import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
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.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
{
this.viewport = viewport;
LoadFile(file, protocol, format);
}
{
this.viewport = viewport;
LoadFile(file, protocol, format);
}
- public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
- String format)
+ public AlignFrame LoadFileWaitTillLoaded(String file,
+ DataSourceType sourceType, FileFormatI format)
{
Desktop.instance.stopLoading();
System.err.println("The input file \"" + file
+ "\" has null or unidentifiable data content!");
if (!Jalview.isHeadlessMode())
{
{
Desktop.instance.stopLoading();
System.err.println("The input file \"" + file
+ "\" has null or unidentifiable data content!");
if (!Jalview.isHeadlessMode())
{
Desktop.desktop,
MessageManager.getString("label.couldnt_read_data")
+ " in " + file + "\n"
+ AppletFormatAdapter.SUPPORTED_FORMATS,
MessageManager.getString("label.couldnt_read_data"),
Desktop.desktop,
MessageManager.getString("label.couldnt_read_data")
+ " in " + file + "\n"
+ AppletFormatAdapter.SUPPORTED_FORMATS,
MessageManager.getString("label.couldnt_read_data"),
// append to existing alignment
viewport.addAlignment(al, title);
}
// append to existing alignment
viewport.addAlignment(al, title);
}
FeaturesDisplayedI fd = ((ComplexAlignFile) source)
.getDisplayedFeatures();
alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
FeaturesDisplayedI fd = ((ComplexAlignFile) source)
.getDisplayedFeatures();
alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- 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);
}
else
{
alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
alignFrame.statusBar.setText(MessageManager.formatMessage(
"label.successfully_loaded_file",
new String[] { title }));
alignFrame.statusBar.setText(MessageManager.formatMessage(
"label.successfully_loaded_file",
new String[] { title }));
errorMessage, MessageManager
.getString("label.error_loading_file"),
errorMessage, MessageManager
.getString("label.error_loading_file"),
Desktop.desktop, MessageManager.formatMessage(
"label.problems_opening_file",
new String[] { file }), MessageManager
.getString("label.file_open_error"),
Desktop.desktop, MessageManager.formatMessage(
"label.problems_opening_file",
new String[] { file }), MessageManager
.getString("label.file_open_error"),
Desktop.desktop, MessageManager.formatMessage(
"warn.out_of_memory_loading_file", new String[]
{ file }), MessageManager
.getString("label.out_of_memory"),
Desktop.desktop, MessageManager.formatMessage(
"warn.out_of_memory_loading_file", new String[]
{ file }), MessageManager
.getString("label.out_of_memory"),