X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=894db79cd4e2ea8f88f21ec6c91bad7f2a504f80;hb=0de37d1a047209510bab82225109ae2a47931f79;hp=56c6e2de45b97e9c5443d6df60fa66acb88f9902;hpb=cb5d856b1304448cae13a333cbd9017f81520d90;p=jalview.git

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 56c6e2d..894db79 100644
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,32 +1,52 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
-import java.util.*;
-import java.util.List;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.util.Locale;
+
+import javax.swing.BoxLayout;
+import javax.swing.ButtonGroup;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.SwingConstants;
+
+import jalview.api.FeatureRenderer;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
+import jalview.io.FeaturesFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
 import jalview.util.MessageManager;
 
 /**
@@ -39,20 +59,45 @@ import jalview.util.MessageManager;
  */
 public class AnnotationExporter extends JPanel
 {
-  JInternalFrame frame;
+  private JInternalFrame frame;
+
+  private AlignmentPanel ap;
+
+  /*
+   * true if exporting features, false if exporting annotations
+   */
+  private boolean exportFeatures = true;
+
+  private AlignmentAnnotation[] annotations;
 
-  AlignmentPanel ap;
+  private boolean wholeView;
 
-  boolean features = true;
+  /*
+   * option to export linked (CDS/peptide) features when shown 
+   * on the alignment, converted to this alignment's coordinates
+   */
+  private JCheckBox includeLinkedFeatures;
 
-  AlignmentAnnotation[] annotations;
+  /*
+   * output format option shown for feature export
+   */
+  JRadioButton GFFFormat = new JRadioButton();
 
-  List<SequenceGroup> sequenceGroups;
+  /*
+   * output format option shown for annotation export
+   */
+  JRadioButton CSVFormat = new JRadioButton();
 
-  Hashtable alignmentProperties;
+  private JPanel linkedFeaturesPanel;
 
-  public AnnotationExporter()
+  /**
+   * Constructor
+   * 
+   * @param panel
+   */
+  public AnnotationExporter(AlignmentPanel panel)
   {
+    this.ap = panel;
     try
     {
       jbInit();
@@ -62,82 +107,84 @@ public class AnnotationExporter extends JPanel
     }
 
     frame = new JInternalFrame();
+    frame.setFrameIcon(null);
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width,
-            frame.getPreferredSize().height);
+    Dimension preferredSize = frame.getPreferredSize();
+    Desktop.addInternalFrame(frame, "", true, preferredSize.width,
+            preferredSize.height, true, true);
   }
 
-  public void exportFeatures(AlignmentPanel ap)
+  /**
+   * Configures the dialog for options to export visible features. If from a
+   * split frame panel showing linked features, make the option to include these
+   * in the export visible.
+   */
+  public void exportFeatures()
   {
-    this.ap = ap;
-    features = true;
+    exportFeatures = true;
     CSVFormat.setVisible(false);
-    frame.setTitle("Export Features");
+    if (ap.av.isShowComplementFeatures())
+    {
+      linkedFeaturesPanel.setVisible(true);
+      frame.pack();
+    }
+    frame.setTitle(MessageManager.getString("label.export_features"));
+  }
+
+  /**
+   * Configures the dialog for options to export all visible annotations
+   */
+  public void exportAnnotations()
+  {
+    boolean showAnnotation = ap.av.isShowAnnotation();
+    exportAnnotation(showAnnotation ? null
+            : ap.av.getAlignment().getAlignmentAnnotation(), true);
+  }
+
+  /**
+   * Configures the dialog for options to export the given annotation row
+   * 
+   * @param toExport
+   */
+  public void exportAnnotation(AlignmentAnnotation toExport)
+  {
+    exportAnnotation(new AlignmentAnnotation[] { toExport }, false);
   }
 
-  public void exportAnnotations(AlignmentPanel ap,
-          AlignmentAnnotation[] annotations, List<SequenceGroup> list,
-          Hashtable alProperties)
+  private void exportAnnotation(AlignmentAnnotation[] toExport,
+          boolean forWholeView)
   {
-    this.ap = ap;
-    features = false;
+    wholeView = forWholeView;
+    annotations = toExport;
+    exportFeatures = false;
     GFFFormat.setVisible(false);
     CSVFormat.setVisible(true);
-    this.annotations = annotations;
-    this.sequenceGroups = list;
-    this.alignmentProperties = alProperties;
-    frame.setTitle("Export Annotations");
+    frame.setTitle(MessageManager.getString("label.export_annotations"));
   }
 
