Merge branch 'develop' into improvement/JAL-4409_implement_extra_schemes_in_getdown

[jalview.git] / src / jalview / gui / CalculationChooser.java

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index af41e58..4e22a74 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -52,12 +52,14 @@ import javax.swing.JRadioButton;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
+import jalview.analysis.AlignmentUtils;
 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.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceGroup;
 import jalview.util.MessageManager;
 
@@ -79,6 +81,21 @@ public class CalculationChooser extends JPanel
   private static final int MIN_TREE_SELECTION = 3;
 
   private static final int MIN_PCA_SELECTION = 4;
+  
+  private String secondaryStructureModelName;
+  
+  private void getSecondaryStructureModelName() {
+    
+    ScoreModels scoreModels = ScoreModels.getInstance();
+    for (ScoreModelI sm : scoreModels.getModels())
+    {
+      if (sm.isSecondaryStructure())
+      {
+        secondaryStructureModelName = sm.getName();
+      }
+    }
+    
+  }
 
   AlignFrame af;
 
@@ -89,6 +106,8 @@ public class CalculationChooser extends JPanel
   JRadioButton averageDistance;
 
   JComboBox<String> modelNames;
+  
+  JComboBox<String> ssSourceDropdown;
 
   JButton calculate;
 
@@ -121,6 +140,7 @@ public class CalculationChooser extends JPanel
     this.af = alignFrame;
     init();
     af.alignPanel.setCalculationDialog(this);
+    
   }
 
   /**
@@ -128,6 +148,7 @@ public class CalculationChooser extends JPanel
    */
   void init()
   {
+    getSecondaryStructureModelName();
     setLayout(new BorderLayout());
     frame = new JInternalFrame();
     frame.setFrameIcon(null);
@@ -208,16 +229,37 @@ public class CalculationChooser extends JPanel
     pca.addActionListener(calcChanged);
     neighbourJoining.addActionListener(calcChanged);
     averageDistance.addActionListener(calcChanged);
+    
+    
+    //to do    
+    ssSourceDropdown = buildSSSourcesOptionsList();
+    ssSourceDropdown.setVisible(false); // Initially hide the dropdown
 
     /*
      * score models drop-down - with added tooltips!
      */
     modelNames = buildModelOptionsList();
+    
+    // Step 3: Show or Hide Dropdown Based on Selection
+    modelNames.addActionListener(new ActionListener() {
+        @Override
+        public void actionPerformed(ActionEvent e) {
+            String selectedModel = modelNames.getSelectedItem().toString();
+            
+            if (selectedModel.equals(secondaryStructureModelName)) {
+              ssSourceDropdown.setVisible(true);
+            } else {
+              ssSourceDropdown.setVisible(false);
+            }
+        }
+    });
+
 
     JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
     scoreModelPanel.setOpaque(false);
     scoreModelPanel.add(modelNames);
-
+    scoreModelPanel.add(ssSourceDropdown);
+    
     /*
      * score model parameters
      */
@@ -232,7 +274,7 @@ public class CalculationChooser extends JPanel
     paramsPanel.add(matchGaps);
     paramsPanel.add(includeGappedColumns);
     paramsPanel.add(shorterSequence);
-
+    
     /*
      * OK / Cancel buttons
      */
@@ -270,7 +312,7 @@ public class CalculationChooser extends JPanel
     }
     this.add(actionPanel, BorderLayout.SOUTH);
 
-    int width = 350;
+    int width = 365;
     int height = includeParams ? 420 : 240;
 
     setMinimumSize(new Dimension(325, height - 10));
@@ -418,7 +460,38 @@ public class CalculationChooser extends JPanel
 
     return scoreModelsCombo;
   }
+  
+
+  private JComboBox<String> buildSSSourcesOptionsList()
+  {
+    final JComboBox<String> comboBox = new JComboBox<>();
+    Object curSel = comboBox.getSelectedItem();
+    DefaultComboBoxModel<String> sourcesModel = new DefaultComboBoxModel<>();
 
