X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=0d47e36bdd5c71d1dec26f62d42113a650ee363c;hb=ee5718cb9339243dd47eeb410fe101217859c2ff;hp=e966c92161916ce48a574a649c6ec4dd0c1c8152;hpb=ffea8e06f34c1004671749a799722f64a83d8161;p=jalview.git

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index e966c92..0d47e36 100644
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,8 +20,9 @@
  */
 package jalview.gui;
 
+import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 import jalview.io.AnnotationFile;
 import jalview.io.FeaturesFile;
 import jalview.io.JalviewFileChooser;
@@ -33,9 +34,7 @@ import java.awt.Color;
 import java.awt.FlowLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
+import java.util.Map;
 
 import javax.swing.BorderFactory;
 import javax.swing.ButtonGroup;
@@ -63,11 +62,9 @@ public class AnnotationExporter extends JPanel
 
   boolean features = true;
 
-  AlignmentAnnotation[] annotations;
+  private AlignmentAnnotation[] annotations;
 
-  List<SequenceGroup> sequenceGroups;
-
-  Hashtable alignmentProperties;
+  private boolean wholeView;
 
   public AnnotationExporter()
   {
@@ -94,17 +91,29 @@ public class AnnotationExporter extends JPanel
     frame.setTitle(MessageManager.getString("label.export_features"));
   }
 
-  public void exportAnnotations(AlignmentPanel ap,
-          AlignmentAnnotation[] annotations, List<SequenceGroup> list,
-          Hashtable alProperties)
+  public void exportAnnotations(AlignmentPanel ap)
   {
     this.ap = ap;
+    annotations = ap.av.isShowAnnotation() ? null : ap.av.getAlignment()
+            .getAlignmentAnnotation();
+    wholeView = true;
+    startExportAnnotation();
+  }
+
+  public void exportAnnotations(AlignmentPanel alp,
+          AlignmentAnnotation[] toExport)
+  {
+    ap = alp;
+    annotations = toExport;
+    wholeView = false;
+    startExportAnnotation();
+  }
+
+  private void startExportAnnotation()
+  {
     features = false;
     GFFFormat.setVisible(false);
     CSVFormat.setVisible(true);
-    this.annotations = annotations;
-    this.sequenceGroups = list;
-    this.alignmentProperties = alProperties;
     frame.setTitle(MessageManager.getString("label.export_annotations"));
   }
 
@@ -114,42 +123,16 @@ public class AnnotationExporter extends JPanel
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(features ? MessageManager.getString("label.save_features_to_file")
-            : MessageManager.getString("label.save_annotation_to_file"));
+    chooser.setDialogTitle(features ? MessageManager
+            .getString("label.save_features_to_file") : MessageManager
+            .getString("label.save_annotation_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      String text = MessageManager.getString("label.no_features_on_alignment");
-      if (features)
-      {
-        if (GFFFormat.isSelected())
-        {
-          text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
-                  .getDataset().getSequencesArray(),
-                  getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
-        }
-        else
-        {
-          text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
-                  .getDataset().getSequencesArray(),
-                  getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
-        }
-      }
-      else
-      {
-        if (CSVFormat.isSelected())
-        {
-          text = new AnnotationFile().printCSVAnnotations(annotations);
-        }
-        else
-        {
-          text = new AnnotationFile().printAnnotations(annotations,
-                  sequenceGroups, alignmentProperties);
-        }
-      }
+      String text = getFileContents();
 
       try
       {
@@ -167,25 +150,37 @@ public class AnnotationExporter extends JPanel
     close_actionPerformed(null);
   }
 
