import jalview.api.ComplexAlignFile;
import jalview.api.FeaturesDisplayedI;
+import jalview.api.FeaturesSourceI;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
loader.start();
}
}
+ @Override
public void run()
{
String title = protocol.equals(AppletFormatAdapter.PASTE) ? "Copied From Clipboard"
// just in case the caller didn't identify the file for us
if (source != null)
{
- format = new IdentifyFile().Identify(source, false); // identify
+ format = new IdentifyFile().identify(source, false); // identify
// stream and
// rewind rather
// than close
}
else
{
- format = new IdentifyFile().Identify(file, protocol);
+ format = new IdentifyFile().identify(file, protocol);
}
}
.getColumnSelection();
SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
.getHiddenSequences();
- boolean showSeqFeatures = ((ComplexAlignFile) source)
- .isShowSeqFeatures();
- ColourSchemeI cs = ((ComplexAlignFile) source)
- .getColourScheme();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
FeaturesDisplayedI fd = ((ComplexAlignFile) source)
.getDisplayedFeatures();
alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
-
- alignFrame.getViewport().setShowSequenceFeatures(
- showSeqFeatures);
alignFrame.getViewport().setFeaturesDisplayed(fd);
- alignFrame.changeColour(cs);
+ alignFrame.getViewport().setShowSequenceFeatures(
+ ((ComplexAlignFile) source).isShowSeqFeatures());
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
+ {
+ alignFrame.changeColour(cs);
+ }
}
else
{
alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
+ if (source instanceof FeaturesSourceI)
+ {
+ alignFrame.getViewport().setShowSequenceFeatures(true);
+ }
}
// add metadata and update ui
if (!protocol.equals(AppletFormatAdapter.PASTE))
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
javax.swing.JOptionPane.showInternalMessageDialog(
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
javax.swing.JOptionPane.showInternalMessageDialog(
*
* @see java.lang.Object#finalize()
*/
+ @Override
protected void finalize() throws Throwable
{
source = null;