JAL-1632 dialog to calculate either Tree or PCA

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index bfd48ed..a9418b5 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -79,6 +79,7 @@ action.scale_right = Scale Right
 action.by_tree_order = By Tree Order
 action.sort = Sort
 action.calculate_tree = Calculate Tree...
+action.calculate_tree_pca = Calculate Tree or PCA...
 action.help = Help
 action.by_annotation = By Annotation...
 action.invert_sequence_selection = Invert Sequence Selection
@@ -892,6 +893,7 @@ label.choose_filename_for_param_file = Choose a filename for this parameter file
 label.save_as_html = Save as HTML
 label.recently_opened = Recently Opened
 label.blasting_for_unidentified_sequence_jobs_running = BLASTing for unidentified sequences - {0}  jobs running.
+label.tree = Tree
 label.tree_from = Tree from {0}
 label.webservice_job_title = {0} using {1}
 label.select_visible_region_of = selected {0} region of {1}

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index d771dd5..def3998 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -823,6 +823,7 @@ label.choose_filename_for_param_file = Escoja un nombre de fichero para este fic
 label.save_as_html = Guardar como HTML
 label.recently_opened = Abiertos recientemente
 label.blasting_for_unidentified_sequence_jobs_running = Ejecutando BLAST de las secuencias no indentificadas - {0}  trabajos en marcha.
+label.tree = Árbol
 label.tree_from = Árbol de {0}
 label.webservice_job_title = {0} usando {1}
 label.select_visible_region_of = seleccionada {0} región de {1}

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 21668d3..efb204e 100644 (file)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -20,7 +20,9 @@
  */
 package jalview.appletgui;
 
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.analysis.ScoreModelI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
@@ -57,7 +59,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
 
   int top = 0;
 
-  public PCAPanel(AlignViewport av)
+  public PCAPanel(AlignViewport viewport)
   {
     try
     {
@@ -74,19 +76,19 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
       zCombobox.addItem("dim " + i);
     }
 
-    this.av = av;
-    boolean selected = av.getSelectionGroup() != null
-            && av.getSelectionGroup().getSize() > 0;
-    AlignmentView seqstrings = av.getAlignmentView(selected);
-    boolean nucleotide = av.getAlignment().isNucleotide();
+    this.av = viewport;
+    boolean selected = viewport.getSelectionGroup() != null
+            && viewport.getSelectionGroup().getSize() > 0;
+    AlignmentView seqstrings = viewport.getAlignmentView(selected);
+    boolean nucleotide = viewport.getAlignment().isNucleotide();
     SequenceI[] seqs;
     if (!selected)
     {
-      seqs = av.getAlignment().getSequencesArray();
+      seqs = viewport.getAlignment().getSequencesArray();
     }
     else
     {
-      seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
+      seqs = viewport.getSelectionGroup().getSequencesInOrder(viewport.getAlignment());
     }
     SeqCigar sq[] = seqstrings.getSequences();
     int length = sq[0].getWidth();
@@ -100,10 +102,14 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
         return;
       }
     }
+
+    ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
+            !nucleotide);
     pcaModel = new PCAModel(seqstrings, seqs, nucleotide,
+ scoreModel,
             SimilarityParams.SeqSpace);
 
-    rc = new RotatableCanvas(av);
+    rc = new RotatableCanvas(viewport);
     embedMenuIfNeeded(rc);
     add(rc, BorderLayout.CENTER);
 

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 57a7422..3b73c5a 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.api.analysis.ViewBasedAnalysisI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -77,18 +78,32 @@ public class PCAPanel extends GPCAPanel implements Runnable,
   int top = 0;
 
   /**
-   * Creates a new PCAPanel object.
+   * Creates a new PCAPanel object using default score model and parameters
    * 
-   * @param av
-   *          DOCUMENT ME!
-   * @param s
-   *          DOCUMENT ME!
+   * @param alignPanel
    */
   public PCAPanel(AlignmentPanel alignPanel)
   {
+    this(alignPanel, ScoreModels.getInstance().getDefaultModel(
+            !alignPanel.av.getAlignment().isNucleotide()),
+            SimilarityParams.SeqSpace);
+  }
+
+  /**
+   * Constructor given sequence data, a similarity (or distance) score model,
+   * and score calculation parameters
+   * 
+   * @param alignPanel
+   * @param scoreModel
+   * @param params
+   */
+  public PCAPanel(AlignmentPanel alignPanel, ScoreModelI scoreModel,
+          SimilarityParamsI params)
+  {
     super();
     this.av = alignPanel.av;
     this.ap = alignPanel;
+    boolean nucleotide = av.getAlignment().isNucleotide();
 
     progressBar = new ProgressBar(statusPanel, statusBar);
 
