import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.awt.geom.AffineTransform;
+import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator;
import jalview.analysis.AlignSeq;
import jalview.analysis.AlignmentUtils;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
+import jalview.io.NewickFile;
import jalview.util.Comparison;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
/**
* The panel that holds the labels for alignment annotations, providing
EditNameDialog dialog = new EditNameDialog(annotation.label,
annotation.description, name, description);
- dialog.showDialog(ap.alignFrame, title, new Runnable()
- {
- @Override
- public void run()
+ dialog.showDialog(ap.alignFrame, title, () -> {
+ annotation.label = dialog.getName();
+ String text = dialog.getDescription();
+ if (text != null && text.length() == 0)
{
- annotation.label = dialog.getName();
- String text = dialog.getDescription();
- if (text != null && text.length() == 0)
- {
- text = null;
- }
- annotation.description = text;
- if (addNew)
- {
- ap.av.getAlignment().addAnnotation(annotation);
- ap.av.getAlignment().setAnnotationIndex(annotation, 0);
- }
- ap.refresh(true);
+ text = null;
}
+ annotation.description = text;
+ if (addNew)
+ {
+ ap.av.getAlignment().addAnnotation(annotation);
+ ap.av.getAlignment().setAnnotationIndex(annotation, 0);
+ }
+ ap.refresh(true);
+ return null;
});
}
consclipbrd.addActionListener(this);
pop.add(consclipbrd);
}
+ if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP
+ && PAEContactMatrix.PAEMATRIX
+ .equals(aa[selectedRow].getCalcId()))
+ {
+ final PAEContactMatrix cm = (PAEContactMatrix) av
+ .getContactMatrix(aa[selectedRow]);
+ if (cm.getNewickString()!=null && cm.getNewickString().length()>0)
+ {
+ item = new JMenuItem("Show Matrix");
+ item.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+
+ ap.alignFrame.showContactMapTree(aa[selectedRow],cm);
+
+ }
+ });
+ pop.addSeparator();
+ pop.add(item);
+ }
+
+ }
}
pop.show(this, evt.getX(), evt.getY());
}
{
if (vertBar)
{
- g.drawLine(x - 40, y, x - 40, y - aa[i].height);
+ g.drawLine(20, y + offset, 20, y - aa[i].height);
+ g.drawLine(20, y + offset, x - 20, y + offset);
+
}
g.drawString(label, x, y + offset);
}