src/jalview/gui/AnnotationExporter.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 \r
  20 package jalview.gui;\r
  21 \r
  22 import javax.swing.*;\r
  23 import java.awt.event.ActionListener;\r
  24 import java.awt.event.ActionEvent;\r
  25 \r
  26 import jalview.io.*;\r
  27 import jalview.datamodel.AlignmentAnnotation;\r
  28 \r
  29 import java.awt.Color;\r
  30 import java.awt.FlowLayout;\r
  31 import java.util.Vector;\r
  32 import javax.swing.BorderFactory;\r
  33 \r
  34 \r
  35 public class AnnotationExporter\r
  36     extends JPanel\r
  37 {\r
  38   JInternalFrame frame;\r
  39   AlignmentPanel ap;\r
  40   boolean features = true;\r
  41   AlignmentAnnotation [] annotations;\r
  42   Vector sequenceGroups;\r
  43 \r
  44   public AnnotationExporter()\r
  45   {\r
  46     try\r
  47     {\r
  48       jbInit();\r
  49     }\r
  50     catch (Exception ex)\r
  51     {\r
  52       ex.printStackTrace();\r
  53     }\r
  54 \r
  55     frame = new JInternalFrame();\r
  56     frame.setContentPane(this);\r
  57     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
  58     Desktop.addInternalFrame(frame,\r
  59                              "",\r
  60                              260, 125);\r
  61   }\r
  62 \r
  63   public void exportFeatures(AlignmentPanel ap)\r
  64   {\r
  65     this.ap = ap;\r
  66     features = true;\r
  67     frame.setTitle("Export Features");\r
  68   }\r
  69 \r
  70   public void exportAnnotations(AlignmentPanel ap,\r
  71                                 AlignmentAnnotation [] annotations,\r
  72                                 Vector sequenceGroups)\r
  73   {\r
  74     this.ap = ap;\r
  75     features = false;\r
  76     GFFFormat.setVisible(false);\r
  77     this.annotations = annotations;\r
  78     this.sequenceGroups = sequenceGroups;\r
  79     frame.setTitle("Export Annotations");\r
  80   }\r
  81 \r
  82   public void toFile_actionPerformed(ActionEvent e)\r
  83   {\r
  84       JalviewFileChooser chooser = new JalviewFileChooser(\r
  85       jalview.bin.Cache.getProperty( "LAST_DIRECTORY"));\r
  86 \r
  87       chooser.setFileView(new JalviewFileView());\r
  88       chooser.setDialogTitle(\r
  89           features ? "Save Features to File" : "Save Annotation to File");\r
  90       chooser.setToolTipText("Save");\r
  91 \r
  92       int value = chooser.showSaveDialog(this);\r
  93 \r
  94       if (value == JalviewFileChooser.APPROVE_OPTION)\r
  95       {\r
  96         String text = "No features found on alignment";\r
  97         if (features)\r
  98         {\r
  99           if (GFFFormat.isSelected())\r
 100             text = new FeaturesFile().printGFFFormat(\r
 101                 ap.av.alignment.getDataset().getSequencesArray(),\r
 102                 ap.av.featuresDisplayed);\r
 103           else\r
 104             text = new FeaturesFile().printJalviewFormat(\r
 105                 ap.av.alignment.getDataset().getSequencesArray(),\r
 106                 ap.av.featuresDisplayed);\r
 107         }\r
 108         else\r
 109         {\r
 110            text = new AnnotationFile().printAnnotations(\r
 111               annotations,\r
 112               sequenceGroups );\r
 113         }\r
 114 \r
 115         try\r
 116         {\r
 117           java.io.PrintWriter out = new java.io.PrintWriter(\r
 118               new java.io.FileWriter(chooser.getSelectedFile()));\r
 119 \r
 120           out.print(text);\r
 121           out.close();\r
 122         }\r
 123         catch (Exception ex)\r
 124         {\r
 125           ex.printStackTrace();\r
 126         }\r
 127       }\r
 128   }\r
 129 \r
