From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 23 May 2024 17:23:50 +0000 (+0100)
Subject: JAL-4423 provide option in calc dialog to re-use the existing MSA rather than compute... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3d119bcaf73c4dbbb1a6c4899614001993b57466;p=jalview.git

JAL-4423 provide option in calc dialog to re-use the existing MSA rather than compute pairwise alignments for pasimap
---

diff --git a/src/jalview/analysis/PaSiMap.java b/src/jalview/analysis/PaSiMap.java
index 86888ee..2d015ce 100755
--- a/src/jalview/analysis/PaSiMap.java
+++ b/src/jalview/analysis/PaSiMap.java
@@ -52,6 +52,8 @@ public class PaSiMap implements Runnable
   final private int openCost = 100;
 
   final private int extendCost = 5;
+  
+  boolean dontRealign = false;
 
   /*
    * outputs
@@ -313,4 +315,9 @@ public class PaSiMap implements Runnable
   {
     return dim;
   }
+
+  public void setDontRealign(boolean dontRealign)
+  {
+    this.dontRealign = dontRealign;
+  }
 }
diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 3775c47..c22c4ba 100644
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -133,6 +133,8 @@ public class CalculationChooser extends JPanel
 
   private JCheckBox matchGaps;
 
+  private JCheckBox reuseAlignment;
+
   private JCheckBox includeGappedColumns;
 
   private JCheckBox shorterSequence;
@@ -308,6 +310,15 @@ public class CalculationChooser extends JPanel
     paramsPanel.add(shorterSequence);
     
     /*
+     * pasimap parameters
+     */
+    reuseAlignment = new JCheckBox("Use aligned similarity");
+    reuseAlignment.setSelected(false);
+    reuseAlignment.setVisible(false);
+    scoreModelPanel.add(reuseAlignment);
+    		
+    
+    /*
      * OK / Cancel buttons
      */
     calculate = new JButton(MessageManager.getString("action.calculate"));
@@ -395,6 +406,7 @@ public class CalculationChooser extends JPanel
     boolean checkAverageDistance = checkEnabled(averageDistance, size,
             MIN_TREE_SELECTION);
 
+    reuseAlignment.setVisible(checkPasimap);
     if (checkPca || checkPasimap || checkNeighbourJoining || checkAverageDistance)
     {
       calculate.setToolTipText(null);
@@ -771,6 +783,7 @@ public class CalculationChooser extends JPanel
      * construct the panel and kick off its calculation thread
      */
     pasimapPanel = new PaSiMapPanel(af.alignPanel, modelName);
+    pasimapPanel.setUseAlignment(reuseAlignment.isSelected());
     new Thread(pasimapPanel).start();
 
   }
diff --git a/src/jalview/gui/PaSiMapPanel.java b/src/jalview/gui/PaSiMapPanel.java
index 4a2d19d..2b6bc14 100644
--- a/src/jalview/gui/PaSiMapPanel.java
+++ b/src/jalview/gui/PaSiMapPanel.java
@@ -92,6 +92,8 @@ public class PaSiMapPanel extends GPaSiMapPanel
 
   private boolean working;
 
+  private boolean useObservedAlignment;
+
   /**
    * Constructor given sequence data, a similarity (or distance) score model
    * name, and score calculation parameters
@@ -132,7 +134,7 @@ public class PaSiMapPanel extends GPaSiMapPanel
     ScoreModelI scoreModel = ScoreModels.getInstance()
             .getScoreModel(modelName, ap);
     setPasimapModel(
-            new PaSiMapModel(av, seqs, nucleotide, scoreModel));
+            new PaSiMapModel(av, seqs, nucleotide, useObservedAlignment, scoreModel));
     PaintRefresher.Register(this, av.getSequenceSetId());
 
     setRotatableCanvas(new RotatableCanvas(alignPanel));
@@ -215,6 +217,7 @@ public class PaSiMapPanel extends GPaSiMapPanel
               GAP_OPEN_COST, GAP_EXTEND_COST, false);
       System.out.println(pap != null);
       setPairwiseAlignPanel(pap);
+      getPasimapModel().setUseObservedAlignment(useObservedAlignment);
       getPasimapModel().calculate(pap);
 
       xCombobox.setSelectedIndex(0);
@@ -879,4 +882,13 @@ public class PaSiMapPanel extends GPaSiMapPanel
   {
     return progressBar.getProgressBar(id);
   }
+
+  /**
+   * enable or disable the pairwise alignment step
+   * @param selected
+   */
+  public void setUseAlignment(boolean selected)
+  {
+    useObservedAlignment = selected;
+  }
 }
diff --git a/src/jalview/viewmodel/PaSiMapModel.java b/src/jalview/viewmodel/PaSiMapModel.java
index a0e5174..d2caa47 100644
--- a/src/jalview/viewmodel/PaSiMapModel.java
+++ b/src/jalview/viewmodel/PaSiMapModel.java
@@ -49,6 +49,8 @@ public class PaSiMapModel
   private ScoreModelI scoreModel;
 
   private boolean nucleotide = false;
+  
+  private boolean dontRealign = false;
 
   /*
    * outputs
@@ -69,12 +71,13 @@ public class PaSiMapModel
    * @param modelName
    * @param params
    */
-  public PaSiMapModel(AlignmentViewport seqData, SequenceI[] sqs, boolean nuc,
+  public PaSiMapModel(AlignmentViewport seqData, SequenceI[] sqs, boolean nuc, boolean dontRealign,
           ScoreModelI modelName)
   {
     inputData = seqData;
     seqs = sqs;
     nucleotide = nuc;
+    this.dontRealign = dontRealign;
     scoreModel = modelName;
   }
 
@@ -85,6 +88,7 @@ public class PaSiMapModel
   public void calculate(PairwiseAlignPanel pap)
   {
     pasimap = new PaSiMap(inputData, scoreModel, pap);
+    pasimap.setDontRealign(dontRealign);
     pasimap.run(); // executes in same thread, wait for completion
 
     // Now find the component coordinates
@@ -258,4 +262,9 @@ public class PaSiMapModel
   {
     pasimap = data;
   }
+
+  public void setUseObservedAlignment(boolean useObservedAlignment)
+  {
+    dontRealign = useObservedAlignment;
+  }
 }