import jalview.io.JalviewFileView;
import jalview.util.MessageManager;
-import java.awt.BorderLayout;
import java.awt.Color;
-import java.awt.FlowLayout;
+import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.FileWriter;
import java.io.PrintWriter;
-import javax.swing.BorderFactory;
+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;
private boolean wholeView;
+ /*
+ * option to export linked (CDS/peptide) features when shown
+ * on the alignment, converted to this alignment's coordinates
+ */
+ private JCheckBox includeLinkedFeatures;
+
+ /*
+ * output format option shown for feature export
+ */
+ JRadioButton GFFFormat = new JRadioButton();
+
+ /*
+ * output format option shown for annotation export
+ */
+ JRadioButton CSVFormat = new JRadioButton();
+
+ private JPanel linkedFeaturesPanel;
+
+ /**
+ * Constructor
+ *
+ * @param panel
+ */
public AnnotationExporter(AlignmentPanel panel)
{
this.ap = panel;
frame = new JInternalFrame();
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);
}
/**
- * Configures the diglog for options to export visible features
+ * 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()
{
exportFeatures = true;
CSVFormat.setVisible(false);
+ if (ap.av.isShowComplementFeatures())
+ {
+ linkedFeaturesPanel.setVisible(true);
+ frame.pack();
+ }
frame.setTitle(MessageManager.getString("label.export_features"));
}
FeaturesFile formatter = new FeaturesFile();
final FeatureRenderer fr = ap.getFeatureRenderer();
+ boolean includeComplement = includeLinkedFeatures.isSelected();
+
if (GFFFormat.isSelected())
{
- text = formatter.printGffFormat(sequences, fr, includeNonPositional);
+ text = formatter.printGffFormat(sequences, fr, includeNonPositional,
+ includeComplement);
}
else
{
text = formatter.printJalviewFormat(sequences, fr,
- includeNonPositional);
+ includeNonPositional, includeComplement);
}
return text;
}
}
}
+ /**
+ * 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()
+ : "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
toFile_actionPerformed();
}
});
- toTextbox.setText(MessageManager.getString("label.to_textbox"));
+ JButton toTextbox = new JButton(
+ MessageManager.getString("label.to_textbox"));
toTextbox.addActionListener(new ActionListener()
{
@Override
toTextbox_actionPerformed();
}
});
- close.setText(MessageManager.getString("action.close"));
+ JButton close = new JButton(MessageManager.getString("action.close"));
close.addActionListener(new ActionListener()
{
@Override
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();
- ButtonGroup buttonGroup = new ButtonGroup();
+ JLabel format = new JLabel(
+ MessageManager.getString("action.format") + " ");
+ format.setHorizontalAlignment(SwingConstants.TRAILING);
- JRadioButton jalviewFormat = new JRadioButton();
+ formatPanel.add(format);
+ formatPanel.add(jalviewFormat);
+ formatPanel.add(GFFFormat);
+ formatPanel.add(CSVFormat);
- JRadioButton GFFFormat = new JRadioButton();
-
- JRadioButton CSVFormat = new JRadioButton();
-
- JLabel jLabel1 = new JLabel();
-
- JPanel jPanel3 = new JPanel();
-
- FlowLayout flowLayout1 = new FlowLayout();
+ return formatPanel;
+ }
}
git://source.jalview.org / jalview.git / blobdiff