JAL-2843 refactor / tidy for feature filter input/output

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index ef87671..fe6b8d9 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1445,9 +1445,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     FeaturesFile formatter = new FeaturesFile();
     if (format.equalsIgnoreCase("Jalview"))
     {
-      features = formatter.printJalviewFormat(viewport.getAlignment()
-              .getSequencesArray(), getDisplayedFeatureCols(),
-              getDisplayedFeatureGroups(), true);
+      features = formatter.printJalviewFormat(
+              viewport.getAlignment().getSequencesArray(),
+              getDisplayedFeatureCols(), null, getDisplayedFeatureGroups(),
+              true);
     }
     else
     {

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8a44f27..4c9360e 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1392,13 +1392,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void exportFeatures_actionPerformed(ActionEvent e)
   {
-    new AnnotationExporter().exportFeatures(alignPanel);
+    new AnnotationExporter(alignPanel).exportFeatures();
   }
 
   @Override
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
-    new AnnotationExporter().exportAnnotations(alignPanel);
+    new AnnotationExporter(alignPanel).exportAnnotations();
   }
 
   @Override

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index a619997..6fefbd0 100644 (file)
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -21,8 +21,10 @@
 package jalview.gui;
 
 import jalview.api.FeatureColourI;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.io.AnnotationFile;
 import jalview.io.FeaturesFile;
 import jalview.io.JalviewFileChooser;
@@ -34,6 +36,8 @@ import java.awt.Color;
 import java.awt.FlowLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.io.FileWriter;
+import java.io.PrintWriter;
 import java.util.List;
 import java.util.Map;
 
@@ -57,18 +61,22 @@ import javax.swing.SwingConstants;
  */
 public class AnnotationExporter extends JPanel
 {
-  JInternalFrame frame;
+  private JInternalFrame frame;
 
-  AlignmentPanel ap;
+  private AlignmentPanel ap;
 
-  boolean features = true;
+  /*
+   * true if exporting features, false if exporting annotations
+   */
+  private boolean exportFeatures = true;
 
   private AlignmentAnnotation[] annotations;
 
   private boolean wholeView;
 
-  public AnnotationExporter()
+  public AnnotationExporter(AlignmentPanel panel)
   {
+    this.ap = panel;
     try
     {
       jbInit();
@@ -84,47 +92,54 @@ public class AnnotationExporter extends JPanel
             frame.getPreferredSize().height);
   }
 
-  public void exportFeatures(AlignmentPanel ap)
+  /**
+   * Configures the diglog for options to export visible features
+   */
+  public void exportFeatures()
   {
-    this.ap = ap;
-    features = true;
+    exportFeatures = true;
     CSVFormat.setVisible(false);
     frame.setTitle(MessageManager.getString("label.export_features"));
   }
 
-  public void exportAnnotations(AlignmentPanel ap)
+  /**
+   * Configures the dialog for options to export all visible annotations
+   */
+  public void exportAnnotations()
   {
-    this.ap = ap;
-    annotations = ap.av.isShowAnnotation() ? null
-            : ap.av.getAlignment().getAlignmentAnnotation();
-    wholeView = true;
-    startExportAnnotation();
+    boolean showAnnotation = ap.av.isShowAnnotation();
+    exportAnnotation(showAnnotation ? null
+            : ap.av.getAlignment().getAlignmentAnnotation(), true);
   }
 
-  public void exportAnnotations(AlignmentPanel alp,
-          AlignmentAnnotation[] toExport)
+  /**
+   * Configures the dialog for options to export the given annotation row
+   * 
+   * @param toExport
+   */
+  public void exportAnnotation(AlignmentAnnotation toExport)
   {
-    ap = alp;
-    annotations = toExport;
-    wholeView = false;
-    startExportAnnotation();
+    exportAnnotation(new AlignmentAnnotation[] { toExport }, false);
   }
 
-  private void startExportAnnotation()
+  private void exportAnnotation(AlignmentAnnotation[] toExport,
+          boolean forWholeView)
   {
-    features = false;
+    wholeView = forWholeView;
+    annotations = toExport;
+    exportFeatures = false;
     GFFFormat.setVisible(false);
     CSVFormat.setVisible(true);
     frame.setTitle(MessageManager.getString("label.export_annotations"));
   }
 
-  public void toFile_actionPerformed(ActionEvent e)
+  private void toFile_actionPerformed()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(features
+    chooser.setDialogTitle(exportFeatures
             ? MessageManager.getString("label.save_features_to_file")
             : MessageManager.getString("label.save_annotation_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
@@ -133,13 +148,12 @@ public class AnnotationExporter extends JPanel
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      String text = getFileContents();
+      String text = getText();
 
       try
       {
-        java.io.PrintWriter out = new java.io.PrintWriter(
-                new java.io.FileWriter(chooser.getSelectedFile()));
-
+        PrintWriter out = new PrintWriter(
+                new FileWriter(chooser.getSelectedFile()));
         out.print(text);
         out.close();
       } catch (Exception ex)
@@ -148,64 +162,89 @@ public class AnnotationExporter extends JPanel
       }
     }
 