 130   public void toTextbox_actionPerformed(ActionEvent e)\r
 131   {\r
 132     String text = "No features found on alignment";\r
 133     if(features)\r
 134     {\r
 135       if (GFFFormat.isSelected())\r
 136         text = new FeaturesFile().printGFFFormat(\r
 137             ap.av.alignment.getDataset().getSequencesArray(),\r
 138             ap.av.featuresDisplayed);\r
 139       else\r
 140         text = new FeaturesFile().printJalviewFormat(\r
 141             ap.av.alignment.getDataset().getSequencesArray(),\r
 142                 ap.av.featuresDisplayed);\r
 143     }\r
 144     else if(!features)\r
 145     {\r
 146       text = new AnnotationFile().printAnnotations(\r
 147           annotations,\r
 148           sequenceGroups );\r
 149     }\r
 150 \r
 151 \r
 152     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 153     cap.setText(text);\r
 154     Desktop.addInternalFrame(cap,\r
 155                              (features ?  "Features for - " : "Annotations for - ")\r
 156                              + ap.alignFrame.getTitle(),\r
 157                              600,\r
 158                              500);\r
 159 \r
 160 \r
 161   }\r
 162 \r
 163   public void close_actionPerformed(ActionEvent e)\r
 164   {\r
 165     try{\r
 166       frame.setClosed(true);\r
 167     }catch(java.beans.PropertyVetoException ex)\r
 168     {}\r
 169   }\r
 170 \r
 171 \r
 172 \r
 173   private void jbInit()\r
 174       throws Exception\r
 175   {\r
 176     this.setLayout(flowLayout1);\r
 177     toFile.setText("to File");\r
 178     toFile.addActionListener(new ActionListener()\r
 179     {\r
 180       public void actionPerformed(ActionEvent e)\r
 181       {\r
 182         toFile_actionPerformed(e);\r
 183       }\r
 184     });\r
 185     toTextbox.setText("to Textbox");\r
 186     toTextbox.addActionListener(new ActionListener()\r
 187     {\r
 188       public void actionPerformed(ActionEvent e)\r
 189       {\r
 190         toTextbox_actionPerformed(e);\r
 191       }\r
 192     });\r
 193     close.setText("Close");\r
 194     close.addActionListener(new ActionListener()\r
 195     {\r
 196       public void actionPerformed(ActionEvent e)\r
 197       {\r
 198         close_actionPerformed(e);\r
 199       }\r
 200     });\r
 201     jalviewFormat.setOpaque(false);\r
 202     jalviewFormat.setSelected(true);\r
 203     jalviewFormat.setText("Jalview");\r
 204     GFFFormat.setOpaque(false);\r
 205     GFFFormat.setText("GFF");\r
 206     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);\r
 207     jLabel1.setText("Format: ");\r
 208     this.setBackground(Color.white);\r
 209     jPanel3.setBorder(BorderFactory.createEtchedBorder());\r
 210     jPanel3.setOpaque(false);\r
 211     jPanel1.setOpaque(false);\r
 212     jPanel1.add(toFile);\r
 213     jPanel1.add(toTextbox);\r
 214     jPanel1.add(close);\r
 215     jPanel3.add(jLabel1);\r
 216     jPanel3.add(jalviewFormat);\r
 217     jPanel3.add(GFFFormat);\r
 218     buttonGroup.add(jalviewFormat);\r
 219     buttonGroup.add(GFFFormat);\r
 220     this.add(jPanel3, null);\r
 221     this.add(jPanel1, null);\r
 222   }\r
 223 \r
 224   JPanel jPanel1 = new JPanel();\r
 225   JButton toFile = new JButton();\r
 226   JButton toTextbox = new JButton();\r
 227   JButton close = new JButton();\r
 228   ButtonGroup buttonGroup = new ButtonGroup();\r
 229   JRadioButton jalviewFormat = new JRadioButton();\r
 230   JRadioButton GFFFormat = new JRadioButton();\r
 231   JLabel jLabel1 = new JLabel();\r
 232   JPanel jPanel3 = new JPanel();\r
 233   FlowLayout flowLayout1 = new FlowLayout();\r
 234 \r
 235 }\r