From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 7 Aug 2024 16:16:25 +0000 (+0100)
Subject: JAL-4447 standardised title formula for reporting score model and other parameters... 
X-Git-Tag: Release_2_11_4_0~14^2~6^2~6
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a51b5f709d28d8a25a3c2c4596cbe086aa34ea43;p=jalview.git

JAL-4447 standardised title formula for reporting score model and other parameters for pairwise alignment, PCA, tree, and Pasimap
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 7f6646f..797e7ec 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3963,7 +3963,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     tp = new TreePanel(alignPanel, type, modelName, options);
     
-    frameTitle = formCalculationTitle(tp.getPanelTitle(),onSelection, viewport.getViewName(),this.title);
+    frameTitle = formCalculationTitle(tp.getPanelTitle(),onSelection,this.title);
     
     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
   }
@@ -3976,8 +3976,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param title - alignment frame title
    * @return <calculation Name> (?on region) from (?viewName of) alignment name 
    */
-  private String formCalculationTitle(String panelTitle,
-          boolean onSelection, String viewName, String title)
+  public String formCalculationTitle(String panelTitle,
+          boolean onSelection, String title)
   {
     String frameTitle = panelTitle;
     
@@ -3985,7 +3985,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     frameTitle += " from ";
 
-    if (viewName!=null)
+    if (viewport.getViewName()!=null)
     {
       frameTitle += viewport.getViewName() + " of ";
     }
diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index 711cac8..bd3c960 100644
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -749,13 +749,16 @@ public class CalculationChooser extends JPanel
       @Override
       public void run()
       {
+        String pairwise_alignment_title = af.formCalculationTitle(
+                MessageManager.getString("action.pairwise_alignment")
+                        + " with " + sm.getName(),
+                af.getViewport().getSelectionGroup() != null,
+                af.getTitle());
         JInternalFrame frame = new JInternalFrame();
         frame.setFrameIcon(null);
         frame.setContentPane(
                 new PairwiseAlignPanel(af.getViewport(), (ScoreMatrix) sm));
-        Desktop.addInternalFrame(frame,
-                MessageManager.getString("action.pairwise_alignment"), 600,
-                500);
+        Desktop.addInternalFrame(frame, pairwise_alignment_title, 600, 500);
       }
     }).start();
   }
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 3f103e2..570fc5d 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -82,6 +82,7 @@ public class PCAPanel extends GPCAPanel
 
   private boolean working;
 
+  String newPcaTitle = null;
   /**
    * Constructor given sequence data, a similarity (or distance) score model
    * name, and score calculation parameters
@@ -127,6 +128,12 @@ public class PCAPanel extends GPCAPanel
             .getScoreModel(modelName, ap);
     setPcaModel(
             new PCAModel(seqstrings, seqs, nucleotide, scoreModel, params));
+    
+    newPcaTitle = alignPanel.alignFrame.formCalculationTitle(
+            MessageManager.formatMessage("label.calc_title", "PCA",
+                    getPcaModel().getScoreModelName()),
+            selected, ap.alignFrame.getTitle());
+
     PaintRefresher.Register(this, av.getSequenceSetId());
 
     setRotatableCanvas(new RotatableCanvas(alignPanel));
@@ -209,9 +216,7 @@ public class PCAPanel extends GPCAPanel
     repaint();
     if (getParent() == null)
     {
-      Desktop.addInternalFrame(this,
-              MessageManager.formatMessage("label.calc_title", "PCA",
-                      getPcaModel().getScoreModelName()),
+      Desktop.addInternalFrame(this, newPcaTitle,
               475, 450);
       this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
     }
diff --git a/src/jalview/gui/PaSiMapPanel.java b/src/jalview/gui/PaSiMapPanel.java
index bf965a5..bb7bf11 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 String newPasimapTitle;
+
   /**
    * Constructor given sequence data, a similarity (or distance) score model
    * name, and score calculation parameters
@@ -132,6 +134,12 @@ public class PaSiMapPanel extends GPaSiMapPanel
     ScoreModelI scoreModel = ScoreModels.getInstance()
             .getScoreModel(modelName, ap);
     setPasimapModel(new PaSiMapModel(av, seqs, nucleotide, scoreModel));
+    
+    newPasimapTitle = alignPanel.alignFrame.formCalculationTitle(
+            MessageManager.formatMessage("label.calc_title", "PaSiMap",
+                    scoreModel.getName()),
+            selected, ap.alignFrame.getTitle());
+
     PaintRefresher.Register(this, av.getSequenceSetId());
 
     setRotatableCanvas(new RotatableCanvas(alignPanel));
@@ -266,8 +274,7 @@ public class PaSiMapPanel extends GPaSiMapPanel
     if (!getPasimapModel().isCancelled() && getParent() == null)
     {
       Desktop.addInternalFrame(this,
-              MessageManager.formatMessage("label.calc_title", "PaSiMap",
-                      ap.alignFrame.getTitle()),
+              newPasimapTitle,
               475, 450);
       this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
     }
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index e9b5ffa..bffaec5 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -335,7 +335,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
           double totscore)
   {
     System.out
-            .println("Pairwise alignment scaled similarity score matrix"+getPairwiseSimscoresAsString()+"\n");
+            .println("Pairwise alignment scaled similarity score matrix "+getPairwiseSimscoresAsString()+"\n");
 
     for (int i = 0; i < seqs.length; i++)
     {