-  public void toTextbox_actionPerformed(ActionEvent e)
+  private String getFileContents()
   {
-    String text = MessageManager.getString("label.no_features_on_alignment");
+    String text = MessageManager
+            .getString("label.no_features_on_alignment");
     if (features)
     {
+      Map<String, FeatureColourI> displayedFeatureColours = ap
+              .getFeatureRenderer().getDisplayedFeatureCols();
+      FeaturesFile formatter = new FeaturesFile();
+      SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
+      Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
+              .getDisplayedFeatureCols();
+      boolean includeNonPositional = ap.av.isShowNPFeats();
       if (GFFFormat.isSelected())
       {
-        text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
-                .getDataset().getSequencesArray(),
-                getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
+        text = new FeaturesFile().printGffFormat(ap.av.getAlignment()
+                .getDataset().getSequencesArray(), displayedFeatureColours,
+                true, ap.av.isShowNPFeats());
+        text = formatter.printGffFormat(sequences, featureColours, true,
+                includeNonPositional);
       }
       else
       {
         text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
-                .getDataset().getSequencesArray(),
-                getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
+                .getDataset().getSequencesArray(), displayedFeatureColours,
+                true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
+        text = formatter.printJalviewFormat(sequences, featureColours,
+                true, includeNonPositional);
       }
     }
-    else if (!features)
+    else
     {
       if (CSVFormat.isSelected())
       {
@@ -193,57 +188,51 @@ public class AnnotationExporter extends JPanel
       }
       else
       {
-        text = new AnnotationFile().printAnnotations(annotations,
-                sequenceGroups, alignmentProperties);
+        if (wholeView)
+        {
+          text = new AnnotationFile().printAnnotationsForView(ap.av);
+        }
+        else
+        {
+          text = new AnnotationFile().printAnnotations(annotations, null,
+                  null);
+        }
       }
     }
+    return text;
+  }
 
+  public void toTextbox_actionPerformed(ActionEvent e)
+  {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
+
     try
     {
+      String text = getFileContents();
       cap.setText(text);
       Desktop.addInternalFrame(
               cap,
               (features ? MessageManager.formatMessage(
-                      "label.features_for_params", new String[]
-                      { ap.alignFrame.getTitle() }) : MessageManager
-                      .formatMessage("label.annotations_for_params",
-                              new String[]
-                              { ap.alignFrame.getTitle() })), 600, 500);
+                      "label.features_for_params",
+                      new String[] { ap.alignFrame.getTitle() })
+                      : MessageManager.formatMessage(
+                              "label.annotations_for_params",
+                              new String[] { ap.alignFrame.getTitle() })),
+              600, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning((features ? MessageManager.formatMessage(
-              "label.generating_features_for_params", new String[]
-              { ap.alignFrame.getTitle() }) : MessageManager.formatMessage(
-              "label.generating_annotations_for_params", new String[]
-              { ap.alignFrame.getTitle() })), oom);
+              "label.generating_features_for_params",
+              new String[] { ap.alignFrame.getTitle() })
+              : MessageManager.formatMessage(
+                      "label.generating_annotations_for_params",
+                      new String[] { ap.alignFrame.getTitle() })), oom);
       cap.dispose();
     }
 
     close_actionPerformed(null);
   }
 
-  private Hashtable getDisplayedFeatureCols()
-  {
-    Hashtable fcols = new Hashtable();
-    if (ap.av.getFeaturesDisplayed() == null)
-    {
-      return fcols;
-    }
-
-    Enumeration en = ap.av.getFeaturesDisplayed().keys();
-    FeatureRenderer fr = ap.getSeqPanel().seqCanvas.getFeatureRenderer(); // consider
-                                                                     // higher
-                                                                     // level
-                                                                     // method ?
-    while (en.hasMoreElements())
-    {
-      Object col = en.nextElement();
-      fcols.put(col, fr.featureColours.get(col));
-    }
-    return fcols;
-  }
-
   public void close_actionPerformed(ActionEvent e)
   {
     try
@@ -261,6 +250,7 @@ public class AnnotationExporter extends JPanel
     toFile.setText(MessageManager.getString("label.to_file"));
     toFile.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         toFile_actionPerformed(e);
@@ -269,6 +259,7 @@ public class AnnotationExporter extends JPanel
     toTextbox.setText(MessageManager.getString("label.to_textbox"));
     toTextbox.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         toTextbox_actionPerformed(e);
@@ -277,6 +268,7 @@ public class AnnotationExporter extends JPanel
     close.setText(MessageManager.getString("action.close"));
     close.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         close_actionPerformed(e);
@@ -330,5 +322,4 @@ public class AnnotationExporter extends JPanel
   JPanel jPanel3 = new JPanel();
 
   FlowLayout flowLayout1 = new FlowLayout();
-
 }