package jalview.gui;
import jalview.analysis.NJTree;
+import jalview.analysis.scoremodels.PIDModel;
import jalview.analysis.scoremodels.ScoreModels;
-import jalview.api.analysis.DistanceModelI;
+import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.FlowLayout;
import java.awt.Font;
+import java.awt.GridLayout;
import java.awt.event.ActionEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.beans.PropertyVetoException;
import javax.swing.ButtonGroup;
import javax.swing.JButton;
+import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
AlignFrame af;
+ JRadioButton pca;
+
+ JRadioButton tree;
+
JRadioButton neighbourJoining;
JRadioButton averageDistance;
- JComboBox<String> matrixNames;
+ JComboBox<String> modelNames;
private JInternalFrame frame;
private ButtonGroup treeTypes;
+ private JCheckBox includeGaps;
+
+ private JCheckBox matchGaps;
+
+ private JCheckBox includeGappedColumns;
+
+ private JCheckBox shorterSequence;
+
/**
* Constructor
*
init();
}
+ /**
+ * Lays out the panel and adds it to the desktop
+ */
void init()
{
frame = new JInternalFrame();
frame.setContentPane(this);
this.setBackground(Color.white);
+ /*
+ * Layout consists of 4 or 5 panels:
+ * - first with choice of Tree or PCA
+ * - second with choice of tree method NJ or AV
+ * - third with choice of score model
+ * - fourth with score model parameter options [suppressed]
+ * - fifth with OK and Cancel
+ */
+ tree = new JRadioButton(MessageManager.getString("label.tree"));
+ tree.setOpaque(false);
+ pca = new JRadioButton(
+ MessageManager.getString("label.principal_component_analysis"));
+ pca.setOpaque(false);
neighbourJoining = new JRadioButton(
MessageManager.getString("label.tree_calc_nj"));
- neighbourJoining.setOpaque(false);
averageDistance = new JRadioButton(
MessageManager.getString("label.tree_calc_av"));
+ ItemListener listener = new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ neighbourJoining.setEnabled(tree.isSelected());
+ averageDistance.setEnabled(tree.isSelected());
+ }
+ };
+ pca.addItemListener(listener);
+ tree.addItemListener(listener);
+ ButtonGroup calcTypes = new ButtonGroup();
+ calcTypes.add(pca);
+ calcTypes.add(tree);
+ JPanel calcChoicePanel = new JPanel();
+ calcChoicePanel.setOpaque(false);
+ tree.setSelected(true);
+ calcChoicePanel.add(tree);
+ calcChoicePanel.add(pca);
+
+ neighbourJoining.setOpaque(false);
treeTypes = new ButtonGroup();
treeTypes.add(neighbourJoining);
treeTypes.add(averageDistance);
neighbourJoining.setSelected(true);
+ JPanel treeChoicePanel = new JPanel();
+ treeChoicePanel.setOpaque(false);
+ treeChoicePanel.add(neighbourJoining);
+ treeChoicePanel.add(averageDistance);
- matrixNames = new JComboBox<String>();
+ /*
+ * score model drop-down
+ */
+ modelNames = new JComboBox<String>();
ScoreModels scoreModels = ScoreModels.getInstance();
- for (DistanceModelI sm : scoreModels.getModels())
+ for (ScoreModelI sm : scoreModels.getModels())
{
boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
{
- matrixNames.addItem(sm.getName());
+ modelNames.addItem(sm.getName());
}
}
+ JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ scoreModelPanel.setOpaque(false);
+ scoreModelPanel.add(modelNames, FlowLayout.LEFT);
+
+ /*
+ * score model parameters
+ */
+ JPanel paramsPanel = new JPanel(new GridLayout(5, 1));
+ paramsPanel.setOpaque(false);
+ includeGaps = new JCheckBox("Include gaps");
+ matchGaps = new JCheckBox("Match gaps");
+ includeGappedColumns = new JCheckBox("Include gapped columns");
+ shorterSequence = new JCheckBox("Match on shorter sequence");
+ paramsPanel.add(new JLabel("Pairwise sequence scoring options"));
+ paramsPanel.add(includeGaps);
+ paramsPanel.add(matchGaps);
+ paramsPanel.add(includeGappedColumns);
+ paramsPanel.add(shorterSequence);
+
+ /*
+ * OK / Cancel buttons
