddenColumns() || hiddenSeqs.getSize() > 0)
     {
       int reply = JOptionPane
               .showInternalConfirmDialog(
@@ -1229,26 +1239,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         omitHidden = viewport.getViewAsString(false);
       }
+      else
+      {
+        alignmentToExport = viewport.getAlignment().getHiddenSequences()
+                .getFullAlignment();
+      }
     }
-
-    CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    cap.setForInput(null);
-
-    try
+    if (alignmentToExport == null)
     {
-      cap.setText(new FormatAdapter(viewport).formatSequences(
-              e.getActionCommand(),
-              viewport.getAlignment(), omitHidden,
-              viewport.getColumnSelection()));
-      Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-              "label.alignment_output_command", new Object[]
-              { e.getActionCommand() }), 600, 500);
-    } catch (OutOfMemoryError oom)
-    {
-      new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
-      cap.dispose();
+      alignmentToExport = viewport.getAlignment();
     }
-
+    return new ExportData(alignmentToExport, omitHidden);
   }
 
   /**
@@ -5993,6 +5994,64 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       sf.setComplementVisible(this, show);
     }
   }
+
+  public class ExportData
+  {
+    private AlignmentI alignment;
+
+    private String[] omitHidden;
+
+    public ExportData(AlignmentI align, String[] ommit)
+    {
+      this.alignment = align;
+      this.omitHidden = ommit;
+      System.out.println();
+    }
+
+    public AlignmentI getAlignment()
+    {
+      return alignment;
+    }
+
+    public void setAlignment(AlignmentI alignment)
+    {
+      this.alignment = alignment;
+    }
+
+    public String[] getOmitHidden()
+    {
+      return omitHidden;
+    }
+
+    public void setOmitHidden(String[] omitHidden)
+    {
+      this.omitHidden = omitHidden;
+    }
+  }
+
+  @Override
+  public void hideColumns(List<int[]> colsToHide)
+  {
+    for (int[] colRange : colsToHide)
+    {
+      viewport.hideColumns(colRange[0], colRange[1]);
+    }
+
+  }
+
+  @Override
+  public void syncHiddenSequences()
+  {
+    AlignmentI al = viewport.getAlignment();
+    HiddenSequences hiddenSeqs = al.getHiddenSequences();
+    for (SequenceI seq : al.getSequencesArray())
+      {
+        if (seq.isHidden())
+        {
+        hiddenSeqs.hideSequence(seq);
+        }
+      }
+  }
 }
 
 class PrintThread extends Thread

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 1981488..6f15ddf 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -228,11 +228,11 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
         if (source instanceof HtmlFile)
         {
-          ((HtmlFile) source).applySettingsToAlignFrame(af);
+          ((HtmlFile) source).applySettingsToAlignmentView(af);
         }
         else if (source instanceof JSONFile)
         {
-          ((JSONFile) source).applySettingsToAlignFrame(af);
+          ((JSONFile) source).applySettingsToAlignmentView(af);
         }
 
 

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 5601f27..e2cd43a 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -20,6 +20,10 @@
  */
 package jalview.io;
 
+import java.io.File;
+import java.io.InputStream;
+import java.util.List;
+
 import jalview.api.AlignViewportI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -28,10 +32,6 @@ import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceGroup;
 import jalview.util.MessageManager;
 
-import java.io.File;
-import java.io.InputStream;
-import java.util.List;
-
 /**
  * A low level class for alignment and feature IO with alignment formatting
  * methods used by both applet and application for generating flat alignment
@@ -292,6 +292,7 @@ public class AppletFormatAdapter
         {
           al.addGroup(sg);
         }
+
         return al;
       }
       else if (format.equals(HtmlFile.FILE_DESC))

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index b49c2e0..a026c57 100644 (file)
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -148,7 +148,7 @@ public class BioJsHTMLOutput
     return sb.toString();
   }
 
-  public void refreshBioJSVersionsInfo(String dirName)
+  public static void refreshBioJSVersionsInfo(String dirName)
           throws URISyntaxException
   {
     File directory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
@@ -181,7 +181,7 @@ public class BioJsHTMLOutput
     setBioJsMSAVersions(versionFileMap);
   }
 
-  public void updateBioJS()
+  public static void updateBioJS()
   {
     Thread updateThread = new Thread()
     {
@@ -205,7 +205,7 @@ public class BioJsHTMLOutput
   }
 
 
-  public void syncUpdates(String localDir, BioJSRepositoryPojo repo)
+  public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)
   {
     for (BioJSReleasePojo bjsRelease : repo.getReleases())
     {

