JAL-1641 fixed broken functionalities after refactor

diff --git a/src/jalview/datamodel/AlignmentExportData.java b/src/jalview/datamodel/AlignmentExportData.java
new file mode 100644 (file)
index 0000000..46da85d
--- /dev/null
+++ b/src/jalview/datamodel/AlignmentExportData.java
@@ -0,0 +1,63 @@
+package jalview.datamodel;
+
+import jalview.gui.AlignExportSettings;
+
+public class AlignmentExportData
+{
+  private AlignmentI alignment;
+
+  private String[] omitHidden;
+
+  private int[] startEnd;
+
+  private AlignExportSettings settings;
+
+  public AlignmentExportData(AlignmentI align, String[] ommit,
+          int[] startEnd, AlignExportSettings settings)
+  {
+    this.alignment = align;
+    this.omitHidden = ommit;
+    this.startEnd = startEnd;
+    this.settings = settings;
+  }
+
+  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;
+  }
+
+  public int[] getStartEndPostions()
+  {
+    return startEnd;
+  }
+
+  public void setStartEndPostions(int[] startEnd)
+  {
+    this.startEnd = startEnd;
+  }
+
+  public AlignExportSettings getSettings()
+  {
+    return settings;
+  }
+
+  public void setSettings(AlignExportSettings settings)
+  {
+    this.settings = settings;
+  }
+}

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 764b192..01a22ed 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -48,6 +48,7 @@ import jalview.commands.TrimRegionCommand;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
@@ -1139,8 +1140,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         return false;
       }
 
-      ExportData exportData = getAlignmentForExport(format);
-      FormatAdapter f = new FormatAdapter(alignPanel);
+      AlignmentExportData exportData = getAlignmentForExport(format, viewport);
+      if (exportData.getSettings().isCancelled())
+      {
+        return false;
+      }
+      FormatAdapter f = new FormatAdapter(alignPanel,
+              exportData.getSettings());
       String output = f.formatSequences(format,
               exportData.getAlignment(), // class cast exceptions will
               // occur in the distant future
@@ -1212,7 +1218,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void outputText_actionPerformed(ActionEvent e)
   {
 
-    ExportData exportData = getAlignmentForExport(e.getActionCommand());
+    AlignmentExportData exportData = getAlignmentForExport(
+            e.getActionCommand(), viewport);
     if (exportData.getSettings().isCancelled())
     {
       return;
@@ -1238,7 +1245,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   }
 
-  public ExportData getAlignmentForExport(String exportFomat)
+  public static AlignmentExportData getAlignmentForExport(String exportFomat,
+          AlignViewportI viewport)
   {
     AlignmentI alignmentToExport = null;
     String[] omitHidden = null;
@@ -1272,8 +1280,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
               .getColumnSelection().getHiddenColumns());
     }
-    return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd,
+    AlignmentExportData ed = new AlignmentExportData(alignmentToExport, omitHidden, alignmentStartEnd,
             settings);
+    return ed;
   }
 
   private static int[] getStartEnd(int[] aligmentStartEnd,
@@ -6070,66 +6079,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
-  public class ExportData
-  {
-    private AlignmentI alignment;
-
-    private String[] omitHidden;
-
-    private int[] startEnd;
-
-    private AlignExportSettings settings;
-
-    public ExportData(AlignmentI align, String[] ommit, int[] startEnd,
-            AlignExportSettings settings)
-    {
-      this.alignment = align;
-      this.omitHidden = ommit;
-      this.startEnd = startEnd;
-      this.settings = settings;
-    }
-
-    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;
-    }
-
-    public int[] getStartEndPostions()
-    {
-      return startEnd;
-    }
-
-    public void setStartEndPostions(int[] startEnd)
-    {
-      this.startEnd = startEnd;
-    }
-
-    public AlignExportSettings getSettings()
-    {
-      return settings;
-    }
-
-    public void setSettings(AlignExportSettings settings)
-    {
-      this.settings = settings;
-    }
-  }
-
 }
 
 class PrintThread extends Thread

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index d3d4d6e..3b81e89 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -483,7 +483,7 @@ public class AppletFormatAdapter
   private AlignmentI buildAlignmentFrom(AlignFile alignFile2)
   {
     // Standard boilerplate for creating alignment from parser
-    alignFile.configureForView(viewpanel);
+    // alignFile.configureForView(viewpanel);
 
     AlignmentI al = new Alignment(alignFile.getSeqsAsArray());
 
@@ -597,6 +597,7 @@ public class AppletFormatAdapter
       {
         throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
       }
+
       afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);
 

