X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=9c6231a2e066a9e0d8892f493cb06389082669e7;hb=822cae4dcebdbf5bd5c42c740d8b5e4798bb6cdc;hp=d4975a6c6196b44a9f8e6eacb1a99c2b21caa3b7;hpb=9922c9eec14599f6b141a8db8a3859cab7227ce0;p=jalview.git
diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index d4975a6..9c6231a 100755
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -1,51 +1,60 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
+import jalview.datamodel.*;
import jalview.io.*;
-import jalview.datamodel.AlignmentAnnotation;
-
-import java.awt.Color;
-import java.awt.FlowLayout;
-import javax.swing.BorderFactory;
-
-public class AnnotationExporter
- extends JPanel
+/**
+ *
+ * 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;
+
+ AlignmentAnnotation[] annotations;
+
+ List sequenceGroups;
+
+ Hashtable alignmentProperties;
public AnnotationExporter()
{
try
{
jbInit();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
@@ -53,119 +62,172 @@ public class AnnotationExporter
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame,
- "",
- 260, 125);
+ 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)
+ 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"));
+ 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");
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(features ? "Save Features to File"
+ : "Save Annotation to File");
+ chooser.setToolTipText("Save");
- int value = chooser.showSaveDialog(this);
+ int value = chooser.showSaveDialog(this);
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ String text = "No features found on alignment";
+ if (features)
{
- String text = "No features found on alignment";
- if (features)
+ if (GFFFormat.isSelected())
{
- 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);
+ text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
+ .getDataset().getSequencesArray(),
+ getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
}
else
{
- text = new AnnotationFile().printAnnotations( annotations );
+ text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
+ .getDataset().getSequencesArray(),
+ getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
}
-
- try
+ }
+ else
+ {
+ if (CSVFormat.isSelected())
{
- java.io.PrintWriter out = new java.io.PrintWriter(
- new java.io.FileWriter(chooser.getSelectedFile()));
-
- out.print(text);
- out.close();
+ text = new AnnotationFile().printCSVAnnotations(annotations);
}
- catch (Exception ex)
+ else
{
- ex.printStackTrace();
+ 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 (features)
{
if (GFFFormat.isSelected())
- text = new FeaturesFile().printGFFFormat(
- ap.av.alignment.getDataset().getSequencesArray(),
- ap.av.featuresDisplayed);
+ {
+ text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
+ .getDataset().getSequencesArray(),
+ getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
+ }
else
- text = new FeaturesFile().printJalviewFormat(
- ap.av.alignment.getDataset().getSequencesArray(),
- ap.av.featuresDisplayed);
+ {
+ text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
+ .getDataset().getSequencesArray(),
+ getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
+ }
}
- else if(!features)
+ else if (!features)
{
- text = new AnnotationFile().printAnnotations( annotations );
+ 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);
+ try
+ {
+ cap.setText(text);
+ Desktop.addInternalFrame(cap, (features ? "Features for - "
+ : "Annotations for - ") + ap.alignFrame.getTitle(), 600, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("generating "
+ + (features ? "Features for - " : "Annotations for - ")
+ + 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{
+ try
+ {
frame.setClosed(true);
- }catch(java.beans.PropertyVetoException ex)
- {}
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
}
-
-
- private void jbInit()
- throws Exception
+ private void jbInit() throws Exception
{
- this.setLayout(flowLayout1);
+ this.setLayout(new BorderLayout());
+
toFile.setText("to File");
toFile.addActionListener(new ActionListener()
{
@@ -195,6 +257,8 @@ public class AnnotationExporter
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);
@@ -207,21 +271,34 @@ public class AnnotationExporter
jPanel3.add(jLabel1);
jPanel3.add(jalviewFormat);
jPanel3.add(GFFFormat);
+ jPanel3.add(CSVFormat);
buttonGroup.add(jalviewFormat);
buttonGroup.add(GFFFormat);
- this.add(jPanel3, null);
- this.add(jPanel1, null);
+ 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();
}