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 6329f58..a27777f 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -348,11 +348,11 @@ public class FileLoader implements Runnable
             }
             if (source instanceof HtmlFile)
             {
-              ((HtmlFile) source).applySettingsToAlignFrame(alignFrame);
+              ((HtmlFile) source).applySettingsToAlignmentView(alignFrame);
             }
             else if (source instanceof JSONFile)
             {
-              ((JSONFile) source).applySettingsToAlignFrame(alignFrame);
+              ((JSONFile) source).applySettingsToAlignmentView(alignFrame);
             }
 
             if (raiseGUI)

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index 75e99a6..3dd937d 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -21,15 +21,16 @@
 
 package jalview.io;
 
-import jalview.api.AlignViewControllerGuiI;
-import jalview.schemes.ColourSchemeI;
-
 import java.io.IOException;
+import java.util.List;
 
 import org.jsoup.Jsoup;
 import org.jsoup.nodes.Document;
 import org.jsoup.nodes.Element;
 
+import jalview.api.AlignViewControllerGuiI;
+import jalview.schemes.ColourSchemeI;
+
 public class HtmlFile extends AlignFile
 {
   public static final String FILE_EXT = "html";
@@ -40,6 +41,8 @@ public class HtmlFile extends AlignFile
 
   private boolean showSeqFeatures;
 
+  private List<int[]> hiddenColumns;
+
   public HtmlFile()
   {
     super();
@@ -72,25 +75,27 @@ public class HtmlFile extends AlignFile
       String alignmentJsonString = content.val();
 
       JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
-      seqs = jsonFile.getSeqs();
-      seqGroups = jsonFile.getSeqGroups();
-      annotations = jsonFile.getAnnotations();
-      showSeqFeatures = jsonFile.isShowSeqFeatures();
-      colourScheme = jsonFile.getColourScheme();
+      this.seqs = jsonFile.getSeqs();
+      this.seqGroups = jsonFile.getSeqGroups();
+      this.annotations = jsonFile.getAnnotations();
+      this.showSeqFeatures = jsonFile.isShowSeqFeatures();
+      this.colourScheme = jsonFile.getColourScheme();
+      this.hiddenColumns = jsonFile.getHiddenColumns();
     } catch (Exception e)
     {
       e.printStackTrace();
     }
   }
 
-  public void applySettingsToAlignFrame(AlignViewControllerGuiI af)
+  public void applySettingsToAlignmentView(AlignViewControllerGuiI avc)
   {
-    af.setShowSeqFeatures(isShowSeqFeatures());
-    af.changeColour(getColourScheme());
-    af.setMenusForViewport();
+    avc.setShowSeqFeatures(isShowSeqFeatures());
+    avc.changeColour(getColourScheme());
+    avc.setMenusForViewport();
+    avc.hideColumns(hiddenColumns);
+    avc.syncHiddenSequences();
   }
 
-
   @Override
   public String print()
   {

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 5e2139e..dca59a3 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -21,6 +21,18 @@
 
 package jalview.io;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureRenderer;
@@ -42,18 +54,6 @@ import jalview.json.binding.v1.SequencePojo;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 
-import java.awt.Color;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Vector;
-
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
-
 public class JSONFile extends AlignFile
 {
   private ColourSchemeI colourScheme;
@@ -80,6 +80,10 @@ public class JSONFile extends AlignFile
 
   private JSONExportSettings jsonExportSettings;
 
+  private List<int[]> hiddenColumns;
+
+  private List<String> hiddenSeqRefs;
+
   public JSONFile()
   {
     super();
@@ -141,7 +145,7 @@ public class JSONFile extends AlignFile
         name.append(seq.getName()).append("/").append(seq.getStart())
                 .append("-").append(seq.getEnd());
         SequencePojo jsonSeqPojo = new SequencePojo();
-        jsonSeqPojo.setId(seq.getName() + "_" + seq.hashCode());
+        jsonSeqPojo.setId(String.valueOf(seq.hashCode()));
         jsonSeqPojo.setOrder(++count);
         jsonSeqPojo.setEnd(seq.getEnd());
         jsonSeqPojo.setStart(seq.getStart());
@@ -199,8 +203,7 @@ public class JSONFile extends AlignFile
           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
           for (SequenceI seq : seqGrp.getSequences())
           {
-            seqGrpPojo.getSeqsHash().add(
-                    seq.getName() + "_" + seq.hashCode());
+            seqGrpPojo.getSeqsHash().add(String.valueOf(seq.hashCode()));
           }
           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
         }
@@ -294,7 +297,7 @@ public class JSONFile extends AlignFile
                 && displayedFeatures.isVisible(sf.getType()))
         {
           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
-                  seq.getName() + "_" + seq.hashCode());
+                  String.valueOf(seq.hashCode()));
           String featureColour = (fr == null) ? null : jalview.util.Format
                   .getHexString(fr
                   .findFeatureColour(Color.white, seq,
@@ -376,6 +379,8 @@ public class JSONFile extends AlignFile
                 "showSeqFeatures").toString());
         setColourScheme(getJalviewColorScheme(jsColourScheme));
         setShowSeqFeatures(showFeatures);
+        parseHiddenSeqRefsAsList(jvSettingsJsonObj);
+        parseHiddenCols(jvSettingsJsonObj);
       }
 
