/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program 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 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\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
-\r
package jalview.gui;\r
\r
import java.util.*;\r
import jalview.datamodel.*;\r
import jalview.io.*;\r
\r
-public class AnnotationExporter\r
- extends JPanel\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
try\r
{\r
jbInit();\r
- }\r
- catch (Exception ex)\r
+ } catch (Exception ex)\r
{\r
ex.printStackTrace();\r
}\r
frame = new JInternalFrame();\r
frame.setContentPane(this);\r
frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- Desktop.addInternalFrame(frame,\r
- "",\r
- 260, 125);\r
+ Desktop.addInternalFrame(frame, "", 260, 125);\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,\r
- Vector sequenceGroups,\r
- Hashtable alProperties)\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
public void toFile_actionPerformed(ActionEvent e)\r
{\r
JalviewFileChooser chooser = new JalviewFileChooser(\r
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
\r
chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle(\r
- features ? "Save Features to File" : "Save Annotation to File");\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 (GFFFormat.isSelected())\r
{\r
- text = new FeaturesFile().printGFFFormat(\r
- ap.av.alignment.getDataset().getSequencesArray(),\r
- ap.av.featuresDisplayed);\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(\r
- ap.av.alignment.getDataset().getSequencesArray(),\r
- ap.av.featuresDisplayed);\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
- text = new AnnotationFile().printAnnotations(\r
- annotations,\r
- sequenceGroups,\r
- alignmentProperties);\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
+ new java.io.FileWriter(chooser.getSelectedFile()));\r
\r
out.print(text);\r
out.close();\r
- }\r
- catch (Exception ex)\r
+ } catch (Exception ex)\r
{\r
ex.printStackTrace();\r
}\r
{\r
if (GFFFormat.isSelected())\r
{\r
- text = new FeaturesFile().printGFFFormat(\r
- ap.av.alignment.getDataset().getSequencesArray(),\r
- ap.av.featuresDisplayed);\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(\r
- ap.av.alignment.getDataset().getSequencesArray(),\r
- ap.av.featuresDisplayed);\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
- text = new AnnotationFile().printAnnotations(\r
- annotations,\r
- sequenceGroups,\r
- alignmentProperties);\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
- cap.setText(text);\r
- Desktop.addInternalFrame(cap,\r
- (features ? "Features for - " :\r
- "Annotations for - ")\r
- + ap.alignFrame.getTitle(),\r
- 600,\r
- 500);\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
- catch (java.beans.PropertyVetoException ex)\r
- {}\r
}\r
\r
- private void jbInit()\r
- throws Exception\r
+ private void jbInit() throws Exception\r
{\r
this.setLayout(flowLayout1);\r
toFile.setText("to File");\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.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, null);\r
this.add(jPanel1, null);\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
git://source.jalview.org / jalview.git / blobdiff