@@ -104,7 +119,6 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     boolean selected = av.getSelectionGroup() != null
             && av.getSelectionGroup().getSize() > 0;
     AlignmentView seqstrings = av.getAlignmentView(selected);
-    boolean nucleotide = av.getAlignment().isNucleotide();
     SequenceI[] seqs;
     if (!selected)
     {
@@ -127,8 +141,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       return;
     }
 
-    pcaModel = new PCAModel(seqstrings, seqs, nucleotide,
-            SimilarityParams.SeqSpace);
+    pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
+            params);
     PaintRefresher.Register(this, av.getSequenceSetId());
 
     rc = new RotatableCanvas(alignPanel);

diff --git a/src/jalview/gui/TreeChooser.java b/src/jalview/gui/TreeChooser.java
index 3542532..aafc1c0 100644 (file)
--- a/src/jalview/gui/TreeChooser.java
+++ b/src/jalview/gui/TreeChooser.java
@@ -32,6 +32,8 @@ 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;
@@ -53,6 +55,10 @@ public class TreeChooser extends JPanel
 
   AlignFrame af;
 
+  JRadioButton pca;
+
+  JRadioButton tree;
+
   JRadioButton neighbourJoining;
 
   JRadioButton averageDistance;
@@ -92,17 +98,43 @@ public class TreeChooser extends JPanel
     this.setBackground(Color.white);
 
     /*
-     * Layout consists of 4 panels:
-     * - first with choice of tree method NJ or AV
-     * - second with choice of score model
-     * - third with score model parameter options
-     * - fourth with OK and Cancel
+     * Layout consists of 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
+     * - 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);
@@ -172,6 +204,7 @@ public class TreeChooser extends JPanel
     actionPanel.add(ok);
     actionPanel.add(cancel);
 
+    this.add(calcChoicePanel);
     this.add(treeChoicePanel);
     this.add(scoreModelPanel);
     this.add(paramsPanel);
@@ -190,13 +223,45 @@ public class TreeChooser extends JPanel
    */
   protected void ok_actionPerformed(ActionEvent e)
   {
-    String treeType = neighbourJoining.isSelected() ? NJTree.NEIGHBOUR_JOINING
-            : NJTree.AVERAGE_DISTANCE;
     ScoreModelI sm = ScoreModels.getInstance().forName(
             matrixNames.getSelectedItem().toString());
     SimilarityParamsI params = getSimilarityParameters();
-    af.newTreePanel(treeType, sm, params);
 
+    if (pca.isSelected())
+    {
+      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();
+  }
+
+  /**
+   * 
+   */
+  protected void closeFrame()
+  {
     try
     {
       frame.setClosed(true);

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 97dcfa0..f7fe1b6 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1199,8 +1199,8 @@ public class GAlignFrame extends JInternalFrame
     });
     sortByAnnotScore.setVisible(false);
 
-    calculateTree
-            .setText(MessageManager.getString("action.calculate_tree"));
+    calculateTree.setText(MessageManager
+            .getString("action.calculate_tree_pca"));
 
     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
     padGapsMenuitem.setState(jalview.bin.Cache
@@ -1801,7 +1801,7 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(calculateTree);
     calculateMenu.addSeparator();
     calculateMenu.add(pairwiseAlignmentMenuItem);
-    calculateMenu.add(PCAMenuItem);
+    // calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
     calculateMenu.add(showReverse);

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index 324c69a..f216009 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -21,7 +21,6 @@
 package jalview.viewmodel;
 
 import jalview.analysis.PCA;
-import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.RotatableCanvasI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
@@ -55,22 +54,22 @@ public class PCAModel
   private SimilarityParamsI similarityParams;
 
   /**
-   * Constructor given sequence data and score calculation parameter options.
-   * The initial state is to compute PCA using a default score model (BLOSUM62
-   * for peptide, DNA for nucleotide).
+   * Constructor given sequence data, score model and score calculation
+   * parameter options.
    * 
    * @param seqData
    * @param sqs
    * @param nuc
+   * @param sm
    * @param params
    */
-  public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
+  public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc, ScoreModelI sm,
           SimilarityParamsI params)
   {
     seqstrings = seqData;
     seqs = sqs;
     nucleotide = nuc;
-    scoreModel = ScoreModels.getInstance().getDefaultModel(!nucleotide);
+    scoreModel = sm;
     similarityParams = params;
   }