JAL-1641 updated applet version

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index b4d2592..34ee209 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -20,6 +20,11 @@
  */
 package jalview.api;
 
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
 import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -31,11 +36,6 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 
-import java.awt.Color;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
 /**
  * @author jimp
  * 
@@ -377,4 +377,6 @@ public interface AlignViewportI extends ViewStyleI
 
   public void setFeatureRenderer(FeatureRenderer featureRenderer);
 
+  public boolean isIncludeHiddenRegion();
+
 }

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index ee64dda..1b1a5b8 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1313,7 +1313,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
             "label.alignment_output_command", new Object[]
             { e.getActionCommand() }), 600, 500);
-    cap.setText(new AppletFormatAdapter().formatSequences(
+
+    FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
+    viewport.setFeatureRenderer(fr);
+    viewport.setIncludeHiddenRegion(false);
+    cap.setText(new AppletFormatAdapter(viewport).formatSequences(
             e.getActionCommand(), viewport.getAlignment(),
             viewport.getShowJVSuffix()));
   }
@@ -4182,9 +4186,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   @Override
   public void setShowSeqFeatures(boolean b)
   {
-    // showSeqFeatures.setSelected(b);
-    // viewport.setShowSequenceFeatures(b);
-
+    this.sequenceFeatures.setState(b);
+    viewport.setShowSequenceFeatures(b);
   }
 
   @Override

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index ef17215..607dc05 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -20,6 +20,8 @@
  */
 package jalview.appletgui;
 
+import java.awt.Font;
+
 import jalview.analysis.NJTree;
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureRenderer;
@@ -39,8 +41,6 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
 
-import java.awt.Font;
-
 public class AlignViewport extends AlignmentViewport implements
         SelectionSource, VamsasSource, CommandListener
 {
@@ -60,6 +60,8 @@ public class AlignViewport extends AlignmentViewport implements
 
   private FeatureRenderer featureRenderer;
 
+  private boolean includeHiddenRegion = true;
+
   public void finalize()
   {
     applet = null;
@@ -483,4 +485,14 @@ public class AlignViewport extends AlignmentViewport implements
 
   }
 
+  public boolean isIncludeHiddenRegion()
+  {
+    return includeHiddenRegion;
+  }
+
+  public void setIncludeHiddenRegion(boolean includeHiddenRegion)
+  {
+    this.includeHiddenRegion = includeHiddenRegion;
+  }
+
 }

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index d33e0cc..5b699a6 100644 (file)
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -41,7 +41,10 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.AnnotationFile;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.FileParse;
+import jalview.io.HtmlFile;
 import jalview.io.IdentifyFile;
+import jalview.io.JSONFile;
 import jalview.io.NewickFile;
 import jalview.io.TCoffeeScoreFile;
 import jalview.schemes.TCoffeeColourScheme;
@@ -60,6 +63,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
   AlignFrame alignFrame;
 
+  FileParse source = null;
+
   public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
   {
     try
@@ -163,7 +168,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     }
     else if (alignFrame != null)
     {
-      loadAlignment(text, newWindow);
+      loadAlignment(text, newWindow, alignFrame.getAlignViewport());
     }
 
     // TODO: dialog should indicate if data was parsed correctly or not - see
@@ -212,16 +217,18 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
    * @param text
    * @param newWindow
    */
-  protected void loadAlignment(String text, boolean newWindow)
+  protected void loadAlignment(String text, boolean newWindow,
+          AlignViewport viewport)
   {
     Alignment al = null;
 
     String format = new IdentifyFile().Identify(text,
             AppletFormatAdapter.PASTE);
+    AppletFormatAdapter afa = new AppletFormatAdapter(viewport);
     try
     {
-      al = new AppletFormatAdapter().readFile(text,
-              AppletFormatAdapter.PASTE, format);
+      al = afa.readFile(text, AppletFormatAdapter.PASTE, format);
+      source = afa.getAlignFile();
     } catch (java.io.IOException ex)
     {
       ex.printStackTrace();
@@ -247,6 +254,15 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
         af.statusBar
                 .setText(MessageManager
                         .getString("label.successfully_pasted_annotation_to_alignment"));
+
+        if (source instanceof HtmlFile)
+        {
+          ((HtmlFile) source).applySettingsToAlignmentView(af);
+        }
+        else if (source instanceof JSONFile)
+        {
+          ((JSONFile) source).applySettingsToAlignmentView(af);
+        }
       }
       else
       {