-    close_actionPerformed(null);
+    close_actionPerformed();
+  }
+
+  /**
+   * Answers the text to output for either Features (in GFF or Jalview format) or
+   * Annotations (in CSV or Jalview format)
+   * 
+   * @return
+   */
+  private String getText()
+  {
+    return exportFeatures ? getFeaturesText() : getAnnotationsText();
   }
 
-  private String getFileContents()
+  /**
+   * Returns the text contents for output of annotations in either CSV or Jalview
+   * format
+   * 
+   * @return
+   */
+  private String getAnnotationsText()
   {
-    String text = MessageManager
-            .getString("label.no_features_on_alignment");
-    if (features)
+    String text;
+    if (CSVFormat.isSelected())
     {
-      FeaturesFile formatter = new FeaturesFile();
-      SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
-      Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
-              .getDisplayedFeatureCols();
-      List<String> featureGroups = ap.getFeatureRenderer()
-              .getDisplayedFeatureGroups();
-      boolean includeNonPositional = ap.av.isShowNPFeats();
-      if (GFFFormat.isSelected())
-      {
-        text = formatter.printGffFormat(sequences, featureColours,
-                featureGroups, includeNonPositional);
-      }
-      else
-      {
-        text = formatter.printJalviewFormat(sequences, featureColours,
-                featureGroups, includeNonPositional);
-      }
+      text = new AnnotationFile().printCSVAnnotations(annotations);
     }
     else
     {
-      if (CSVFormat.isSelected())
+      if (wholeView)
       {
-        text = new AnnotationFile().printCSVAnnotations(annotations);
+        text = new AnnotationFile().printAnnotationsForView(ap.av);
       }
       else
       {
-        if (wholeView)
-        {
-          text = new AnnotationFile().printAnnotationsForView(ap.av);
-        }
-        else
-        {
-          text = new AnnotationFile().printAnnotations(annotations, null,
-                  null);
-        }
+        text = new AnnotationFile().printAnnotations(annotations, null,
+                null);
       }
     }
     return text;
   }
 
-  public void toTextbox_actionPerformed(ActionEvent e)
+  /**
+   * Returns the text contents for output of features in either GFF or Jalview
+   * format
+   * 
+   * @return
+   */
+  private String getFeaturesText()
+  {
+    String text;
+    SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
+    Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
+            .getDisplayedFeatureCols();
+    Map<String, FeatureMatcherSetI> featureFilters = ap.getFeatureRenderer()
+            .getFeatureFilters();
+    List<String> featureGroups = ap.getFeatureRenderer()
+            .getDisplayedFeatureGroups();
+    boolean includeNonPositional = ap.av.isShowNPFeats();
+
+    FeaturesFile formatter = new FeaturesFile();
+    if (GFFFormat.isSelected())
+    {
+      text = formatter.printGffFormat(sequences, featureColours,
+              featureGroups, includeNonPositional);
+    }
+    else
+    {
+      text = formatter.printJalviewFormat(sequences, featureColours,
+              featureFilters, featureGroups, includeNonPositional);
+    }
+    return text;
+  }
+
+  private void toTextbox_actionPerformed()
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 
     try
     {
-      String text = getFileContents();
+      String text = getText();
       cap.setText(text);
-      Desktop.addInternalFrame(cap, (features ? MessageManager
+      Desktop.addInternalFrame(cap, (exportFeatures ? MessageManager
               .formatMessage("label.features_for_params", new String[]
               { ap.alignFrame.getTitle() })
               : MessageManager.formatMessage("label.annotations_for_params",
@@ -214,7 +253,7 @@ public class AnnotationExporter extends JPanel
               600, 500);
     } catch (OutOfMemoryError oom)
     {
-      new OOMWarning((features ? MessageManager.formatMessage(
+      new OOMWarning((exportFeatures ? MessageManager.formatMessage(
               "label.generating_features_for_params", new String[]
               { ap.alignFrame.getTitle() })
               : MessageManager.formatMessage(
@@ -225,10 +264,10 @@ public class AnnotationExporter extends JPanel
       cap.dispose();
     }
 
-    close_actionPerformed(null);
+    close_actionPerformed();
   }
 
-  public void close_actionPerformed(ActionEvent e)
+  private void close_actionPerformed()
   {
     try
     {
@@ -248,7 +287,7 @@ public class AnnotationExporter extends JPanel
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        toFile_actionPerformed(e);
+        toFile_actionPerformed();
       }
     });
     toTextbox.setText(MessageManager.getString("label.to_textbox"));
@@ -257,7 +296,7 @@ public class AnnotationExporter extends JPanel
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        toTextbox_actionPerformed(e);
+        toTextbox_actionPerformed();
       }
     });
     close.setText(MessageManager.getString("action.close"));
@@ -266,7 +305,7 @@ public class AnnotationExporter extends JPanel
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        close_actionPerformed(e);
+        close_actionPerformed();
       }
     });
     jalviewFormat.setOpaque(false);

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index b94a615..de69907 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -266,9 +266,7 @@ public class AnnotationLabels extends JPanel
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
-      new AnnotationExporter().exportAnnotations(ap,
-              new AlignmentAnnotation[]
-              { aa[selectedRow] });
+      new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]);
     }
     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
     {