action.scale_right = Scale Right
action.by_tree_order = By Tree Order
action.sort = Sort
-action.calculate_tree = Calculate Tree
+action.calculate_tree = Calculate Tree...
action.help = Help
action.by_annotation = By Annotation...
action.invert_sequence_selection = Invert Sequence Selection
*/
package jalview.analysis;
+import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
-import jalview.schemes.ScoreMatrix;
import jalview.util.Comparison;
import jalview.util.Format;
import jalview.util.MapList;
*/
package jalview.analysis;
+import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.datamodel.BinarySequence;
import jalview.datamodel.BinarySequence.InvalidSequenceTypeException;
import jalview.math.Matrix;
import jalview.schemes.ResidueProperties;
-import jalview.schemes.ScoreMatrix;
import java.io.PrintStream;
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.schemes;
+package jalview.analysis.scoremodels;
-import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
import jalview.api.analysis.ScoreModelI;
+import jalview.schemes.ResidueProperties;
public class ScoreMatrix extends PairwiseSeqScoreModel implements
ScoreModelI
* @param type
* 0 for Protein, 1 for NA
*/
- ScoreMatrix(String name, int[][] matrix, int type)
+ public ScoreMatrix(String name, int[][] matrix, int type)
{
this.matrix = matrix;
this.type = type;
return getPairwiseScore(A1.charAt(0), A2.charAt(0));
}
+ @Override
public int getPairwiseScore(char c, char d)
{
int pog = 0;
/**
* pretty print the matrix
*/
+ @Override
public String toString()
{
return outputMatrix(false);
--- /dev/null
+package jalview.analysis.scoremodels;
+
+import jalview.api.analysis.ScoreModelI;
+import jalview.schemes.ResidueProperties;
+
+import java.util.Map;
+import java.util.TreeMap;
+
+/**
+ * A class that can register and serve instances of ScoreModelI
+ */
+public class ScoreModels
+{
+ private static ScoreModels instance = new ScoreModels();
+
+ private Map<String, ScoreModelI> models;
+
+ public static ScoreModels getInstance()
+ {
+ return instance;
+ }
+
+ /**
+ * Private constructor to enforce use of singleton. Registers Jalview's
+ * "built-in" score models:
+ * <ul>
+ * <li>BLOSUM62</li>
+ * <li>PAM250</li>
+ * <li>DNA</li>
+ * <li>Sequence Feature Similarity</li>
+ * <li>Percentage Identity</li>
+ * </ul>
+ */
+ private ScoreModels()
+ {
+ /*
+ * using TreeMap keeps models ordered alphabetically by name
+ */
+ models = new TreeMap<String, ScoreModelI>(String.CASE_INSENSITIVE_ORDER);
+ registerScoreModel(new ScoreMatrix("BLOSUM62",
+ ResidueProperties.BLOSUM62, 0));
+ registerScoreModel(new ScoreMatrix("PAM250", ResidueProperties.PAM250,
+ 0));
+ registerScoreModel(new ScoreMatrix("DNA", ResidueProperties.DNA, 1));
+ registerScoreModel(new FeatureScoreModel());
+ registerScoreModel(new PIDScoreModel());
+ }
+
+ public Iterable<String> getModelNames()
+ {
+ return models.keySet();
+ }
+
+ public ScoreModelI forName(String s)
+ {
+ return models.get(s);
+ }
+
+ public void registerScoreModel(ScoreModelI sm)
+ {
+ ScoreModelI sm2 = models.get(sm.getName());
+ if (sm2 != null)
+ {
+ System.err.println("Warning: replacing score model " + sm2.getName());
+ }
+ models.put(sm.getName(), sm);
+ }
+}
String getName();
+ /**
+ * Answers true if this model is applicable for nucleotide data (so should be
+ * shown in menus in that context)
+ *
+ * @return
+ */
boolean isDNA();
+ /**
+ * Answers true if this model is applicable for peptide data (so should be
+ * shown in menus in that context)
+ *
+ * @return
+ */
boolean isProtein();
}
*/
package jalview.datamodel;
+import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.schemes.ResidueProperties;
-import jalview.schemes.ScoreMatrix;
/**
* Encode a sequence as a numeric vector using either classic residue binary
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
- buildTreeMenu();
+ calculateTree.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new TreeChooser(AlignFrame.this);
+ }
+ });
buildColourMenu();
if (Desktop.desktop != null)
/**
* DOCUMENT ME!
