import jalview.commands.RemoveGapsCommand;
import jalview.commands.SlideSequencesCommand;
import jalview.commands.TrimRegionCommand;
import jalview.commands.RemoveGapsCommand;
import jalview.commands.SlideSequencesCommand;
import jalview.commands.TrimRegionCommand;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.io.FeaturesFile;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.io.FeaturesFile;
import jalview.io.TCoffeeScoreFile;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.io.TCoffeeScoreFile;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ZappoColourScheme;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.schemes.ZappoColourScheme;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
.parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
.getFeatureRenderer().getFeatureColours(), featureLinks,
true, viewport.applet.getDefaultParameter(
.parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
.getFeatureRenderer().getFeatureColours(), featureLinks,
true, viewport.applet.getDefaultParameter(
viewport.getAlignment()).formatAsString();
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
cap.setText(contents.toString());
Frame frame = new Frame();
frame.add(cap);
viewport.getAlignment()).formatAsString();
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
cap.setText(contents.toString());
Frame frame = new Frame();
frame.add(cap);
"label.alignment_properties", new String[]
{ getTitle() }), 400, 250);
}
"label.alignment_properties", new String[]
{ getTitle() }), 400, 250);
}
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
"label.alignment_output_command", new Object[]
{ e.getActionCommand() }), 600, 500);
"label.alignment_output_command", new Object[]
{ e.getActionCommand() }), 600, 500);
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
Frame frame = new Frame();
frame.add(cap);
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
+ JalviewLite.addFrame(af, newtitle, frameWidth,
"label.overview_params", new String[]
{ this.getTitle() }), overview.getPreferredSize().width,
overview.getPreferredSize().height + 50);
"label.overview_params", new String[]
{ this.getTitle() }), overview.getPreferredSize().width,
overview.getPreferredSize().height + 50);
- jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
+ JalviewLite.addFrame(tp, title, 600, 500);
{
TreePanel tp = new TreePanel(alignPanel, treeFile,
MessageManager.getString("label.load_tree_from_file"), tree);
{
TreePanel tp = new TreePanel(alignPanel, treeFile,
MessageManager.getString("label.load_tree_from_file"), tree);
- jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
+ JalviewLite.addFrame(tp, treeFile, 600, 500);
Frame frame = new Frame();
frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
.getBuildDate()));
Frame frame = new Frame();
frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
.getBuildDate()));
inputText.addActionListener(this);
Menu outputTextboxMenu = new Menu(
MessageManager.getString("label.out_to_textbox"));
inputText.addActionListener(this);
Menu outputTextboxMenu = new Menu(
MessageManager.getString("label.out_to_textbox"));
add(statusBar, BorderLayout.SOUTH);
add(alignPanel, BorderLayout.CENTER);
// and register with the applet so it can pass external API calls to us
add(statusBar, BorderLayout.SOUTH);
add(alignPanel, BorderLayout.CENTER);
// and register with the applet so it can pass external API calls to us
// otherwise, create a new window
if (applet.jmolAvailable)
{
// otherwise, create a new window
if (applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
- protocol);
+ new AppletJmol(pdb, seqs, chains, alignPanel, protocol);