-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.getAlignment()\r
- .getDataset().getSequencesArray(),\r
- getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);\r
- }\r
- else\r
- {\r
- text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()\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.getAlignment()\r
- .getDataset().getSequencesArray(),\r
- getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());\r
- }\r
- else\r
- {\r
- text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()\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 jalview.api.FeatureColourI;
+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.BorderLayout;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Map;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JButton;
+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
+{
+ JInternalFrame frame;
+
+ AlignmentPanel ap;
+
+ boolean features = true;
+
+ private AlignmentAnnotation[] annotations;
+
+ private boolean wholeView;
+
+ public AnnotationExporter()
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width,
+ frame.getPreferredSize().height);
+ }
+
+ public void exportFeatures(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ features = true;
+ CSVFormat.setVisible(false);
+ frame.setTitle(MessageManager.getString("label.export_features"));
+ }
+
+ 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);
+ frame.setTitle(MessageManager.getString("label.export_annotations"));
+ }
+
+ public void toFile_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ 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.setToolTipText(MessageManager.getString("action.save"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String text = getFileContents();
+
+ try
+ {
+ java.io.PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter(chooser.getSelectedFile()));
+
+ out.print(text);
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ close_actionPerformed(null);
+ }
+
+ private String getFileContents()
+ {
+ 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(), 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);
+ }
+ }
+ else
+ {
+ 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;
+ }
+
+ 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);
+ } 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);
+ cap.dispose();
+ }
+
+ close_actionPerformed(null);
+ }
+
+ public void close_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ frame.setClosed(true);
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
+ }
+
+ private void jbInit() throws Exception
+ {
+ this.setLayout(new BorderLayout());
+
+ toFile.setText(MessageManager.getString("label.to_file"));
+ toFile.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ toFile_actionPerformed(e);
+ }
+ });
+ toTextbox.setText(MessageManager.getString("label.to_textbox"));
+ toTextbox.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ toTextbox_actionPerformed(e);
+ }
+ });
+ close.setText(MessageManager.getString("action.close"));
+ close.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ close_actionPerformed(e);
+ }
+ });
+ 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.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();
+
+ JRadioButton jalviewFormat = new JRadioButton();
+
+ JRadioButton GFFFormat = new JRadioButton();
+
+ JRadioButton CSVFormat = new JRadioButton();
+
+ JLabel jLabel1 = new JLabel();
+
+ JPanel jPanel3 = new JPanel();
+
+ FlowLayout flowLayout1 = new FlowLayout();
+}
git://source.jalview.org / jalview.git / blobdiff