+ */
JButton ok = new JButton(MessageManager.getString("action.ok"));
ok.setFont(VERDANA_11PT);
ok.addActionListener(new java.awt.event.ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- ok_actionPerformed(e);
+ ok_actionPerformed();
}
});
-
JButton cancel = new JButton(MessageManager.getString("action.cancel"));
cancel.setFont(VERDANA_11PT);
cancel.addActionListener(new java.awt.event.ActionListener()
cancel_actionPerformed(e);
}
});
+ JPanel actionPanel = new JPanel();
+ actionPanel.setOpaque(false);
+ actionPanel.add(ok);
+ actionPanel.add(cancel);
- JPanel p1 = new JPanel();
- p1.setOpaque(false);
- p1.add(neighbourJoining);
- p1.add(averageDistance);
- this.add(p1);
- JPanel p2 = new JPanel(new FlowLayout(FlowLayout.LEFT));
- p2.setOpaque(false);
- p2.add(matrixNames, FlowLayout.LEFT);
- this.add(p2);
- JPanel p3 = new JPanel();
- p3.setOpaque(false);
- p3.add(ok);
- p3.add(cancel);
- this.add(p3);
+ boolean includeParams = false;
+ this.add(calcChoicePanel);
+ this.add(treeChoicePanel);
+ this.add(scoreModelPanel);
+ if (includeParams)
+ {
+ this.add(paramsPanel);
+ }
+ this.add(actionPanel);
+ int width = 380;
+ int height = includeParams ? 400 : 220;
Desktop.addInternalFrame(frame,
- MessageManager.getString("label.choose_tree"),
- 400, 200, false);
+ MessageManager.getString("label.choose_tree"), width, height,
+ false);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
/**
* Open and calculate the selected tree on 'OK'
+ */
+ protected void ok_actionPerformed()
+ {
+ boolean doPCA = pca.isSelected();
+ ScoreModelI sm = ScoreModels.getInstance().forName(
+ modelNames.getSelectedItem().toString());
+ SimilarityParamsI params = getSimilarityParameters(doPCA, sm);
+
+ if (doPCA)
+ {
+ AlignViewport viewport = af.getViewport();
+ if (((viewport.getSelectionGroup() != null)
+ && (viewport.getSelectionGroup().getSize() < 4) && (viewport
+ .getSelectionGroup().getSize() > 0))
+ || (viewport.getAlignment().getHeight() < 4))
+ {
+ JvOptionPane
+ .showInternalMessageDialog(
+ this,
+ MessageManager
+ .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
+ MessageManager
+ .getString("label.sequence_selection_insufficient"),
+ JvOptionPane.WARNING_MESSAGE);
+ return;
+ }
+ new PCAPanel(af.alignPanel, sm, params);
+ }
+ else
+ {
+ String treeType = neighbourJoining.isSelected() ? NJTree.NEIGHBOUR_JOINING
+ : NJTree.AVERAGE_DISTANCE;
+ af.newTreePanel(treeType, sm, params);
+ }
+
+ // closeFrame();
+ }
+
+ /**
*
- * @param e
*/
- protected void ok_actionPerformed(ActionEvent e)
+ protected void closeFrame()
{
try
{
frame.setClosed(true);
- String treeType = neighbourJoining.isSelected() ? NJTree.NEIGHBOUR_JOINING
- : NJTree.AVERAGE_DISTANCE;
- DistanceModelI sm = ScoreModels.getInstance().forName(
- matrixNames.getSelectedItem().toString());
- af.newTreePanel(treeType, sm);
- } catch (Exception ex)
+ } catch (PropertyVetoException ex)
+ {
+ }
+ }
+
+ /**
+ * Returns a data bean holding parameters for similarity (or distance) model
+ * calculation
+ *
+ * @param doPCA
+ * @param sm
+ * @return
+ */
+ protected SimilarityParamsI getSimilarityParameters(boolean doPCA,
+ ScoreModelI sm)
+ {
+ // commented out: parameter choices read from gui widgets
+ // SimilarityParamsI params = new SimilarityParams(
+ // includeGappedColumns.isSelected(), matchGaps.isSelected(),
+ // includeGaps.isSelected(), shorterSequence.isSelected());
+
+ /*
+ * for now we want
+ * includeGappedColumns = true
+ * includeGaps = true
+ * matchOnShortestSequence = false
+ * matchGaps = true except false for PCA by PID (to match SeqSpace)
+ */
+ boolean matchGap = true;
+ if (doPCA && (sm instanceof PIDModel))
{
+ matchGap = false;
}
+ return new SimilarityParams(true, matchGap, true, false);
}
/**
git://source.jalview.org / jalview.git / blobdiff