--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+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.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;
+
+/**
+ * A dialog where a user can choose and action Tree or PCA calculation options
+ */
+public class CalculationChooser extends JPanel
+{
+ /*
+ * flag for whether gap matches residue in the PID calculation for a Tree
+ * - true gives Jalview 2.10.1 behaviour
+ * - set to false (using Groovy) for a more correct tree
+ * (JAL-374)
+ */
+ private static boolean treeMatchGaps = true;
+
+ private static final Font VERDANA_11PT = new Font("Verdana", 0, 11);
+
+ AlignFrame af;
+
+ JRadioButton pca;
+
+ JRadioButton tree;
+
+ JRadioButton neighbourJoining;
+
+ JRadioButton averageDistance;
+
+ JComboBox<String> modelNames;
+
+ private JInternalFrame frame;
+
+ private ButtonGroup treeTypes;
+
+ private JCheckBox includeGaps;
+
+ private JCheckBox matchGaps;
+
+ private JCheckBox includeGappedColumns;
+
+ private JCheckBox shorterSequence;
+
+ /**
+ * Constructor
+ *
+ * @param af
+ */
+ public CalculationChooser(AlignFrame alignFrame)
+ {
+ this.af = alignFrame;
+ 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"));
+ 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);
+
+ /*
+ * score model drop-down
+ */
+ modelNames = new JComboBox<String>();
+ ScoreModels scoreModels = ScoreModels.getInstance();
+ for (ScoreModelI sm : scoreModels.getModels())
+ {
+ boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+ if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
+ {
+ 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();
+ }
+ });
+ JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+ cancel.setFont(VERDANA_11PT);
+ cancel.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ cancel_actionPerformed(e);
+ }
+ });
+ JPanel actionPanel = new JPanel();
+ actionPanel.setOpaque(false);
+ actionPanel.add(ok);
+ actionPanel.add(cancel);
+
+ boolean includeParams = false;
+ this.add(calcChoicePanel);
+ this.add(treeChoicePanel);
+ this.add(scoreModelPanel);
+ if (includeParams)
+ {
+ this.add(paramsPanel);
+ }
+ this.add(actionPanel);
+
+ int width = 350;
+ int height = includeParams ? 400 : 220;
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.choose_calculation"), 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);
+
+ if (doPCA)
+ {
+ openPcaPanel(sm, params);
+ }
+ else
+ {
+ openTreePanel(sm, params);
+ }
+
+ // closeFrame();
+ }
+
+ /**
+ * Open a new Tree panel on the desktop
+ *
+ * @param sm
+ * @param params
+ */
+ protected void openTreePanel(ScoreModelI sm, SimilarityParamsI params)
+ {
+ String treeType = neighbourJoining.isSelected() ? TreeBuilder.NEIGHBOUR_JOINING
+ : TreeBuilder.AVERAGE_DISTANCE;
+ af.newTreePanel(treeType, sm, params);
+ }
+
+ /**
+ * Open a new PCA panel on the desktop
+ *
+ * @param sm
+ * @param params
+ */
+ protected void openPcaPanel(ScoreModelI sm, SimilarityParamsI params)
+ {
+ 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);
+ }
+
+ /**
+ *
+ */
+ protected void closeFrame()
+ {
+ try
+ {
+ frame.setClosed(true);
+ } catch (PropertyVetoException ex)
+ {
+ }
+ }
+
+ /**
+ * Returns a data bean holding parameters for similarity (or distance) model
+ * calculation
+ *
+ * @param doPCA
+ * @return
+ */
+ protected SimilarityParamsI getSimilarityParameters(boolean doPCA)
+ {
+ // commented out: parameter choices read from gui widgets
+ // SimilarityParamsI params = new SimilarityParams(
+ // includeGappedColumns.isSelected(), matchGaps.isSelected(),
+ // includeGaps.isSelected(), shorterSequence.isSelected());
+
+ boolean includeGapGap = true;
+ boolean includeGapResidue = true;
+ boolean matchOnShortestLength = false;
+
+ /*
+ * 'matchGaps' flag is only used in the PID calculation
+ * - set to false for PCA so that PCA using PID reproduces SeqSpace PCA
+ * - set to true for Tree to reproduce Jalview 2.10.1 calculation
+ * - set to false for Tree for a more correct calculation (JAL-374)
+ */
+ boolean matchGap = doPCA ? false : treeMatchGaps;
+
+ return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, matchOnShortestLength);
+ }
+
+ /**
+ * Closes dialog on cancel
+ *
+ * @param e
+ */
+ protected void cancel_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+}