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 6481855..b646d5b 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1250,11 +1250,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         alignmentToExport = viewport.getAlignment();
         alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
                 .getColumnSelection().getHiddenColumns());
+        viewport.setIncludeHiddenRegion(false);
       }
       else
       {
         // export all region including visible
         alignmentToExport = hiddenSeqs.getFullAlignment();
+        viewport.setIncludeHiddenRegion(true);
       }
     }
 
@@ -6126,13 +6128,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     AlignmentI al = viewport.getAlignment();
     HiddenSequences hiddenSeqs = al.getHiddenSequences();
+    boolean hasHiddenRows = false;
     for (SequenceI seq : al.getSequencesArray())
       {
         if (seq.isHidden())
         {
         hiddenSeqs.hideSequence(seq);
+        hasHiddenRows = true;
         }
       }
+    viewport.setHasHiddenRows(hasHiddenRows);
+    firePropertyChange("alignment", null, al.getSequences());
   }
 }
 

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 8ecf19d..2224021 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -99,6 +99,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   private FeatureRenderer featureRenderer;
 
+  private boolean includeHiddenRegion = true;
   String viewName;
 
   /*
@@ -1051,4 +1052,14 @@ public class AlignViewport extends AlignmentViewport implements
   {
     this.featureRenderer = featureRenderer;
   }
+
+  public boolean isIncludeHiddenRegion()
+  {
+    return includeHiddenRegion;
+  }
+
+  public void setIncludeHiddenRegion(boolean includeHiddenRegion)
+  {
+    this.includeHiddenRegion = includeHiddenRegion;
+  }
 }

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index dca59a3..8882f97 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -164,12 +164,18 @@ public class JSONFile extends AlignFile
                 String.valueOf(showSeqFeatures));
 
         String[] hiddenSections = exportHiddenSections();
-        if (hiddenSections != null)
+        if (hiddenSections != null && getViewport().isIncludeHiddenRegion())
         {
-          jsonAlignmentPojo.getAppSettings().put("hiddenCols",
-                  String.valueOf(hiddenSections[0]));
-          jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
-                  String.valueOf(hiddenSections[1]));
+          if (hiddenSections[0] != null)
+          {
+            jsonAlignmentPojo.getAppSettings().put("hiddenCols",
+                    String.valueOf(hiddenSections[0]));
+          }
+          if (hiddenSections[1] != null)
+          {
+            jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
+                    String.valueOf(hiddenSections[1]));
+          }
         }
       }
 
@@ -250,13 +256,14 @@ public class JSONFile extends AlignFile
     // hidden rows/seqs business
     HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
             .getHiddenSequences();
-    if (hiddenSeqsObj == null)
+    if (hiddenSeqsObj == null || hiddenSeqsObj.hiddenSequences == null)
     {
       return hiddenSections;
     }
 
     SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
     System.out.print("Hidden Seqs : ");
+    // if(hiddenSeqs != null){
     StringBuilder hiddenSeqsBuilder = new StringBuilder();
     for (SequenceI hiddenSeq : hiddenSeqs)
     {
@@ -266,11 +273,13 @@ public class JSONFile extends AlignFile
       }
     }
     if (hiddenSeqsBuilder.length() > 0)
-    {
+      {
       hiddenSeqsBuilder.deleteCharAt(0);
-    }
+      }
     hiddenSections[1] = hiddenSeqsBuilder.toString();
     System.out.println(hiddenSections[1]);
+    // }
+
     return hiddenSections;
   }
 
@@ -286,6 +295,8 @@ public class JSONFile extends AlignFile
       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
               : seq.getDatasetSequence().getSequenceFeatures();
 
+      seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
+              : seqFeatures;
       if (seqFeatures == null)
       {
         continue;
@@ -395,7 +406,7 @@ 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))
+        if (hiddenSeqRefs != null && hiddenSeqRefs.contains(seqUniqueId))
         {
           seq.setHidden(true);
         }

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 302b0ef..399347b 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1063,6 +1063,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return hasHiddenRows;
   }
 
+  public void setHasHiddenRows(boolean hasHiddenRows)
+  {
+    this.hasHiddenRows = hasHiddenRows;
+  }
+
   protected SequenceGroup selectionGroup;
 
   public void setSequenceSetId(String newid)