-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.gui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-\r
-/**\r
- * \r
- * GUI dialog for exporting features or alignment annotations depending upon\r
- * which method is called.\r
- * \r
- * @author AMW\r
- * \r
- */\r
-public class AnnotationExporter extends JPanel\r
-{\r
- JInternalFrame frame;\r
-\r
- AlignmentPanel ap;\r
-\r
- boolean features = true;\r
-\r
- AlignmentAnnotation[] annotations;\r
-\r
- Vector sequenceGroups;\r
-\r
- Hashtable alignmentProperties;\r
-\r
- public AnnotationExporter()\r
- {\r
- try\r
- {\r
- jbInit();\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width, frame.getPreferredSize().height);\r
- }\r
-\r
- public void exportFeatures(AlignmentPanel ap)\r
- {\r
- this.ap = ap;\r
- features = true;\r
- CSVFormat.setVisible(false);\r
- frame.setTitle("Export Features");\r
- }\r
-\r
- public void exportAnnotations(AlignmentPanel ap,\r
- AlignmentAnnotation[] annotations, Vector sequenceGroups,\r
- Hashtable alProperties)\r
- {\r
- this.ap = ap;\r
- features = false;\r
- GFFFormat.setVisible(false);\r
- CSVFormat.setVisible(true);\r
- this.annotations = annotations;\r
- this.sequenceGroups = sequenceGroups;\r
- this.alignmentProperties = alProperties;\r
- frame.setTitle("Export Annotations");\r
- }\r
-\r
- public void toFile_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(\r
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle(features ? "Save Features to File"\r
- : "Save Annotation to File");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String text = "No features found on alignment";\r
- if (features)\r
- {\r
- if (GFFFormat.isSelected())\r
- {\r
- text = new FeaturesFile().printGFFFormat(ap.av.alignment\r
- .getDataset().getSequencesArray(),\r
- getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);\r
- }\r
- else\r
- {\r
- text = new FeaturesFile().printJalviewFormat(ap.av.alignment\r
- .getDataset().getSequencesArray(),\r
- getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);\r
- }\r
- }\r
- else\r
- {\r
- if (CSVFormat.isSelected())\r
- {\r
- text = new AnnotationFile().printCSVAnnotations(annotations);\r
- }\r
- else\r
- {\r
- text = new AnnotationFile().printAnnotations(annotations,\r
- sequenceGroups, alignmentProperties);\r
- }\r
- }\r
-\r
- try\r
- {\r
- java.io.PrintWriter out = new java.io.PrintWriter(\r
- new java.io.FileWriter(chooser.getSelectedFile()));\r
-\r
- out.print(text);\r
- out.close();\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- close_actionPerformed(null);\r
- }\r
-\r
- public void toTextbox_actionPerformed(ActionEvent e)\r
- {\r
- String text = "No features found on alignment";\r
- if (features)\r
- {\r
- if (GFFFormat.isSelected())\r
- {\r
- text = new FeaturesFile().printGFFFormat(ap.av.alignment\r
- .getDataset().getSequencesArray(),\r
- getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());\r
- }\r
- else\r
- {\r
- text = new FeaturesFile().printJalviewFormat(ap.av.alignment\r
- .getDataset().getSequencesArray(),\r
- getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());\r
- }\r
- }\r
- else if (!features)\r
- {\r
- if (CSVFormat.isSelected())\r
- {\r
- text = new AnnotationFile().printCSVAnnotations(annotations);\r
- }\r
- else\r
- {\r
- text = new AnnotationFile().printAnnotations(annotations,\r
- sequenceGroups, alignmentProperties);\r
- }\r
- }\r
-\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- try\r
- {\r
- cap.setText(text);\r
- Desktop.addInternalFrame(cap, (features ? "Features for - "\r
- : "Annotations for - ") + ap.alignFrame.getTitle(), 600, 500);\r
- } catch (OutOfMemoryError oom)\r
- {\r
- new OOMWarning("generating "\r
- + (features ? "Features for - " : "Annotations for - ")\r
- + ap.alignFrame.getTitle(), oom);\r
- cap.dispose();\r
- }\r
-\r
- close_actionPerformed(null);\r
- }\r
-\r
- private Hashtable getDisplayedFeatureCols()\r
- {\r
- Hashtable fcols = new Hashtable();\r
- if (ap.av.featuresDisplayed == null)\r
- {\r
- return fcols;\r
- }\r
- Enumeration en = ap.av.featuresDisplayed.keys();\r
- FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider\r
- // higher\r
- // level\r
- // method ?\r
- while (en.hasMoreElements())\r
- {\r
- Object col = en.nextElement();\r
- fcols.put(col, fr.featureColours.get(col));\r
- }\r
- return fcols;\r
- }\r
-\r
- public void close_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- frame.setClosed(true);\r
- } catch (java.beans.PropertyVetoException ex)\r
- {\r
- }\r
- }\r
-\r
- private void jbInit() throws Exception\r
- {\r
- this.setLayout(new BorderLayout());\r
- \r
- toFile.setText("to File");\r
- toFile.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- toFile_actionPerformed(e);\r
- }\r
- });\r
- toTextbox.setText("to Textbox");\r
- toTextbox.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- toTextbox_actionPerformed(e);\r
- }\r
- });\r
- close.setText("Close");\r
- close.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- close_actionPerformed(e);\r
- }\r
- });\r
- jalviewFormat.setOpaque(false);\r
- jalviewFormat.setSelected(true);\r
- jalviewFormat.setText("Jalview");\r
- GFFFormat.setOpaque(false);\r
- GFFFormat.setText("GFF");\r
- CSVFormat.setOpaque(false);\r
- CSVFormat.setText("CSV(Spreadsheet)");\r
- jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);\r
