import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.HtmlSvgOutput;
import java.awt.print.PrinterJob;
import java.beans.PropertyChangeEvent;
import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
showReverse.setVisible(nucleotide);
showReverseComplement.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
- modifyConservation.setEnabled(!nucleotide);
+ modifyConservation.setEnabled(!nucleotide
+ && conservationMenuItem.isSelected());
showGroupConservation.setEnabled(!nucleotide);
showComplementMenuItem.setText(nucleotide ? MessageManager
padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.isShowColourText());
abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
+ modifyPID.setEnabled(abovePIDThreshold.isSelected());
conservationMenuItem.setSelected(av.getConservationSelected());
+ modifyConservation.setEnabled(conservationMenuItem.isSelected());
seqLimits.setSelected(av.getShowJVSuffix());
idRightAlign.setSelected(av.isRightAlignIds());
centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
public void saveAs_actionPerformed(ActionEvent e)
{
String format = currentFileFormat == null ? null : currentFileFormat
- .toString();
+ .getName();
JalviewFileChooser chooser = JalviewFileChooser.forWrite(
Cache.getProperty("LAST_DIRECTORY"), format);
fileName = chooser.getSelectedFile().getPath();
- Cache.setProperty("DEFAULT_FILE_FORMAT",
- currentFileFormat.toString());
+ Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
Cache.setProperty("LAST_DIRECTORY", fileName);
saveAlignment(fileName, currentFileFormat);
}
else
{
- // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
- // {
- // warningMessage("Cannot save file " + fileName + " using format "
- // + format, "Alignment output format not supported");
- // if (!Jalview.isHeadlessMode())
- // {
- // saveAs_actionPerformed(null);
- // }
- // return false;
- // }
-
AlignmentExportData exportData = getAlignmentForExport(format,
viewport, null);
if (exportData.getSettings().isCancelled())
{
try
{
- java.io.PrintWriter out = new java.io.PrintWriter(
- new java.io.FileWriter(file));
+ PrintWriter out = new PrintWriter(new FileWriter(file));
out.print(output);
out.close();
this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format",
- new Object[] { fileName, format }));
+ new Object[] { fileName, format.getName() }));
} catch (Exception ex)
{
success = false;
@Override
protected void outputText_actionPerformed(ActionEvent e)
{
-
- FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
+ FileFormatI fileFormat = FileFormats.getInstance().forName(
+ e.getActionCommand());
AlignmentExportData exportData = getAlignmentForExport(fileFormat,
viewport, null);
if (exportData.getSettings().isCancelled())
{
ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
// Make sure viewport is up to date w.r.t. any sliders
- if (viewport.getAbovePIDThreshold())
- {
- int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
- viewport.setThreshold(threshold);
- }
-
- if (viewport.getConservationSelected())
- {
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
- cs, "Background"));
- }
+ // ? not needed as handled by SliderPanel.valueChanged?
+// if (viewport.getAbovePIDThreshold())
+// {
+ // int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+// "Background");
+ //todo is threshold held in viewport style or in colour scheme?
+// viewport.setThreshold(threshold);
+ // }
+ //
+ // if (viewport.getConservationSelected())
+ // {
+ // cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+ // cs, "Background"));
+ // }
}
viewport.setGlobalColourScheme(cs);
+ if (viewport.getConservationSelected())
+ {
+ int conservationInc = SliderPanel.getConservationValue();
+ viewport.getViewportColourScheme()
+ .setConservationInc(conservationInc);
+ }
alignPanel.paintAlignment(true);
}
@Override
protected void modifyPID_actionPerformed()
{
- if (viewport.getAbovePIDThreshold()
- && viewport.getGlobalColourScheme() != null)
+ if (viewport.getAbovePIDThreshold())
{
SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
+ viewport.getViewportColourScheme(), "Background");
SliderPanel.showPIDSlider();
}
}
&& viewport.getGlobalColourScheme() != null)
{
SliderPanel.setConservationSlider(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
+ viewport.getViewportColourScheme(), "Background");
SliderPanel.showConservationSlider();
}
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action on selecting or deselecting (Colour) By Conservation
*/
@Override
protected void conservationMenuItem_actionPerformed()
{
- viewport.setConservationSelected(conservationMenuItem.isSelected());
-
- viewport.setAbovePIDThreshold(false);
- abovePIDThreshold.setSelected(false);
+ boolean selected = conservationMenuItem.isSelected();
+ modifyConservation.setEnabled(selected);
+ viewport.setConservationSelected(selected);
changeColour(viewport.getGlobalColourScheme());
-
- modifyConservation_actionPerformed();
+ if (selected)
+ {
+ modifyConservation_actionPerformed();
+ }
+ else
+ {
+ SliderPanel.hideConservationSlider();
+ }
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action on selecting or deselecting (Colour) Above PID Threshold
*/
@Override
public void abovePIDThreshold_actionPerformed()
{
- viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
-
- conservationMenuItem.setSelected(false);
- viewport.setConservationSelected(false);
+ boolean selected = abovePIDThreshold.isSelected();
+ modifyPID.setEnabled(selected);
+ viewport.setAbovePIDThreshold(selected);
changeColour(viewport.getGlobalColourScheme());
-
- modifyPID_actionPerformed();
+ if (selected)
+ {
+ modifyPID_actionPerformed();
+ }
+ else
+ {
+ SliderPanel.hidePIDSlider();
+ }
}
/**
colourMenu.add(textColour);
colourMenu.addSeparator();
- ColourMenuHelper
- .addMenuItems(colourMenu, this, viewport.getAlignment());
+ ColourMenuHelper.addMenuItems(colourMenu, this,
+ viewport.getAlignment(), false);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
- /*
- * select the default colour for the alignment (this may be
- * overridden later)
- */
- boolean nucleotide = viewport.getAlignment().isNucleotide();
- String defaultColourScheme = Cache.getDefault(
- nucleotide ? Preferences.DEFAULT_COLOUR_NUC
- : Preferences.DEFAULT_COLOUR_PROT,
- ResidueColourScheme.NONE);
+ ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
+ String schemeName = colourScheme == null ? null : colourScheme
+ .getSchemeName();
- ColourMenuHelper.setColourSelected(colourMenu, defaultColourScheme);
+ ColourMenuHelper.setColourSelected(colourMenu, schemeName);
}
}