*/
package jalview.gui;
-import jalview.api.FeatureColourI;
+import java.util.Locale;
+
+import jalview.api.FeatureRenderer;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
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.util.Map;
+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;
*/
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()
+ /*
+ * 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;
try
{
jbInit();
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);
}
- 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);
+ if (ap.av.isShowComplementFeatures())
+ {
+ linkedFeaturesPanel.setVisible(true);
+ frame.pack();
+ }
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()
{
+ // 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 ? MessageManager
- .getString("label.save_features_to_file") : MessageManager
- .getString("label.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 = 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)
}
}
- 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())
{
- 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(), displayedFeatureColours,
- true, ap.av.isShowNPFeats());
- text = formatter.printGffFormat(sequences, featureColours, true,
- includeNonPositional);
- }
- else
- {
- text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
- .getDataset().getSequencesArray(), displayedFeatureColours,
- true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
- text = formatter.printJalviewFormat(sequences, featureColours,
- true, 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();
+ boolean includeNonPositional = ap.av.isShowNPFeats();
+
+ FeaturesFile formatter = new FeaturesFile();
+ final FeatureRenderer fr = ap.getFeatureRenderer();
+ boolean includeComplement = includeLinkedFeatures.isSelected();
+
+ if (GFFFormat.isSelected())
+ {
+ text = formatter.printGffFormat(sequences, fr, includeNonPositional,
+ includeComplement);
+ }
+ else
+ {
+ text = formatter.printJalviewFormat(sequences, fr,
+ includeNonPositional, includeComplement);
+ }
+ 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.formatMessage(
- "label.features_for_params",
- new String[] { ap.alignFrame.getTitle() })
- : MessageManager.formatMessage(
- "label.annotations_for_params",
- new String[] { ap.alignFrame.getTitle() })),
+ 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)
{
- new OOMWarning((features ? MessageManager.formatMessage(
- "label.generating_features_for_params",
- new String[] { ap.alignFrame.getTitle() })
+ 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);
+ new String[]
+ { ap.alignFrame.getTitle() })),
+ oom);
cap.dispose();
}
- close_actionPerformed(null);
+ close_actionPerformed();
}
- public void close_actionPerformed(ActionEvent e)
+ private void close_actionPerformed()
{
try
{
}
}
+ /**
+ * 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;
+ }
- toFile.setText(MessageManager.getString("label.to_file"));
+ /**
+ * Builds the panel with to File or Textbox or Close actions
+ *
+ * @return
+ */
+ JPanel buildActionsPanel()
+ {
+ JPanel actionsPanel = new JPanel();
+ actionsPanel.setOpaque(false);
+
+ 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();
- 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