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 74fb147..089f50b 100644 (file)
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,6 +1,7 @@
 package jalview.io;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentExportData;
 import jalview.exceptions.NoFileSelectedException;
 import jalview.json.binding.v1.BioJSReleasePojo;
 import jalview.json.binding.v1.BioJSRepositoryPojo;
@@ -51,7 +52,20 @@ public class BioJsHTMLOutput
     try
     {
       String outputFile = getOutputFile();
-      String jalviewAlignmentJson = JSONFile.getJSONData(ap);
+      // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
+      AlignmentExportData exportData = jalview.gui.AlignFrame
+              .getAlignmentForExport(
+              JSONFile.FILE_DESC, ap.getAlignViewport());
+      if (exportData.getSettings().isCancelled())
+      {
+        return;
+      }
+      String jalviewAlignmentJson = new FormatAdapter(ap,
+              exportData.getSettings()).formatSequences(JSONFile.FILE_DESC,
+              exportData.getAlignment(), exportData.getOmitHidden(),
+              exportData.getStartEndPostions(), ap.getAlignViewport()
+                      .getColumnSelection());
+
       String bioJSTemplateString = getBioJsTemplateAsString();
       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
               .replaceAll(

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index e795925..8a563fa 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -29,7 +29,6 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.gui.AlignmentPanel;
 
 /**
  * Additional formatting methods used by the application in a number of places.
@@ -51,7 +50,7 @@ public class FormatAdapter extends AppletFormatAdapter
     init();
   }
 
-  public FormatAdapter(AlignmentPanel alignPanel,
+  public FormatAdapter(AlignmentViewPanel alignPanel,
           AlignExportSettingI settings)
   {
     super(alignPanel, settings);

diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index 7e02118..781eace 100644 (file)
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -1,6 +1,7 @@
 package jalview.io;
 
 import jalview.api.FeatureRenderer;
+import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
@@ -93,13 +94,26 @@ public class HtmlSvgOutput
       }
       printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, g1,
               g2);
-      FileOutputStream out = new FileOutputStream(file);
 
       String titleSvgData = g1.getSVGDocument();
       String alignSvgData = g2.getSVGDocument();
-      String jsonData = JSONFile.getJSONData(ap);
+
+      AlignmentExportData exportData = ap.alignFrame.getAlignmentForExport(
+              JSONFile.FILE_DESC, av);
+      if (exportData.getSettings().isCancelled())
+      {
+        return;
+      }
+      String jsonData = new FormatAdapter(ap, exportData.getSettings())
+              .formatSequences(JSONFile.FILE_DESC, exportData
+                      .getAlignment(), exportData.getOmitHidden(),
+                      exportData.getStartEndPostions(), ap
+                              .getAlignViewport().getColumnSelection());
+
+      // String jsonData = JSONFile.getJSONData(ap);
       String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
 
+      FileOutputStream out = new FileOutputStream(file);
       out.write(htmlData.getBytes());
       out.flush();
       out.close();

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index ce70ea5..25a0064 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -594,46 +594,29 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   public void configureForView(AlignmentViewPanel avpanel)
   {
     super.configureForView(avpanel);
-    if (isExporting())
-    {
-      setViewport(avpanel.getAlignViewport());
-      seqGroups = avpanel.getAlignment().getGroups();
-      setDisplayedFeatures(getViewport().getFeaturesDisplayed());
-      fr = avpanel.cloneFeatureRenderer();
 
-      for (SequenceI seq : getViewport().getAlignment().getSequences())
-      {
-        seqs.add(seq);
-      }
+    seqGroups = avpanel.getAlignment().getGroups();
+    setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+    fr = avpanel.cloneFeatureRenderer();
 
-      // Add non auto calculated annotation to AlignFile
-      for (AlignmentAnnotation annot : getViewport().getAlignment()
-              .getAlignmentAnnotation())
+    // Add non auto calculated annotation to AlignFile
+    for (AlignmentAnnotation annot : getViewport().getAlignment()
+            .getAlignmentAnnotation())
+    {
+      if (annot != null && !annot.autoCalculated)
       {
-        if (annot != null && !annot.autoCalculated)
+        if (!annot.visible)
         {
-          if (annot.label.equals("PDB.CATempFactor"))
-          {
-            continue;
-          }
-          annotations.add(annot);
+          continue;
         }
+        annotations.add(annot);
       }
-
-      globalColorScheme = ColourSchemeProperty.getColourName(getViewport()
-              .getGlobalColourScheme());
-      setDisplayedFeatures(getViewport().getFeaturesDisplayed());
-      showSeqFeatures = getViewport().isShowSequenceFeatures();
     }
-  }
+    globalColorScheme = ColourSchemeProperty.getColourName(getViewport()
+            .getGlobalColourScheme());
+    setDisplayedFeatures(getViewport().getFeaturesDisplayed());
+    showSeqFeatures = getViewport().isShowSequenceFeatures();
 
-
-  public static String getJSONData(AlignmentViewPanel av)
-  {
-    JSONFile jsonFile = new JSONFile();
-    jsonFile.configureForView(av);
-    String jsonString = jsonFile.print();
-    return jsonString;
   }
 
   public boolean isShowSeqFeatures()