*
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("AV", "PID", "Average distance tree using PID");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
- }
-
- /**
- * DOCUMENT ME!
- *
* @param type
* DOCUMENT ME!
* @param pwType
* call. Listeners are added to remove the menu item when the treePanel is
* closed, and adjust the tree leaf to sequence mapping when the alignment is
* modified.
- *
- * @param treePanel
- * Displayed tree window.
- * @param title
- * SortBy menu item title.
*/
@Override
- public void buildTreeMenu()
+ public void buildTreeSortMenu()
{
- calculateTree.removeAll();
- // build the calculate menu
-
- for (final String type : new String[] { "NJ", "AV" })
- {
- String treecalcnm = MessageManager.getString("label.tree_calc_"
- + type.toLowerCase());
- for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
- {
- JMenuItem tm = new JMenuItem();
- ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
- if (sm.isDNA() == viewport.getAlignment().isNucleotide()
- || sm.isProtein() == !viewport.getAlignment()
- .isNucleotide())
- {
- String smn = MessageManager.getStringOrReturn(
- "label.score_model_", sm.getName());
- final String title = MessageManager.formatMessage(
- "label.treecalc_title", treecalcnm, smn);
- tm.setText(title);//
- tm.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- newTreePanel(type, pwtype, title);
- }
- });
- calculateTree.add(tm);
- }
-
- }
- }
sortByTreeMenu.removeAll();
List<Component> comps = PaintRefresher.components.get(viewport
ColourMenuHelper.setColourSelected(colourMenu, schemeName);
}
+
+ public void newTreePanel(String treeType, ScoreModelI sm)
+ {
+ String treecalcnm = MessageManager.getString("label.tree_calc_"
+ + treeType.toLowerCase());
+ String smn = MessageManager.getStringOrReturn("label.score_model_",
+ sm.getName());
+ final String ttl = MessageManager.formatMessage("label.treecalc_title",
+ treecalcnm, smn);
+ newTreePanel(treeType, sm.getName(), ttl);
+ }
}
class PrintThread extends Thread
--- /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.scoremodels.ScoreModels;
+import jalview.api.analysis.ScoreModelI;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+
+/**
+ * A dialog to allow a user to select and action Tree calculation options
+ */
+public class TreeChooser extends JPanel
+{
+ private static final Font VERDANA_11PT = new Font("Verdana", 0, 11);
+
+ AlignFrame af;
+
+ JRadioButton neighbourJoining;
+
+ JRadioButton averageDistance;
+
+ JComboBox<String> matrixNames;
+
+ private JInternalFrame frame;
+
+ private ButtonGroup treeTypes;
+
+ /**
+ * Constructor
+ *
+ * @param af
+ */
+ public TreeChooser(AlignFrame alignFrame)
+ {
+ this.af = alignFrame;
+ init();
+ }
+
+ void init()
+ {
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ this.setBackground(Color.white);
+
+ neighbourJoining = new JRadioButton(
+ MessageManager.getString("label.tree_calc_nj"));
+ neighbourJoining.setOpaque(false);
+ averageDistance = new JRadioButton(
+ MessageManager.getString("label.tree_calc_av"));
+ treeTypes = new ButtonGroup();
+ treeTypes.add(neighbourJoining);
+ treeTypes.add(averageDistance);
+ neighbourJoining.setSelected(true);
+
+ matrixNames = new JComboBox<String>();
+ ScoreModels scoreModels = ScoreModels.getInstance();
+ for (String scoreType : scoreModels.getModelNames())
+ {
+ ScoreModelI sm = scoreModels.forName(scoreType);
+ if (sm.isDNA() == af.getViewport().getAlignment().isNucleotide()
+ || sm.isProtein() == !af.getViewport().getAlignment()
+ .isNucleotide())
+ {
+ matrixNames.addItem(sm.getName());
+ }
+ }
+
+ 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);
+ }
+ });
+
+ 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 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);
+
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.choose_tree"),
+ 400, 200, false);
+
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ }
+
+ /**
+ * Open and calculate the selected tree on 'OK'
+ *
+ * @param e
+ */
+ protected void ok_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ frame.setClosed(true);
