import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
import jalview.io.IdentifyFile;
import jalview.io.JPredFile;
import jalview.io.FileParse;
import jalview.io.IdentifyFile;
import jalview.io.JPredFile;
import jalview.javascript.MouseOverStructureListener;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
import jalview.javascript.MouseOverStructureListener;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.BufferedReader;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.BufferedReader;
boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
if (alf.viewport.getSelectionGroup() != null)
{
// JBPNote: getSelectionAsNewSequence behaviour has changed - this
// method now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
if (alf.viewport.getSelectionGroup() != null)
{
// JBPNote: getSelectionAsNewSequence behaviour has changed - this
// method now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
- String reply = new AppletFormatAdapter().formatSequences(format,
+ FileFormatI theFormat = FileFormats.getInstance().forName(format);
+ String reply = new AppletFormatAdapter().formatSequences(theFormat,
public void loadAnnotationFrom(AlignFrame alf, String annotation)
{
if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
public void loadAnnotationFrom(AlignFrame alf, String annotation)
{
if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
{
alf.alignPanel.fontChanged();
alf.alignPanel.setScrollValues(0, 0);
}
else
{
{
alf.alignPanel.fontChanged();
alf.alignPanel.setScrollValues(0, 0);
}
else
{
public boolean loadFeaturesFrom(AlignFrame alf, String features,
boolean autoenabledisplay)
{
public boolean loadFeaturesFrom(AlignFrame alf, String features,
boolean autoenabledisplay)
{
- al = new AppletFormatAdapter().readFile(text,
- AppletFormatAdapter.PASTE, format);
+ FileFormatI format = new IdentifyFile().identify(text,
+ DataSourceType.PASTE);
+ al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE,
+ format);
if (al.getHeight() > 0)
{
return new AlignFrame(al, this, title, false);
}
if (al.getHeight() > 0)
{
return new AlignFrame(al, this, title, false);
}
al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
format);
if ((al != null) && (al.getHeight() > 0))
al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
format);
if ((al != null) && (al.getHeight() > 0))
{
newAlignFrame.setTitle(MessageManager.formatMessage(
"label.sequences_from", new Object[] { applet
{
newAlignFrame.setTitle(MessageManager.formatMessage(
"label.sequences_from", new Object[] { applet
- pdbs.addElement(new Object[] { pdb, seqs, chains,
- new String(protocol) });
+ pdbs.addElement(new Object[] { pdb, seqs, chains, protocol });
- try
- {
- col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
- } catch (Exception ex)
- {
- System.err.println("Couldn't parse '" + colprop
- + "' as a colour for " + colparam);
- col = null;
- }
+ System.err.println("Couldn't parse '" + colprop
+ + "' as a colour for " + colparam);