- jLabel1.setText("Format: ");\r
- this.setBackground(Color.white);\r
- jPanel3.setBorder(BorderFactory.createEtchedBorder());\r
- jPanel3.setOpaque(false);\r
- jPanel1.setOpaque(false);\r
- jPanel1.add(toFile);\r
- jPanel1.add(toTextbox);\r
- jPanel1.add(close);\r
- jPanel3.add(jLabel1);\r
- jPanel3.add(jalviewFormat);\r
- jPanel3.add(GFFFormat);\r
- jPanel3.add(CSVFormat);\r
- buttonGroup.add(jalviewFormat);\r
- buttonGroup.add(GFFFormat);\r
- buttonGroup.add(CSVFormat);\r
- this.add(jPanel3, BorderLayout.CENTER);\r
- this.add(jPanel1, BorderLayout.SOUTH);\r
- }\r
-\r
- JPanel jPanel1 = new JPanel();\r
-\r
- JButton toFile = new JButton();\r
-\r
- JButton toTextbox = new JButton();\r
-\r
- JButton close = new JButton();\r
-\r
- ButtonGroup buttonGroup = new ButtonGroup();\r
-\r
- JRadioButton jalviewFormat = new JRadioButton();\r
-\r
- JRadioButton GFFFormat = new JRadioButton();\r
-\r
- JRadioButton CSVFormat = new JRadioButton();\r
-\r
- JLabel jLabel1 = new JLabel();\r
-\r
- JPanel jPanel3 = new JPanel();\r
-\r
- FlowLayout flowLayout1 = new FlowLayout();\r
-\r
-}\r
+/*
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+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.FeaturesFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.util.MessageManager;
+
+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 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;
+
+/**
+ *
+ * GUI dialog for exporting features or alignment annotations depending upon
+ * which method is called.
+ *
+ * @author AMW
+ *
+ */
+public class AnnotationExporter extends JPanel
+{
+ private JInternalFrame frame;
+
+ private AlignmentPanel ap;
+
+ /*
+ * true if exporting features, false if exporting annotations
+ */
+ private boolean exportFeatures = true;
+
+ private AlignmentAnnotation[] annotations;
+
+ 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;
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ Dimension preferredSize = frame.getPreferredSize();
+ Desktop.addInternalFrame(frame, "", true, preferredSize.width,
+ preferredSize.height, true, true);
+ }
+
+ /**
+ * 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"));
+ }
+
+ /**
+ * 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);
+ }
+
+ private void exportAnnotation(AlignmentAnnotation[] toExport,
+ boolean forWholeView)
+ {
+ wholeView = forWholeView;
+ annotations = toExport;
+ exportFeatures = false;
+ GFFFormat.setVisible(false);
+ CSVFormat.setVisible(true);
+ frame.setTitle(MessageManager.getString("label.export_annotations"));
+ }
+
+ private void toFile_actionPerformed()
+ {
+ // TODO: JAL-3048 JalviewFileChooser - Save option
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ Cache.getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ 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 = getText();
+
+ try
+ {
+ PrintWriter out = new PrintWriter(
+ new FileWriter(chooser.getSelectedFile()));
+ out.print(text);
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ 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();
+ }
+
+ /**
+ * Returns the text contents for output of annotations in either CSV or
+ * Jalview format
+ *
+ * @return
+ */
+ private String getAnnotationsText()
+ {
+ String text;
+ if (CSVFormat.isSelected())
+ {
+ text = new AnnotationFile().printCSVAnnotations(annotations);
+ }
+ else
+ {
+ if (wholeView)
+ {
+ text = new AnnotationFile().printAnnotationsForView(ap.av);
+ }
+ else
+ {
+ text = new AnnotationFile().printAnnotations(annotations, null,
+ null);
+ }
+ }
+ return text;
+ }
+
+ /**
+ * 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 = 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)
+ {
+ 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();
+ }
+
+ close_actionPerformed();
+ }
+
+ private void close_actionPerformed()
+ {
+ try
+ {
+ frame.setClosed(true);
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
+ }
+
+ /**
+ * Adds widgets to the panel
+ *
+ * @throws Exception
+ */
+ private void jbInit() throws Exception
+ {
+ 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);
+
+ JButton toFile = new JButton(MessageManager.getString("label.to_file"));
+ toFile.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ toFile_actionPerformed();
+ }
+ });
+ JButton toTextbox = new JButton(
+ MessageManager.getString("label.to_textbox"));
+ toTextbox.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ toTextbox_actionPerformed();
+ }
+ });
+ JButton close = new JButton(MessageManager.getString("action.close"));
+ close.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent 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);
+ GFFFormat.setOpaque(false);
+ GFFFormat.setText("GFF");
+ CSVFormat.setOpaque(false);
+ CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
+
+ ButtonGroup buttonGroup = new ButtonGroup();
+ buttonGroup.add(jalviewFormat);
+ buttonGroup.add(GFFFormat);
+ buttonGroup.add(CSVFormat);
+
+ JLabel format = new JLabel(
+ MessageManager.getString("action.format") + " ");
+ format.setHorizontalAlignment(SwingConstants.TRAILING);
+
+ formatPanel.add(format);
+ formatPanel.add(jalviewFormat);
+ formatPanel.add(GFFFormat);
+ formatPanel.add(CSVFormat);
+
+ return formatPanel;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff