src/jalview/gui/AnnotationExporter.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2007 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 java.util.*;\r
  23 \r
  24 import java.awt.*;\r
  25 import java.awt.event.*;\r
  26 import javax.swing.*;\r
  27 \r
  28 import jalview.datamodel.*;\r
  29 import jalview.io.*;\r
  30 \r
  31 public class AnnotationExporter\r
  32     extends JPanel\r
  33 {\r
  34   JInternalFrame frame;\r
  35   AlignmentPanel ap;\r
  36   boolean features = true;\r
  37   AlignmentAnnotation[] annotations;\r
  38   Vector sequenceGroups;\r
  39   Hashtable alignmentProperties;\r
  40 \r
  41   public AnnotationExporter()\r
  42   {\r
  43     try\r
  44     {\r
  45       jbInit();\r
  46     }\r
  47     catch (Exception ex)\r
  48     {\r
  49       ex.printStackTrace();\r
  50     }\r
  51 \r
  52     frame = new JInternalFrame();\r
  53     frame.setContentPane(this);\r
  54     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
  55     Desktop.addInternalFrame(frame,\r
  56                              "",\r
  57                              260, 125);\r
  58   }\r
  59 \r
  60   public void exportFeatures(AlignmentPanel ap)\r
  61   {\r
  62     this.ap = ap;\r
  63     features = true;\r
  64     frame.setTitle("Export Features");\r
  65   }\r
  66 \r
  67   public void exportAnnotations(AlignmentPanel ap,\r
  68                                 AlignmentAnnotation[] annotations,\r
  69                                 Vector sequenceGroups,\r
  70                                 Hashtable alProperties)\r
  71   {\r
  72     this.ap = ap;\r
  73     features = false;\r
  74     GFFFormat.setVisible(false);\r
  75     this.annotations = annotations;\r
  76     this.sequenceGroups = sequenceGroups;\r
  77     this.alignmentProperties = alProperties;\r
  78     frame.setTitle("Export Annotations");\r
  79   }\r
  80 \r
  81   public void toFile_actionPerformed(ActionEvent e)\r
  82   {\r
  83     JalviewFileChooser chooser = new JalviewFileChooser(\r
  84         jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
  85 \r
  86     chooser.setFileView(new JalviewFileView());\r
  87     chooser.setDialogTitle(\r
  88         features ? "Save Features to File" : "Save Annotation to File");\r
  89     chooser.setToolTipText("Save");\r
  90 \r
  91     int value = chooser.showSaveDialog(this);\r
  92 \r
  93     if (value == JalviewFileChooser.APPROVE_OPTION)\r
  94     {\r
  95       String text = "No features found on alignment";\r
  96       if (features)\r
  97       {\r
  98         if (GFFFormat.isSelected())\r
  99         {\r
 100           text = new FeaturesFile().printGFFFormat(\r
 101               ap.av.alignment.getDataset().getSequencesArray(),\r
 102               ap.av.featuresDisplayed);\r
 103         }\r
 104         else\r
 105         {\r
 106           text = new FeaturesFile().printJalviewFormat(\r
 107               ap.av.alignment.getDataset().getSequencesArray(),\r
 108               ap.av.featuresDisplayed);\r
 109         }\r
 110       }\r
 111       else\r
 112       {\r
 113         text = new AnnotationFile().printAnnotations(\r
 114             annotations,\r
 115             sequenceGroups,\r
 116             alignmentProperties);\r
 117       }\r
 118 \r
 119       try\r
 120       {\r
 121         java.io.PrintWriter out = new java.io.PrintWriter(\r
 122             new java.io.FileWriter(chooser.getSelectedFile()));\r
 123 \r
 124         out.print(text);\r
 125         out.close();\r
 126       }\r
 127       catch (Exception ex)\r
 128       {\r
 129         ex.printStackTrace();\r
 130       }\r
 131     }\r
 132   }\r
 133 \r
 134   public void toTextbox_actionPerformed(ActionEvent e)\r
 135   {\r
 136     String text = "No features found on alignment";\r
 137     if (features)\r
 138     {\r
 139       if (GFFFormat.isSelected())\r
 140       {\r
 141         text = new FeaturesFile().printGFFFormat(\r
 142             ap.av.alignment.getDataset().getSequencesArray(),\r
 143             ap.av.featuresDisplayed);\r
 144       }\r
 145       else\r
 146       {\r
 147         text = new FeaturesFile().printJalviewFormat(\r
 148             ap.av.alignment.getDataset().getSequencesArray(),\r
 149             ap.av.featuresDisplayed);\r
 150       }\r
 151     }\r
 152     else if (!features)\r
 153     {\r
 154       text = new AnnotationFile().printAnnotations(\r
 155           annotations,\r
 156           sequenceGroups,\r
 157           alignmentProperties);\r
 158     }\r
 159 \r
 160     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 161     cap.setText(text);\r
 162     Desktop.addInternalFrame(cap,\r
 163                              (features ? "Features for - " :\r
 164                               "Annotations for - ")\r
 165                              + ap.alignFrame.getTitle(),\r
 166                              600,\r
 167                              500);\r
 168 \r
 169   }\r
 170 \r
 171   public void close_actionPerformed(ActionEvent e)\r
 172   {\r
 173     try\r
 174     {\r
 175       frame.setClosed(true);\r
 176     }\r
 177     catch (java.beans.PropertyVetoException ex)\r
 178     {}\r
 179   }\r
 180 \r
 181   private void jbInit()\r
 182       throws Exception\r
 183   {\r
 184     this.setLayout(flowLayout1);\r
 185     toFile.setText("to File");\r
 186     toFile.addActionListener(new ActionListener()\r
 187     {\r
 188       public void actionPerformed(ActionEvent e)\r
 189       {\r
 190         toFile_actionPerformed(e);\r
 191       }\r
 192     });\r
 193     toTextbox.setText("to Textbox");\r
 194     toTextbox.addActionListener(new ActionListener()\r
 195     {\r
 196       public void actionPerformed(ActionEvent e)\r
 197       {\r
 198         toTextbox_actionPerformed(e);\r
 199       }\r
 200     });\r
 201     close.setText("Close");\r
 202     close.addActionListener(new ActionListener()\r
 203     {\r
 204       public void actionPerformed(ActionEvent e)\r
 205       {\r
 206         close_actionPerformed(e);\r
 207       }\r
 208     });\r
 209     jalviewFormat.setOpaque(false);\r
 210     jalviewFormat.setSelected(true);\r
 211     jalviewFormat.setText("Jalview");\r
 212     GFFFormat.setOpaque(false);\r
 213     GFFFormat.setText("GFF");\r
 214     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);\r
 215     jLabel1.setText("Format: ");\r
 216     this.setBackground(Color.white);\r
 217     jPanel3.setBorder(BorderFactory.createEtchedBorder());\r
 218     jPanel3.setOpaque(false);\r
 219     jPanel1.setOpaque(false);\r
 220     jPanel1.add(toFile);\r
 221     jPanel1.add(toTextbox);\r
 222     jPanel1.add(close);\r
 223     jPanel3.add(jLabel1);\r
 224     jPanel3.add(jalviewFormat);\r
 225     jPanel3.add(GFFFormat);\r
 226     buttonGroup.add(jalviewFormat);\r
 227     buttonGroup.add(GFFFormat);\r
 228     this.add(jPanel3, null);\r
 229     this.add(jPanel1, null);\r
 230   }\r
 231 \r
 232   JPanel jPanel1 = new JPanel();\r
 233   JButton toFile = new JButton();\r
 234   JButton toTextbox = new JButton();\r
 235   JButton close = new JButton();\r
 236   ButtonGroup buttonGroup = new ButtonGroup();\r
 237   JRadioButton jalviewFormat = new JRadioButton();\r
 238   JRadioButton GFFFormat = new JRadioButton();\r
 239   JLabel jLabel1 = new JLabel();\r
 240   JPanel jPanel3 = new JPanel();\r
 241   FlowLayout flowLayout1 = new FlowLayout();\r
 242 \r
 243 }\r