X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=3f14544ed3d9e7f405c5108a85c65a6cb560f3df;hb=4cea7a0328724b90a6a7c16ae8c926e0cc12cedd;hp=be0ef742a5b5fd8a59b9b812209834b6e6f7a19b;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
old mode 100755
new mode 100644
index be0ef74..3f14544
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,273 +1,305 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-
-/**
- *
- * 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;
-
- AlignmentAnnotation[] annotations;
-
- Vector sequenceGroups;
-
- Hashtable alignmentProperties;
-
- public AnnotationExporter()
- {
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- frame = new JInternalFrame();
- frame.setContentPane(this);
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "", 260, 125);
- }
-
- public void exportFeatures(AlignmentPanel ap)
- {
- this.ap = ap;
- features = true;
- CSVFormat.setVisible(false);
- frame.setTitle("Export Features");
- }
-
- public void exportAnnotations(AlignmentPanel ap,
- AlignmentAnnotation[] annotations, Vector sequenceGroups,
- Hashtable alProperties)
- {
- this.ap = ap;
- features = false;
- GFFFormat.setVisible(false);
- CSVFormat.setVisible(true);
- this.annotations = annotations;
- this.sequenceGroups = sequenceGroups;
- this.alignmentProperties = alProperties;
- frame.setTitle("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 ? "Save Features to File"
- : "Save Annotation to File");
- chooser.setToolTipText("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.alignment
- .getDataset().getSequencesArray(),
- ap.av.featuresDisplayed);
- }
- else
- {
- text = new FeaturesFile().printJalviewFormat(ap.av.alignment
- .getDataset().getSequencesArray(),
- ap.av.featuresDisplayed);
- }
- }
- else
- {
- if (CSVFormat.isSelected())
- {
- text = new AnnotationFile().printCSVAnnotations(annotations);
- }
- else
- {
- text = new AnnotationFile().printAnnotations(annotations,
- sequenceGroups, alignmentProperties);
- }
- }
-
- 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);
- }
-
- public void toTextbox_actionPerformed(ActionEvent e)
- {
- String text = "No features found on alignment";
- if (features)
- {
- if (GFFFormat.isSelected())
- {
- text = new FeaturesFile().printGFFFormat(ap.av.alignment
- .getDataset().getSequencesArray(), ap.av.featuresDisplayed);
- }
- else
- {
- text = new FeaturesFile().printJalviewFormat(ap.av.alignment
- .getDataset().getSequencesArray(), ap.av.featuresDisplayed);
- }
- }
- else if (!features)
- {
- if (CSVFormat.isSelected())
- {
- text = new AnnotationFile().printCSVAnnotations(annotations);
- }
- else
- {
- text = new AnnotationFile().printAnnotations(annotations,
- sequenceGroups, alignmentProperties);
- }
- }
-
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setText(text);
- Desktop.addInternalFrame(cap, (features ? "Features for - "
- : "Annotations for - ")
- + ap.alignFrame.getTitle(), 600, 500);
-
- 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(flowLayout1);
- toFile.setText("to File");
- toFile.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- toFile_actionPerformed(e);
- }
- });
- toTextbox.setText("to Textbox");
- toTextbox.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- toTextbox_actionPerformed(e);
- }
- });
- close.setText("Close");
- close.addActionListener(new ActionListener()
- {
- 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("CSV(Spreadsheet)");
- jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
- jLabel1.setText("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, null);
- this.add(jPanel1, null);
- }
-
- 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();
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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 .
+ */
+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 jalview.util.MessageManager;
+
+/**
+ *
+ * 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;
+
+ AlignmentAnnotation[] annotations;
+
+ List sequenceGroups;
+
+ Hashtable alignmentProperties;
+
+ 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("Export Features");
+ }
+
+ public void exportAnnotations(AlignmentPanel ap,
+ AlignmentAnnotation[] annotations, List list,
+ Hashtable alProperties)
+ {
+ this.ap = ap;
+ features = false;
+ GFFFormat.setVisible(false);
+ CSVFormat.setVisible(true);
+ this.annotations = annotations;
+ this.sequenceGroups = list;
+ this.alignmentProperties = alProperties;
+ frame.setTitle("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 ? "Save Features to File"
+ : "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);
+ }
+ }
+
+ 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);
+ }
+
+ public void toTextbox_actionPerformed(ActionEvent e)
+ {
+ 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());
+ }
+ else
+ {
+ text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
+ .getDataset().getSequencesArray(),
+ getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
+ }
+ }
+ else if (!features)
+ {
+ if (CSVFormat.isSelected())
+ {
+ text = new AnnotationFile().printCSVAnnotations(annotations);
+ }
+ else
+ {
+ text = new AnnotationFile().printAnnotations(annotations,
+ sequenceGroups, alignmentProperties);
+ }
+ }
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ try
+ {
+ 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);
+ }
+
+ private Hashtable getDisplayedFeatureCols()
+ {
+ Hashtable fcols = new Hashtable();
+ if (ap.av.featuresDisplayed == null)
+ {
+ return fcols;
+ }
+ Enumeration en = ap.av.featuresDisplayed.keys();
+ FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider
+ // higher
+ // level
+ // method ?
+ while (en.hasMoreElements())
+ {
+ Object col = en.nextElement();
+ fcols.put(col, fr.featureColours.get(col));
+ }
+ return fcols;
+ }
+
+ 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()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ toFile_actionPerformed(e);
+ }
+ });
+ toTextbox.setText(MessageManager.getString("label.to_textbox"));
+ toTextbox.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ toTextbox_actionPerformed(e);
+ }
+ });
+ close.setText(MessageManager.getString("action.close"));
+ close.addActionListener(new ActionListener()
+ {
+ 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();
+
+}