import jalview.commands.RemoveGapsCommand;
import jalview.commands.SlideSequencesCommand;
import jalview.commands.TrimRegionCommand;
+import jalview.controller.AlignViewController;
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.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.io.FeaturesFile;
+import jalview.io.NewickFile;
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.util.Comparison;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
}
alignPanel = new AlignmentPanel(this, viewport);
- avc = new jalview.controller.AlignViewController(this, viewport,
+ avc = new AlignViewController(this, viewport,
alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
boolean featuresFile = false;
try
{
- featuresFile = new jalview.io.FeaturesFile(file, type)
+ featuresFile = new FeaturesFile(file, type)
.parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
.getFeatureRenderer().getFeatureColours(), featureLinks,
true, viewport.applet.getDefaultParameter(
}
else if (source == alProperties)
{
- StringBuffer contents = new jalview.io.AlignmentProperties(
+ StringBuffer contents = new AlignmentProperties(
viewport.getAlignment()).formatAsString();
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
cap.setText(contents.toString());
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(
"label.alignment_properties", new String[]
{ getTitle() }), 400, 250);
}
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
+ JalviewLite.addFrame(frame,
MessageManager.getString("label.input_cut_paste"), 500, 500);
}
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(
"label.alignment_output_command", new Object[]
{ e.getActionCommand() }), 600, 500);
cap.setAnnotationImport();
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
+ JalviewLite.addFrame(frame,
MessageManager.getString("action.paste_annotations"), 400, 300);
}
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
+ JalviewLite.addFrame(frame,
MessageManager.getString("label.annotations"), 600, 500);
cap.setText(annotation);
}
}
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
+ JalviewLite.addFrame(frame,
MessageManager.getString("label.features"), 600, 500);
cap.setText(features);
}
for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
{
ch = seq.getCharAt(j);
- if (!jalview.util.Comparison.isGap((ch)))
+ if (!Comparison.isGap((ch)))
{
endRes++;
}
}
}
- jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
+ JalviewLite.addFrame(af, newtitle, frameWidth,
frameHeight);
}
else
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.add(overview);
// +50 must allow for applet frame window
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(
"label.overview_params", new String[]
{ this.getTitle() }), overview.getPreferredSize().width,
overview.getPreferredSize().height + 50);
alignPanel.getOverviewPanel().updateOverviewImage();
}
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(viewport.applet)
+ StructureSelectionManager.getStructureSelectionManager(viewport.applet)
.sequenceColoursChanged(alignPanel);
alignPanel.paintAlignment(true);
{
Frame frame = new Frame();
frame.add(new PairwiseAlignPanel(alignPanel));
- jalview.bin.JalviewLite.addFrame(frame,
+ JalviewLite.addFrame(frame,
MessageManager.getString("action.pairwise_alignment"), 600,
500);
}
addTreeMenuItem(tp, title);
- jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
+ JalviewLite.addFrame(tp, title, 600, 500);
}
}
cap.setTreeImport();
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
+ JalviewLite.addFrame(frame,
MessageManager.getString("label.paste_newick_file"), 400, 300);
}
- public void loadTree(jalview.io.NewickFile tree, String treeFile)
+ public void loadTree(NewickFile tree, String treeFile)
{
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);
addTreeMenuItem(tp, treeFile);
}
Frame frame = new Frame();
frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
.getBuildDate()));
- jalview.bin.JalviewLite.addFrame(frame,
+ JalviewLite.addFrame(frame,
MessageManager.getString("label.jalview"), 580, 220);
}
inputText.addActionListener(this);
Menu outputTextboxMenu = new Menu(
MessageManager.getString("label.out_to_textbox"));
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+ for (int i = 0; i < AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
{
- MenuItem item = new MenuItem(
- jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+ MenuItem item = new MenuItem(AppletFormatAdapter.WRITEABLE_FORMATS[i]);
item.addActionListener(new java.awt.event.ActionListener()
{
add(statusBar, BorderLayout.SOUTH);
add(alignPanel, BorderLayout.CENTER);
// and register with the applet so it can pass external API calls to us
- jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
+ JalviewLite.addFrame(this, this.getTitle(),
frameWidth,
frameHeight);
}
{
// can only do alignments with Jmol
// find the last jmol window assigned to this alignment
- jalview.appletgui.AppletJmol ajm = null, tajm;
+ AppletJmol ajm = null, tajm;
Vector jmols = applet
- .getAppletWindow(jalview.appletgui.AppletJmol.class);
+.getAppletWindow(AppletJmol.class);
for (int i = 0, iSize = jmols.size(); i < iSize; i++)
{
- tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
+ tajm = (AppletJmol) jmols.elementAt(i);
if (tajm.ap.alignFrame == this)
{
ajm = tajm;
// otherwise, create a new window
if (applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
- protocol);
+ new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
applet.lastFrameX += 40;
applet.lastFrameY += 40;
}