Includes the PaSiMap button in the CalculationChooser

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 3843ddb..980e9bc 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -83,7 +83,7 @@ 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.calculate_tree_pca = Calculate Tree, PCA or PaSiMap...
 action.help = Help
 action.by_annotation = By Annotation...
 action.invert_sequence_selection = Invert Sequence Selection
@@ -170,6 +170,7 @@ label.amend = Amend
 label.undo_command = Undo {0}
 label.redo_command = Redo {0}
 label.principal_component_analysis = Principal Component Analysis
+label.pasimap = PaSiMap
 label.average_distance_identity = Average Distance Using % Identity
 label.neighbour_joining_identity = Neighbour Joining Using % Identity
 label.choose_calculation = Choose Calculation

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index d0bfd65..547d95b 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -81,7 +81,7 @@ action.scale_right = Escala derecha
 action.by_tree_order = Por orden del árbol
 action.sort = Ordenar
 action.calculate_tree = Calcular árbol...
-action.calculate_tree_pca = Calcular árbol o ACP...
+action.calculate_tree_pca = Calcular árbol, ACP o PaSiMap...
 action.help = Ayuda
 action.by_annotation = Por anotación...
 action.invert_sequence_selection = Invertir selección de secuencias
@@ -164,6 +164,7 @@ label.amend = Modificar
 label.undo_command = Deshacer {0}
 label.redo_command = Rehacer {0}
 label.principal_component_analysis = Análisis del Componente Principal
+label.pasimap = PaSiMap
 label.average_distance_identity = Distancia Media Usando % de Identidad
 label.neighbour_joining_identity = Unir vecinos utilizando % de Identidad
 label.choose_calculation = Elegir el cálculo

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index f7e5413..0f6c257 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -80,10 +80,14 @@ public class CalculationChooser extends JPanel
 
   private static final int MIN_PCA_SELECTION = 4;
 
+  private static final int MIN_PASIMAP_SELECTION = 4; //&! <++>!! chekc how many
+
   AlignFrame af;
 
   JRadioButton pca;
 
+  JRadioButton pasimap;        //&! initialize JRadioButton object for pasimap
+
   JRadioButton neighbourJoining;
 
   JRadioButton averageDistance;
@@ -111,6 +115,9 @@ public class CalculationChooser extends JPanel
    */
   private PCAPanel pcaPanel;
 
+  //&! change to PaSiMapPanel
+  private PCAPanel pasimapPanel;
+
   /**
    * Constructor
    * 
@@ -157,6 +164,10 @@ public class CalculationChooser extends JPanel
             MessageManager.getString("label.principal_component_analysis"));
     pca.setOpaque(false);
 
+    pasimap = new JRadioButton(                        // create the JRadioButton for pasimap with label.pasimap as its text
+           MessageManager.getString("label.pasimap"));
+    pasimap.setOpaque(false);
+
     neighbourJoining = new JRadioButton(
             MessageManager.getString("label.tree_calc_nj"));
     neighbourJoining.setSelected(true);
@@ -186,6 +197,14 @@ public class CalculationChooser extends JPanel
     pcaBorderless.add(pca, FlowLayout.LEFT);
     calcChoicePanel.add(pcaBorderless, FlowLayout.LEFT);
 
+    //&! 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)
+    pasimapBorderless.setOpaque(false);                // false -> stops every pixel inside border from being painted
+    pasimapBorderless.add(pasimap, FlowLayout.LEFT);   // add pasimap button to the JPanel
+    calcChoicePanel.add(pasimapBorderless, FlowLayout.LEFT);   // add button with border and everything to the overall ChoicePanel
+
     treePanel.add(neighbourJoining);
     treePanel.add(averageDistance);
 
@@ -193,6 +212,7 @@ public class CalculationChooser extends JPanel
 
     ButtonGroup calcTypes = new ButtonGroup();
     calcTypes.add(pca);
+    calcTypes.add(pasimap);    //&! add pasimap to the calculation types
     calcTypes.add(neighbourJoining);
     calcTypes.add(averageDistance);
 
@@ -205,6 +225,7 @@ public class CalculationChooser extends JPanel
       }
     };
     pca.addActionListener(calcChanged);
+    pasimap.addActionListener(calcChanged);    // add the calcChanged ActionListener to pasimap --> <++> idk
     neighbourJoining.addActionListener(calcChanged);
     averageDistance.addActionListener(calcChanged);
 
@@ -314,12 +335,13 @@ public class CalculationChooser extends JPanel
      * return value of true means enabled and selected
      */
     boolean checkPca = checkEnabled(pca, size, MIN_PCA_SELECTION);
+    boolean checkPasimap = checkEnabled(pasimap, size, MIN_PASIMAP_SELECTION);         // check if pasimap is enabled and min_size is fulfilled
     boolean checkNeighbourJoining = checkEnabled(neighbourJoining, size,
             MIN_TREE_SELECTION);
     boolean checkAverageDistance = checkEnabled(averageDistance, size,
             MIN_TREE_SELECTION);
 
-    if (checkPca || checkNeighbourJoining || checkAverageDistance)
+    if (checkPca || checkPasimap || checkNeighbourJoining || checkAverageDistance)
     {
       calculate.setToolTipText(null);
       calculate.setEnabled(true);
@@ -514,19 +536,24 @@ public class CalculationChooser extends JPanel
   protected void calculate_actionPerformed()
   {
     boolean doPCA = pca.isSelected();
+    boolean doPaSiMap = pasimap.isSelected();
     String modelName = modelNames.getSelectedItem().toString();
     SimilarityParamsI params = getSimilarityParameters(doPCA);
 
-    if (doPCA)
+    if (doPCA && !doPaSiMap)
     {
       openPcaPanel(modelName, params);
     }
+    else if (doPaSiMap && !doPCA)
+    {
+      openPasimapPanel(modelName, params);
+    }
     else
     {
       openTreePanel(modelName, params);
     }
 
-    // closeFrame();
+    closeFrame();
   }
 
   /**
@@ -598,6 +625,44 @@ public class CalculationChooser extends JPanel
   }
 
   /**
+   * Open a new PaSiMap panel on the desktop
+   * 
+   * @param modelName
+   * @param params
+   */
+  protected void openPasimapPanel(String modelName, SimilarityParamsI params)
+  {
+    AlignViewport viewport = af.getViewport();
+
+    /*
+     * gui validation shouldn't allow insufficient sequences here, but leave
+     * this check in in case this method gets exposed programmatically in future
+     */
+    if (((viewport.getSelectionGroup() != null)
+            && (viewport.getSelectionGroup().getSize() < MIN_PASIMAP_SELECTION)
+            && (viewport.getSelectionGroup().getSize() > 0))
+            || (viewport.getAlignment().getHeight() < MIN_PASIMAP_SELECTION))
+    {
+      JvOptionPane.showInternalMessageDialog(this,
+              MessageManager.formatMessage(
+                      "label.you_need_at_least_n_sequences",
+                      MIN_PASIMAP_SELECTION),
+              MessageManager
+                      .getString("label.sequence_selection_insufficient"),
+              JvOptionPane.WARNING_MESSAGE);
+      return;
+    }
+
+    /*
+     * construct the panel and kick off its calculation thread
+     */
+    //&! change to PaSiMapPanel
+    pasimapPanel = new PCAPanel(af.alignPanel, modelName, params);
+    new Thread(pasimapPanel).start();
+
+  }
+
+  /**
    * 
    */
   protected void closeFrame()