+ String treeType = neighbourJoining.isSelected() ? "NJ" : "AV";
+ ScoreModelI sm = ScoreModels.getInstance().forName(
+ matrixNames.getSelectedItem().toString());
+ af.newTreePanel(treeType, sm);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * Closes dialog on cancel
+ *
+ * @param e
+ */
+ protected void cancel_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+}
protected JMenu sort = new JMenu();
- protected JMenu calculateTree = new JMenu();
+ protected JMenuItem calculateTree = new JMenuItem();
protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
PCAMenuItem_actionPerformed(e);
}
});
- JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
- MessageManager.getString("label.average_distance_identity"));
- averageDistanceTreeMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- averageDistanceTreeMenuItem_actionPerformed(e);
- }
- });
- JMenuItem neighbourTreeMenuItem = new JMenuItem(
- MessageManager.getString("label.neighbour_joining_identity"));
- neighbourTreeMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- neighbourTreeMenuItem_actionPerformed(e);
- }
- });
this.getContentPane().setLayout(new BorderLayout());
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
outputTextboxMenu.setText(MessageManager
.getString("label.out_to_textbox"));
-
- JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
- MessageManager.getString("label.average_distance_blosum62"));
- avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- avTreeBlosumMenuItem_actionPerformed(e);
- }
- });
- JMenuItem njTreeBlosumMenuItem = new JMenuItem(
- MessageManager.getString("label.neighbour_blosum62"));
- njTreeBlosumMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- njTreeBlosumMenuItem_actionPerformed(e);
- }
- });
annotationPanelMenuItem.setActionCommand("");
annotationPanelMenuItem.setText(MessageManager
.getString("label.show_annotations"));
@Override
public void menuSelected(MenuEvent e)
{
- buildTreeMenu();
+ buildTreeSortMenu();
}
@Override
{
}
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
protected void conservationMenuItem_actionPerformed(boolean selected)
{
}
}
- public void buildTreeMenu()
+ public void buildTreeSortMenu()
{
}
import jalview.analysis.scoremodels.FeatureScoreModel;
import jalview.analysis.scoremodels.PIDScoreModel;
+import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.api.analysis.ScoreModelI;
import java.awt.Color;
// public static final double hydmax = 1.38;
// public static final double hydmin = -2.53;
- private static final int[][] BLOSUM62 = {
+ public static final int[][] BLOSUM62 = {
{ 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,
-2, 0, -2, -1, 0, -4 },
{ -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3,
{ -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,
-4, -4, -4, -4, -4, -4, 1 }, };
- static final int[][] PAM250 = {
+ public static final int[][] PAM250 = {
{ 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3,
0, 0, 0, 0, -8 },
{ -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,
// treats T and U identically. R and Y weak equivalence with AG and CTU.
// N matches any other base weakly
//
- static final int[][] DNA = { { 10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1 }, // A
+ public static final int[][] DNA = {
+ { 10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1 }, // A
{ -8, 10, -8, -8, -8, 1, 1, -8, 1, 1, 1 }, // C
{ -8, -8, 10, -8, -8, 1, 1, 1, -8, 1, 1 }, // G
{ -8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1 }, // T
// scoreMatrices.put("Conservation EnhPos", new
// ScoreMatrix("Conservation EnhPos",propMatrixEpos,0));
scoreMatrices.put("PID", new PIDScoreModel());
- scoreMatrices.put("Displayed Features", new FeatureScoreModel());
+ scoreMatrices.put("Sequence Feature Similarity",
+ new FeatureScoreModel());
}
private ResidueProperties()
*/
package jalview.schemes;
+import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.api.analysis.ScoreModelI;
import jalview.gui.JvOptionPane;
git://source.jalview.org / jalview.git / commitdiff