+    List<String> ssSources = getApplicableSecondaryStructureSources();
+
+    boolean selectedIsPresent = false;
+    for (String source : ssSources)
+    {
+      if (curSel != null && source.equals(curSel))
+      {
+        selectedIsPresent = true;
+        curSel = source;
+      }
+      sourcesModel.addElement(source);
+      
+    }
+
+    if (selectedIsPresent)
+    {
+      sourcesModel.setSelectedItem(curSel);
+    }
+    comboBox.setModel(sourcesModel);
+    
+    return comboBox;
+  }
+  
+  
   private void updateScoreModels(JComboBox<String> comboBox,
           List<String> toolTips)
   {
@@ -430,8 +503,12 @@ public class CalculationChooser extends JPanel
      * select the score models applicable to the alignment type
      */
     boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
-    List<ScoreModelI> models = getApplicableScoreModels(nucleotide,
-            pca.isSelected());
+    AlignmentAnnotation[] alignmentAnnotations = af.getViewport().getAlignment().getAlignmentAnnotation();
+
+    boolean ssPresent = AlignmentUtils.isSecondaryStructurePresent(alignmentAnnotations);
+
+    List<ScoreModelI> models = getApplicableScoreModels(nucleotide, pca.isSelected(),
+            ssPresent);
 
     /*
      * now we can actually add entries to the combobox,
@@ -466,6 +543,7 @@ public class CalculationChooser extends JPanel
     }
     // finally, update the model
     comboBox.setModel(model);
+    
   }
 
   /**
@@ -483,14 +561,15 @@ public class CalculationChooser extends JPanel
    * @return
    */
   protected static List<ScoreModelI> getApplicableScoreModels(
-          boolean nucleotide, boolean forPca)
+          boolean nucleotide, boolean forPca, boolean ssPresent)
   {
     List<ScoreModelI> filtered = new ArrayList<>();
 
     ScoreModels scoreModels = ScoreModels.getInstance();
     for (ScoreModelI sm : scoreModels.getModels())
     {
-      if (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA())
+      if (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA() 
+              || ssPresent && sm.isSecondaryStructure())
       {
         filtered.add(sm);
       }
@@ -505,10 +584,22 @@ public class CalculationChooser extends JPanel
     {
       filtered.add(scoreModels.getBlosum62());
     }
-
+    
     return filtered;
   }
 
+  
+  protected List<String> getApplicableSecondaryStructureSources()
+  {
+    AlignmentAnnotation[] annotations = af.getViewport().getAlignment().getAlignmentAnnotation();
+    
+    List<String> ssSources = AlignmentUtils.getSecondaryStructureSources(annotations);
+    //List<String> ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations);
+    
+                 
+    return ssSources;
+  }
+  
   /**
    * Open and calculate the selected tree or PCA on 'OK'
    */
@@ -516,8 +607,16 @@ public class CalculationChooser extends JPanel
   {
     boolean doPCA = pca.isSelected();
     String modelName = modelNames.getSelectedItem().toString();
-    SimilarityParamsI params = getSimilarityParameters(doPCA);
-
+    String ssSource = "";
+    Object selectedItem = ssSourceDropdown.getSelectedItem();
+    if (selectedItem != null) {
+        ssSource = selectedItem.toString();
+    }
+    SimilarityParams params = getSimilarityParameters(doPCA);
+    if(ssSource.length()>0)
+    {
+      params.setSecondaryStructureSource(ssSource);
+    }
     if (doPCA)
     {
       openPcaPanel(modelName, params);
@@ -618,7 +717,7 @@ public class CalculationChooser extends JPanel
    * @param doPCA
    * @return
    */
-  protected SimilarityParamsI getSimilarityParameters(boolean doPCA)
+  protected SimilarityParams getSimilarityParameters(boolean doPCA)
   {
     // commented out: parameter choices read from gui widgets
     // SimilarityParamsI params = new SimilarityParams(