*/
package jalview.gui;
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AlignmentUtils;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.Sequence;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.seqfetcher.DbSourceProxy;
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Set;
-import java.util.Vector;
-
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
-import javax.swing.JLayeredPane;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JRadioButtonMenuItem;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
-
/**
* DOCUMENT ME!
*
return false;
}
- String[] omitHidden = null;
-
- if (viewport.hasHiddenColumns())
- {
- int reply = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.alignment_contains_hidden_columns"),
- MessageManager
- .getString("action.save_omit_hidden_columns"),
- JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
-
- if (reply == JOptionPane.YES_OPTION)
- {
- omitHidden = viewport.getViewAsString(false);
- }
- }
- FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
- viewport.setFeatureRenderer(fr);
+ ExportData exportData = getAlignmentForExport();
FormatAdapter f = new FormatAdapter(viewport);
String output = f.formatSequences(format,
- viewport.getAlignment(), // class cast exceptions will
+ exportData.getAlignment(), // class cast exceptions will
// occur in the distant future
- omitHidden, f.getCacheSuffixDefault(format),
+ exportData.getOmitHidden(), f.getCacheSuffixDefault(format),
viewport.getColumnSelection());
if (output == null)
return success;
}
+
private void warningMessage(String warning, String title)
{
if (new jalview.util.Platform().isHeadless())
@Override
protected void outputText_actionPerformed(ActionEvent e)
{
+
+ ExportData exportData = getAlignmentForExport();
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(null);
+
+ try
+ {
+ cap.setText(new FormatAdapter(viewport).formatSequences(
+ e.getActionCommand(),
+ exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ viewport.getColumnSelection()));
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new Object[]
+ { e.getActionCommand() }), 600, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
+ cap.dispose();
+ }
+
+ }
+
+ public ExportData getAlignmentForExport()
+ {
+ AlignmentI alignmentToExport = null;
String[] omitHidden = null;
FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
viewport.setFeatureRenderer(fr);
- if (viewport.hasHiddenColumns())
+ HiddenSequences hiddenSeqs = viewport.getAlignment()
+ .getHiddenSequences();
+ if (viewport.hasHiddenColumns() || hiddenSeqs.getSize() > 0)
{
int reply = JOptionPane
.showInternalConfirmDialog(
{
omitHidden = viewport.getViewAsString(false);
}
+ else
+ {
+ alignmentToExport = viewport.getAlignment().getHiddenSequences()
+ .getFullAlignment();
+ }
}
-
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput(null);
-
- try
+ if (alignmentToExport == null)
{
- cap.setText(new FormatAdapter(viewport).formatSequences(
- e.getActionCommand(),
- viewport.getAlignment(), omitHidden,
- viewport.getColumnSelection()));
- Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.alignment_output_command", new Object[]
- { e.getActionCommand() }), 600, 500);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
- cap.dispose();
+ alignmentToExport = viewport.getAlignment();
}
-
+ return new ExportData(alignmentToExport, omitHidden);
}
/**
sf.setComplementVisible(this, show);
}
}
+
+ public class ExportData
+ {
+ private AlignmentI alignment;
+
+ private String[] omitHidden;
+
+ public ExportData(AlignmentI align, String[] ommit)
+ {
+ this.alignment = align;
+ this.omitHidden = ommit;
+ System.out.println();
+ }
+
+ public AlignmentI getAlignment()
+ {
+ return alignment;
+ }
+
+ public void setAlignment(AlignmentI alignment)
+ {
+ this.alignment = alignment;
+ }
+
+ public String[] getOmitHidden()
+ {
+ return omitHidden;
+ }
+
+ public void setOmitHidden(String[] omitHidden)
+ {
+ this.omitHidden = omitHidden;
+ }
+ }
+
+ @Override
+ public void hideColumns(List<int[]> colsToHide)
+ {
+ for (int[] colRange : colsToHide)
+ {
+ viewport.hideColumns(colRange[0], colRange[1]);
+ }
+
+ }
+
+ @Override
+ public void syncHiddenSequences()
+ {
+ AlignmentI al = viewport.getAlignment();
+ HiddenSequences hiddenSeqs = al.getHiddenSequences();
+ for (SequenceI seq : al.getSequencesArray())
+ {
+ if (seq.isHidden())
+ {
+ hiddenSeqs.hideSequence(seq);
+ }
+ }
+ }
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / blobdiff