import jalview.bin.Cache;
import jalview.datamodel.SequenceGroup;
import jalview.util.MessageManager;
-
+import jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
+import jalview.datamodel.SequenceGroup;
+import jalview.util.MessageManager;
+
/**
* A dialog where a user can choose and action Tree or PCA calculation options
*/
private static final int MIN_PCA_SELECTION = 4;
- private static final int MIN_PASIMAP_SELECTION = 4; //&! <++>!! chekc how many
+ private static final int MIN_PASIMAP_SELECTION = 8;
AlignFrame af;
JRadioButton pca;
- JRadioButton pasimap; //&! initialize JRadioButton object for pasimap
+ JRadioButton pasimap;
JRadioButton neighbourJoining;
*/
private PCAPanel pcaPanel;
- //&! change to PaSiMapPanel
- private PCAPanel pasimapPanel;
+ private PaSiMapPanel pasimapPanel;
/**
* Constructor
{
setLayout(new BorderLayout());
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
this.setBackground(Color.white);
frame.addFocusListener(new FocusListener()
pcaBorderless.add(pca, FlowLayout.LEFT);
calcChoicePanel.add(pcaBorderless, FlowLayout.LEFT);
- //&! create pasimap panel
+ // create pasimap panel
JPanel pasimapBorderless = new JPanel(new FlowLayout(FlowLayout.LEFT)); // create new JPanel (button) for pasimap
pasimapBorderless.setBorder(
BorderFactory.createEmptyBorder(2, b.left, 2, b.right)); // set border (margin) for button (same as treePanel and pca)
ButtonGroup calcTypes = new ButtonGroup();
calcTypes.add(pca);
- calcTypes.add(pasimap); //&! add pasimap to the calculation types
+ calcTypes.add(pasimap);
calcTypes.add(neighbourJoining);
calcTypes.add(averageDistance);
/*
* construct the panel and kick off its calculation thread
*/
- //&! change to PaSiMapPanel
- pasimapPanel = new PCAPanel(af.alignPanel, modelName, params);
+ pasimapPanel = new PaSiMapPanel(af.alignPanel, modelName, params);
new Thread(pasimapPanel).start();
}