-  public void toFile_actionPerformed(ActionEvent e)
+  private void toFile_actionPerformed()
   {
+    // TODO: JAL-3048 JalviewFileChooser - Save option
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(features ? "Save Features to File"
-            : "Save Annotation to File");
+    chooser.setDialogTitle(exportFeatures
+            ? 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 = "No features found 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 = 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)
@@ -146,77 +193,109 @@ public class AnnotationExporter extends JPanel
       }
     }
 
-    close_actionPerformed(null);
+    close_actionPerformed();
   }
 
-  public void toTextbox_actionPerformed(ActionEvent e)
+  /**
+   * Answers the text to output for either Features (in GFF or Jalview format)
+   * or Annotations (in CSV or Jalview format)
+   * 
+   * @return
+   */
+  private String getText()
   {
-    String text = "No features found on alignment";
-    if (features)
+    return exportFeatures ? getFeaturesText() : getAnnotationsText();
+  }
+
+  /**
+   * Returns the text contents for output of annotations in either CSV or
+   * Jalview format
+   * 
+   * @return
+   */
+  private String getAnnotationsText()
+  {
+    String text;
+    if (CSVFormat.isSelected())
     {
-      if (GFFFormat.isSelected())
-      {
-        text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
-                .getDataset().getSequencesArray(),
-                getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
-      }
-      else
-      {
-        text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
-                .getDataset().getSequencesArray(),
-                getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
-      }
+      text = new AnnotationFile().printCSVAnnotations(annotations);
     }
-    else if (!features)
+    else
     {
-      if (CSVFormat.isSelected())
+      if (wholeView)
       {
-        text = new AnnotationFile().printCSVAnnotations(annotations);
+        text = new AnnotationFile().printAnnotationsForView(ap.av);
       }
       else
       {
-        text = new AnnotationFile().printAnnotations(annotations,
-                sequenceGroups, alignmentProperties);
+        text = new AnnotationFile().printAnnotations(annotations, null,
+                null);
       }
     }
+    return text;
+  }
 
-    CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    try
+  /**
+   * 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();
+    boolean includeNonPositional = ap.av.isShowNPFeats();
+
+    FeaturesFile formatter = new FeaturesFile();
+    final FeatureRenderer fr = ap.getFeatureRenderer();
+    boolean includeComplement = includeLinkedFeatures.isSelected();
+
+    if (GFFFormat.isSelected())
     {
-      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);
-    } catch (OutOfMemoryError oom)
+      text = formatter.printGffFormat(sequences, fr, includeNonPositional,
+              includeComplement);
+    }
+    else
     {
-      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);
-      cap.dispose();
+      text = formatter.printJalviewFormat(sequences, fr,
+              includeNonPositional, includeComplement);
     }
-
-    close_actionPerformed(null);
+    return text;
   }
 
-  private Hashtable getDisplayedFeatureCols()
+  private void toTextbox_actionPerformed()
   {
-    Hashtable fcols = new Hashtable();
-    if (ap.av.featuresDisplayed == null)
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+
+    try
     {
-      return fcols;
-    }
-    Enumeration en = ap.av.featuresDisplayed.keys();
-    FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider
-                                                                     // higher
-                                                                     // level
-                                                                     // method ?
-    while (en.hasMoreElements())
+      String text = getText();
+      cap.setText(text);
+      Desktop.addInternalFrame(cap, (exportFeatures ? MessageManager
+              .formatMessage("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)
     {
-      Object col = en.nextElement();
-      fcols.put(col, fr.featureColours.get(col));
+      new OOMWarning((exportFeatures ? 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);
+      cap.dispose();
     }
-    return fcols;
+
+    close_actionPerformed();
   }
 
-  public void close_actionPerformed(ActionEvent e)
+  private void close_actionPerformed()
   {
     try
     {
@@ -226,81 +305,137 @@ public class AnnotationExporter extends JPanel
     }
   }
 
