From 01dd0eed037513b5b2dbcd499dfd0cdd957cf0bd Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 5 Aug 2024 18:39:23 +0100
Subject: [PATCH] JAL-4446 calculate and report PaSiMap ETA in progress bar

---
 src/jalview/gui/PaSiMapPanel.java       |   49 +++++++++++++------------------
 src/jalview/gui/PairwiseAlignPanel.java |   41 ++++++++++++++++++++++++--
 2 files changed, 59 insertions(+), 31 deletions(-)

diff --git a/src/jalview/gui/PaSiMapPanel.java b/src/jalview/gui/PaSiMapPanel.java
index 2a6d6a9..98a366e 100644
--- a/src/jalview/gui/PaSiMapPanel.java
+++ b/src/jalview/gui/PaSiMapPanel.java
@@ -181,7 +181,7 @@ public class PaSiMapPanel extends GPaSiMapPanel
   {
     working = true;
     progId = System.currentTimeMillis();
-    progressBar = this;
+    progressBar = new jalview.gui.ProgressBar(statusPanel, statusBar);
     String message = MessageManager
             .getString("label.pasimap_recalculating");
     if (getParent() == null)
@@ -657,6 +657,24 @@ public class PaSiMapPanel extends GPaSiMapPanel
     updateProgressBar(progress);
   }
 
+  public void updateProgressBarWithEta(int progress, double minutes)
+  {
+    JProgressBar pBar = progressBar.getProgressBar(progId);
+
+    if (pBar == null)
+    {
+      return;
+    }
+    int max=pBar.getMaximum();
+    progressBar.setProgressBarMessage(progId,
+            progressBar.getMessage(progId) + " ("
+                    + (Double.isNaN(minutes) ? " .. working ..)"
+                            : (minutes < 1.0 ? "Less than a minute)"
+                                    : ((int) Math.ceil(minutes)) + " mins. to go)")));
+    pBar.setMaximum(max);
+    pBar.setValue(progress);
+
+  }
   public void updateProgressBar(int progress)
   {
     JProgressBar pBar = progressBar.getProgressBar(progId);
@@ -685,7 +703,8 @@ public class PaSiMapPanel extends GPaSiMapPanel
       {
         if (PairwiseAlignPanel.PROGRESS.equals(pcEvent.getPropertyName()))
         {
-          updateProgressBar((int) pcEvent.getNewValue());
+          updateProgressBarWithEta((int) pcEvent.getNewValue(), pap.getEta());
+          
         }
         else if (PairwiseAlignPanel.TOTAL.equals(pcEvent.getPropertyName()))
         {
@@ -700,32 +719,6 @@ public class PaSiMapPanel extends GPaSiMapPanel
           final IProgressIndicatorHandler handler)
   {
     progressBar.registerHandler(id, handler);
-    // if (progressBarHandlers == null ||
-    // !progressBars.contains(Long.valueOf(id)))
-    // {
-    // throw new
-    // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
-    // }
-    // progressBarHandlers.put(Long.valueOf(id), handler);
-    // final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
-    // if (handler.canCancel())
-    // {
-    // JButton cancel = new JButton(
-    // MessageManager.getString("action.cancel"));
-    // final IProgressIndicator us = this;
-    // cancel.addActionListener(new ActionListener()
-    // {
-    //
-    // @Override
-    // public void actionPerformed(ActionEvent e)
-    // {
-    // handler.cancelActivity(id);
-    // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
-    // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
-    // }
-    // });
-    // progressPanel.add(cancel, BorderLayout.EAST);
-    // }
   }
 
   /**
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 77ec0f5..4c3b30c 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -84,6 +84,11 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
   private ScoreMatrix scoreMatrix;
 
   /**
+   * remaining time
+   */
+  private double etime=Double.NaN;
+
+  /**
    * Creates a new PairwiseAlignPanel object.
    * 
    * @param viewport
@@ -191,7 +196,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     int count = seqs.length;
 
     boolean first = true;
-
+    long time=System.currentTimeMillis();
     progress = 0;
     firePropertyChange(TOTAL, 0, total);
 
@@ -251,6 +256,11 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         }
         firePropertyChange(PROGRESS, progress, ++progress);
       }
+      if (i<count)
+      {
+        // remaining time in minutes ~ is (elapsed time)/ 0.5*(n*n)
+        etime = 0.0001*(total-progress)*(System.currentTimeMillis()-time)/progress;
+      }
     }
     alignmentScores[count - 1][count - 1] = Float.NaN;
 
@@ -264,6 +274,22 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
     alignmentOutput = sb.toString();
   }
+  
+  public boolean hasEta()
+  {
+    return !Double.isNaN(etime);
+  }
+  public double getEta()
+  {
+    return etime;
+  }
+  /**
+   * stops the run() loop ASAP
+   */
+  public void cancel()
+  {
+    cancelled=true;
+  }
 
   public float[][] getScores()
   {
@@ -291,7 +317,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
           double totscore)
   {
     System.out
-            .println("Pairwise alignment scaled similarity score matrix\n");
+            .println("Pairwise alignment scaled similarity score matrix"+getPairwiseSimscoresAsString()+"\n");
 
     for (int i = 0; i < seqs.length; i++)
     {
@@ -324,6 +350,15 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
     jalview.bin.Console.outPrintln("\n");
   }
+  
+  public String getPairwiseSimscoresAsString()
+  {
+    return (scoreMatrix != null
+            ? " (" + scoreMatrix.getName() + ", open=" + GAP_OPEN_COST
+                    + ", extend=" + GAP_EXTEND_COST
+                    + (endGaps ? ", with endGaps" : ", no endGaps") + ")"
+            : "");
+  }
 
   /**
    * DOCUMENT ME!
@@ -345,7 +380,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 
     Desktop.addInternalFrame(af,
-            MessageManager.getString("label.pairwise_aligned_sequences"),
+            MessageManager.getString("label.pairwise_aligned_sequences")+" "+getPairwiseSimscoresAsString(),
             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
   }
 
-- 
1.7.10.2