JAL-1780 more support for export setting for flatfile output

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 34ee209..fa73194 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -373,10 +373,25 @@ public interface AlignViewportI extends ViewStyleI
    */
   void setFollowHighlight(boolean b);
 
+  /**
+   * Returns a FeatureRenderer instance
+   * 
+   * @return
+   */
   public FeatureRenderer getFeatureRenderer();
 
+  /**
+   * Sets a FeatureRenderer for a viewport
+   * 
+   * @param featureRenderer
+   */
   public void setFeatureRenderer(FeatureRenderer featureRenderer);
 
-  public boolean isIncludeHiddenRegion();
+  /**
+   * Returns Settings for exporting an Alignment
+   * 
+   * @return
+   */
+  public AlignExportSettingI getExportSettings();
 
 }

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 1510a14..4f7e2b9 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1341,7 +1341,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
     viewport.setFeatureRenderer(fr);
-    viewport.setIncludeHiddenRegion(false);
     cap.setText(new AppletFormatAdapter(viewport).formatSequences(
             e.getActionCommand(), viewport.getAlignment(),
             viewport.getShowJVSuffix()));

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 607dc05..d7ec681 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -23,6 +23,7 @@ package jalview.appletgui;
 import java.awt.Font;
 
 import jalview.analysis.NJTree;
+import jalview.api.AlignExportSettingI;
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureRenderer;
 import jalview.bin.JalviewLite;
@@ -60,7 +61,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   private FeatureRenderer featureRenderer;
 
-  private boolean includeHiddenRegion = true;
+  private AlignExportSettingI exportSettings;
 
   public void finalize()
   {
@@ -485,14 +486,15 @@ public class AlignViewport extends AlignmentViewport implements
 
   }
 
-  public boolean isIncludeHiddenRegion()
+  public AlignExportSettingI getExportSettings()
   {
-    return includeHiddenRegion;
+    return exportSettings;
   }
 
-  public void setIncludeHiddenRegion(boolean includeHiddenRegion)
+  public void setExportSettings(AlignExportSettingI exportSettings)
   {
-    this.includeHiddenRegion = includeHiddenRegion;
+    this.exportSettings = exportSettings;
   }
 
+
 }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index db61f77..85b6767 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -74,6 +74,7 @@ import jalview.analysis.CrossRef;
 import jalview.analysis.Dna;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignExportSettingI;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
@@ -1140,7 +1141,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         return false;
       }
 
-      ExportData exportData = getAlignmentForExport();
+      ExportData exportData = getAlignmentForExport(format);
       FormatAdapter f = new FormatAdapter(viewport);
       String output = f.formatSequences(format,
               exportData.getAlignment(), // class cast exceptions will
@@ -1213,10 +1214,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void outputText_actionPerformed(ActionEvent e)
   {
 
-    ExportData exportData = getAlignmentForExport();
+    ExportData exportData = getAlignmentForExport(e.getActionCommand());
+    if (exportData.getSettings().isCancelled())
+    {
+      return;
+    }
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(null);
-
     try
     {
       cap.setText(new FormatAdapter(viewport).formatSequences(
@@ -1235,7 +1239,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   }
 
-  public ExportData getAlignmentForExport()
+  public ExportData getAlignmentForExport(String exportFomat)
   {
     AlignmentI alignmentToExport = null;
     String[] omitHidden = null;
@@ -1250,36 +1254,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignmentStartEnd = new int[]
     { 0, alignmentToExport.getWidth() - 1 };
 
-    if (viewport.hasHiddenColumns() || hiddenSeqs.getSize() > 0)
-    {
-      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);
+    boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
+    AlignExportSettingI settings = new AlignExportSettings(hasHiddenSeqs,
+            viewport.hasHiddenColumns(), exportFomat);
+    viewport.setExportSettings(settings);
+    settings.isExportAnnotations();
 
-      if (reply == JOptionPane.YES_OPTION)
-      {
-        // export only visible region
-        omitHidden = viewport.getViewAsString(false);
-        alignmentToExport = viewport.getAlignment();
-        alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
-                .getColumnSelection().getHiddenColumns());
-        viewport.setIncludeHiddenRegion(false);
-      }
-      else
-      {
-        // export all region including visible
-        alignmentToExport = hiddenSeqs.getFullAlignment();
-        viewport.setIncludeHiddenRegion(true);
-      }
+    if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
+    {
+      omitHidden = viewport.getViewAsString(false);
     }
 
-    return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd);
+    if (hasHiddenSeqs && settings.isExportHiddenSequences())
+    {
+      alignmentToExport = hiddenSeqs.getFullAlignment();
+    }
+    else
+    {
+      alignmentToExport = viewport.getAlignment();
+      alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
+              .getColumnSelection().getHiddenColumns());
+    }
+    return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd,
+            settings);
   }
 
   private static int[] getStartEnd(int[] aligmentStartEnd,
@@ -1352,9 +1349,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    // new HTMLOutput(alignPanel,
-    // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
-    // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
     new HtmlSvgOutput(null, alignPanel);
   }
 
@@ -6094,11 +6088,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     private int[] startEnd;
 