+  /**
+   * Adds widgets to the panel
+   * 
+   * @throws Exception
+   */
   private void jbInit() throws Exception
   {
-    this.setLayout(new BorderLayout());
+    this.setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
+    this.setBackground(Color.white);
+
+    JPanel formatPanel = buildFormatOptionsPanel();
+    JPanel linkedFeatures = buildLinkedFeaturesPanel();
+    JPanel actionsPanel = buildActionsPanel();
+
+    this.add(formatPanel);
+    this.add(linkedFeatures);
+    this.add(actionsPanel);
+  }
+
+  /**
+   * Builds a panel with a checkbox for the option to export linked
+   * (CDS/peptide) features. This is hidden by default, and only made visible if
+   * exporting features from a split frame panel which is configured to show
+   * linked features.
+   * 
+   * @return
+   */
+  private JPanel buildLinkedFeaturesPanel()
+  {
+    linkedFeaturesPanel = new JPanel();
+    linkedFeaturesPanel.setOpaque(false);
+
+    boolean nucleotide = ap.av.isNucleotide();
+    String complement = nucleotide ? MessageManager
+            .getString("label.protein").toLowerCase(Locale.ROOT) : "CDS";
+    JLabel label = new JLabel(MessageManager
+            .formatMessage("label.include_linked_features", complement));
+    label.setHorizontalAlignment(SwingConstants.TRAILING);
+    String tooltip = MessageManager
+            .formatMessage("label.include_linked_tooltip", complement);
+    label.setToolTipText(JvSwingUtils.wrapTooltip(true, tooltip));
+
+    includeLinkedFeatures = new JCheckBox();
+    linkedFeaturesPanel.add(label);
+    linkedFeaturesPanel.add(includeLinkedFeatures);
+    linkedFeaturesPanel.setVisible(false);
+
+    return linkedFeaturesPanel;
+  }
+
+  /**
+   * Builds the panel with to File or Textbox or Close actions
+   * 
+   * @return
+   */
+  JPanel buildActionsPanel()
+  {
+    JPanel actionsPanel = new JPanel();
+    actionsPanel.setOpaque(false);
 
-    toFile.setText(MessageManager.getString("label.to_file"));
+    JButton toFile = new JButton(MessageManager.getString("label.to_file"));
     toFile.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        toFile_actionPerformed(e);
+        toFile_actionPerformed();
       }
     });
-    toTextbox.setText(MessageManager.getString("label.to_textbox"));
+    JButton toTextbox = new JButton(
+            MessageManager.getString("label.to_textbox"));
     toTextbox.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        toTextbox_actionPerformed(e);
+        toTextbox_actionPerformed();
       }
     });
-    close.setText(MessageManager.getString("action.close"));
+    JButton close = new JButton(MessageManager.getString("action.close"));
     close.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        close_actionPerformed(e);
+        close_actionPerformed();
       }
     });
+
+    actionsPanel.add(toFile);
+    actionsPanel.add(toTextbox);
+    actionsPanel.add(close);
+
+    return actionsPanel;
+  }
+
+  /**
+   * Builds the panel with options to output in Jalview, GFF or CSV format. GFF
+   * is only made visible when exporting features, CSV only when exporting
+   * annotation.
+   * 
+   * @return
+   */
+  JPanel buildFormatOptionsPanel()
+  {
+    JPanel formatPanel = new JPanel();
+    // formatPanel.setBorder(BorderFactory.createEtchedBorder());
+    formatPanel.setOpaque(false);
+
+    JRadioButton jalviewFormat = new JRadioButton("Jalview");
     jalviewFormat.setOpaque(false);
     jalviewFormat.setSelected(true);
-    jalviewFormat.setText("Jalview");
     GFFFormat.setOpaque(false);
     GFFFormat.setText("GFF");
     CSVFormat.setOpaque(false);
     CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
-    jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
-    jLabel1.setText(MessageManager.getString("action.format") + " ");
-    this.setBackground(Color.white);
-    jPanel3.setBorder(BorderFactory.createEtchedBorder());
-    jPanel3.setOpaque(false);
-    jPanel1.setOpaque(false);
-    jPanel1.add(toFile);
-    jPanel1.add(toTextbox);
-    jPanel1.add(close);
-    jPanel3.add(jLabel1);
-    jPanel3.add(jalviewFormat);
-    jPanel3.add(GFFFormat);
-    jPanel3.add(CSVFormat);
+
+    ButtonGroup buttonGroup = new ButtonGroup();
     buttonGroup.add(jalviewFormat);
     buttonGroup.add(GFFFormat);
     buttonGroup.add(CSVFormat);
-    this.add(jPanel3, BorderLayout.CENTER);
-    this.add(jPanel1, BorderLayout.SOUTH);
-  }
-
-  JPanel jPanel1 = new JPanel();
-
-  JButton toFile = new JButton();
-
-  JButton toTextbox = new JButton();
 
-  JButton close = new JButton();
+    JLabel format = new JLabel(
+            MessageManager.getString("action.format") + " ");
+    format.setHorizontalAlignment(SwingConstants.TRAILING);
 
-  ButtonGroup buttonGroup = new ButtonGroup();
-
-  JRadioButton jalviewFormat = new JRadioButton();
-
-  JRadioButton GFFFormat = new JRadioButton();
-
-  JRadioButton CSVFormat = new JRadioButton();
-
-  JLabel jLabel1 = new JLabel();
-
-  JPanel jPanel3 = new JPanel();
-
-  FlowLayout flowLayout1 = new FlowLayout();
+    formatPanel.add(format);
+    formatPanel.add(jalviewFormat);
+    formatPanel.add(GFFFormat);
+    formatPanel.add(CSVFormat);
 
+    return formatPanel;
+  }
 }