       seqMap = new Hashtable<String, Sequence>();
@@ -390,6 +395,10 @@ public class JSONFile extends AlignFile
         int end = Integer.valueOf(sequence.get("end").toString());
         Sequence seq = new Sequence(sequenceName, sequcenceString, start,
                 end);
+        if (hiddenSeqRefs.contains(seqUniqueId))
+        {
+          seq.setHidden(true);
+        }
         seqs.add(seq);
         seqMap.put(seqUniqueId, seq);
       }
@@ -483,6 +492,31 @@ public class JSONFile extends AlignFile
     return this;
   }
 
+  public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
+  {
+    hiddenSeqRefs = new ArrayList<String>();
+    String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
+    if(hiddenSeqs != null && !hiddenSeqs.isEmpty()){
+      String[] seqRefs = hiddenSeqs.split(";");
+      for(String seqRef : seqRefs){
+        hiddenSeqRefs.add(seqRef);
+      }
+    }
+  }
+
+  public void parseHiddenCols(JSONObject jvSettingsJson)
+  {
+    hiddenColumns = new ArrayList<int[]>();
+    String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
+    if(hiddenCols != null && !hiddenCols.isEmpty()){
+      String[] rangeStrings = hiddenCols.split(";");
+      for(String rangeString : rangeStrings){
+        String[] range = rangeString.split("-");
+        hiddenColumns.add(new int[]
+        { Integer.valueOf(range[0]), Integer.valueOf(range[1]) });
+      }
+    }
+  }
 
   @SuppressWarnings("unchecked")
   private void parseFeatures(JSONArray jsonSeqFeatures)
@@ -543,11 +577,13 @@ public class JSONFile extends AlignFile
     return jalviewColor;
   }
 
-  public void applySettingsToAlignFrame(AlignViewControllerGuiI af)
+  public void applySettingsToAlignmentView(AlignViewControllerGuiI avc)
   {
-    af.setShowSeqFeatures(isShowSeqFeatures());
-    af.changeColour(getColourScheme());
-    af.setMenusForViewport();
+    avc.setShowSeqFeatures(isShowSeqFeatures());
+    avc.changeColour(getColourScheme());
+    avc.setMenusForViewport();
+    avc.hideColumns(hiddenColumns);
+    avc.syncHiddenSequences();
   }
 
   public String getGlobalColorScheme()
@@ -634,6 +670,11 @@ public class JSONFile extends AlignFile
     return annotations;
   }
 
+  public List<int[]> getHiddenColumns()
+  {
+    return hiddenColumns;
+  }
+
   public class JSONExportSettings
   {
     private boolean exportSequence;

diff --git a/test/jalview/io/BioJsHTMLOutputTest.java b/test/jalview/io/BioJsHTMLOutputTest.java
index 134d84f..ac2b599 100644 (file)
--- a/test/jalview/io/BioJsHTMLOutputTest.java
+++ b/test/jalview/io/BioJsHTMLOutputTest.java
@@ -21,11 +21,10 @@ public class BioJsHTMLOutputTest
   @Test
   public void getJalviewAlignmentAsJsonString()
   {
-    BioJsHTMLOutput bioJsHtmlOutput = new BioJsHTMLOutput(null, null);
     String bjsTemplate = null;
     try
     {
-      bioJsHtmlOutput.updateBioJS();
+      BioJsHTMLOutput.updateBioJS();
       try
       {
         // allow the update some three seconds to complete before getting latest
@@ -47,10 +46,9 @@ public class BioJsHTMLOutputTest
   @Test(expected = NullPointerException.class)
   public void expectedNullPointerException()
   {
-    BioJsHTMLOutput bjs = new BioJsHTMLOutput(null, null);
     try
     {
-      bjs.refreshBioJSVersionsInfo(null);
+      BioJsHTMLOutput.refreshBioJSVersionsInfo(null);
     } catch (URISyntaxException e)
     {
       Assert.fail("Expception occured while testing!");
@@ -61,11 +59,11 @@ public class BioJsHTMLOutputTest
   @Test
   public void getBioJsMSAVersions()
   {
-    BioJsHTMLOutput bjs = new BioJsHTMLOutput(null, null);
     TreeMap<String, File> versions = null;
     try
     {
-      bjs.refreshBioJSVersionsInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+      BioJsHTMLOutput
+              .refreshBioJSVersionsInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
       versions = BioJsHTMLOutput.getBioJsMSAVersions();
     } catch (URISyntaxException e)
     {