-    public ExportData(AlignmentI align, String[] ommit, int[] startEnd)
+    private AlignExportSettingI settings;
+
+    public ExportData(AlignmentI align, String[] ommit, int[] startEnd,
+            AlignExportSettingI settings)
     {
       this.alignment = align;
       this.omitHidden = ommit;
       this.startEnd = startEnd;
+      this.settings = settings;
     }
 
     public AlignmentI getAlignment()
@@ -6130,6 +6128,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       this.startEnd = startEnd;
     }
+
+    public AlignExportSettingI getSettings()
+    {
+      return settings;
+    }
+
+    public void setSettings(AlignExportSettingI settings)
+    {
+      this.settings = settings;
+    }
   }
 
 }

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 2224021..a6f7d41 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -54,6 +54,7 @@ import javax.swing.JOptionPane;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.NJTree;
+import jalview.api.AlignExportSettingI;
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureRenderer;
 import jalview.api.ViewStyleI;
@@ -100,6 +101,9 @@ public class AlignViewport extends AlignmentViewport implements
   private FeatureRenderer featureRenderer;
 
   private boolean includeHiddenRegion = true;
+
+  private AlignExportSettingI exportSettings;
+
   String viewName;
 
   /*
@@ -1053,13 +1057,13 @@ public class AlignViewport extends AlignmentViewport implements
     this.featureRenderer = featureRenderer;
   }
 
-  public boolean isIncludeHiddenRegion()
+  public AlignExportSettingI getExportSettings()
   {
-    return includeHiddenRegion;
+    return exportSettings;
   }
 
-  public void setIncludeHiddenRegion(boolean includeHiddenRegion)
+  public void setExportSettings(AlignExportSettingI exportSettings)
   {
-    this.includeHiddenRegion = includeHiddenRegion;
+    this.exportSettings = exportSettings;
   }
 }

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index d2b8412..f977b04 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -79,8 +79,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   private FeatureRenderer fr;
 
-  private JSONExportSettings jsonExportSettings;
-
   private List<int[]> hiddenColumns;
 
   private ColumnSelection columnSelection;
@@ -123,15 +121,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     String jsonOutput = null;
     try
     {
-      if (getJsonExportSettings() == null)
-      {
-        jsonExportSettings = new JSONExportSettings();
-        jsonExportSettings.setExportAnnotations(true);
-        jsonExportSettings.setExportGroups(true);
-        jsonExportSettings.setExportJalviewSettings(true);
-        jsonExportSettings.setExportSequenceFeatures(true);
-      }
-
       AlignmentPojo jsonAlignmentPojo = new AlignmentPojo();
       if (getViewport() != null)
       {
@@ -159,44 +148,46 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
       }
 
-      if (jsonExportSettings.isExportJalviewSettings())
+      jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
+      jsonAlignmentPojo.getAppSettings().put("application", application);
+      jsonAlignmentPojo.getAppSettings().put("version", version);
+      jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
+      jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
+              String.valueOf(showSeqFeatures));
+
+      String[] hiddenSections = getHiddenSections();
+      if (hiddenSections != null)
       {
-        jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
-        jsonAlignmentPojo.getAppSettings().put("application", application);
-        jsonAlignmentPojo.getAppSettings().put("version", version);
-        jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
-        jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
-                String.valueOf(showSeqFeatures));
-
-        String[] hiddenSections = exportHiddenSections();
-        if (hiddenSections != null && getViewport().isIncludeHiddenRegion())
+        if (hiddenSections[0] != null
+                && getViewport().getExportSettings()
+                        .isExportHiddenColumns())
         {
-          if (hiddenSections[0] != null)
-          {
-            jsonAlignmentPojo.getAppSettings().put("hiddenCols",
-                    String.valueOf(hiddenSections[0]));
-          }
-          if (hiddenSections[1] != null)
-          {
-            jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
-                    String.valueOf(hiddenSections[1]));
-          }
+          jsonAlignmentPojo.getAppSettings().put("hiddenCols",
+                  String.valueOf(hiddenSections[0]));
+        }
+        if (hiddenSections[1] != null
+                && getViewport().getExportSettings()
+                        .isExportHiddenSequences())
+        {
+          jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
+                  String.valueOf(hiddenSections[1]));
         }
       }
 
-      if (jsonExportSettings.isExportAnnotations())
+      if (getViewport().getExportSettings().isExportAnnotations())
       {
         jsonAlignmentPojo
                 .setAlignAnnotation(annotationToJsonPojo(annotations));
       }
 
-      if (jsonExportSettings.isExportSequenceFeatures())
+      if (getViewport().getExportSettings().isExportFeatures())
       {
         jsonAlignmentPojo
                 .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
       }
 
-      if (jsonExportSettings.isExportGroups() && seqGroups != null
+      if (getViewport().getExportSettings().isExportGroups()
+              && seqGroups != null
               && seqGroups.size() > 0)
       {
         for (SequenceGroup seqGrp : seqGroups)
@@ -231,7 +222,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     return jsonOutput;
   }
 
-  public String[] exportHiddenSections()
+  public String[] getHiddenSections()
   {
     String[] hiddenSections = new String[2];
     if (getViewport() == null)
@@ -614,16 +605,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     this.displayedFeatures = displayedFeatures;
   }
 
-  public JSONExportSettings getJsonExportSettings()
-  {
-    return jsonExportSettings;
-  }
-
-  public void setJsonExportSettings(JSONExportSettings jsonExportSettings)
-  {
-    this.jsonExportSettings = jsonExportSettings;
-  }
-
 
   public static String getJSONData(AlignViewportI av)
   {