From 39ef2c483d62e04129703d6acff8a594cc7e9b16 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 7 Aug 2024 15:07:51 +0100
Subject: [PATCH] JAL-4446 better reporting of ETA estimation - particularly
 for large alignments

---
 src/jalview/gui/PaSiMapPanel.java       |   27 +++++++++++++++++++++------
 src/jalview/gui/PairwiseAlignPanel.java |   31 +++++++++++++++++++++----------
 2 files changed, 42 insertions(+), 16 deletions(-)

diff --git a/src/jalview/gui/PaSiMapPanel.java b/src/jalview/gui/PaSiMapPanel.java
index edf7deb..bc6e477 100644
--- a/src/jalview/gui/PaSiMapPanel.java
+++ b/src/jalview/gui/PaSiMapPanel.java
@@ -687,15 +687,27 @@ public class PaSiMapPanel extends GPaSiMapPanel
       return;
     }
     int max=pBar.getMaximum();
+    updateProgressBarEta(minutes);
+    pBar.setMaximum(max);
+    pBar.setValue(progress);
+  }
+    
+  public void updateProgressBarEta(double minutes)
+  {
+    JProgressBar pBar = progressBar.getProgressBar(progId);
+
+    if (pBar == null)
+    {
+      return;
+    }
     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);
-
+                                    : ((int) Math.ceil(minutes))
+                                            + " mins. to go)")));
   }
+  
   public void updateProgressBar(int progress)
   {
     JProgressBar pBar = progressBar.getProgressBar(progId);
@@ -724,13 +736,16 @@ public class PaSiMapPanel extends GPaSiMapPanel
       {
         if (PairwiseAlignPanel.PROGRESS.equals(pcEvent.getPropertyName()))
         {
-          updateProgressBarWithEta((int) pcEvent.getNewValue(), pap.getEta());
-          
+            updateProgressBar((int) pcEvent.getNewValue());
         }
         else if (PairwiseAlignPanel.TOTAL.equals(pcEvent.getPropertyName()))
         {
           updateProgressBar((int) pcEvent.getNewValue(), 0);
         }
+        else if (PairwiseAlignPanel.ETA.equals(pcEvent.getPropertyName()))
+        {
+          updateProgressBarEta((double) pcEvent.getNewValue());
+        }
       }
     });
   }
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index ca97aaf..9071c31 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -70,11 +70,13 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
   public static final String PROGRESS = "progress";
 
+  protected static final String ETA = "eta_in_minutes";
+
   private volatile boolean cancelled;
   
-  private int total;
+  private long total;
 
-  private int progress;
+  private long progress;
 
   private SequenceGroup selection;
 
@@ -138,7 +140,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     this.GAP_EXTEND_COST = gapExtendCost;
     this.endGaps = endGaps;
     this.selection = selection;
-    this.total = MiscMath.combinations(av.getAlignment().getHeight(), 2);
+    this.total = av.getAlignment().getHeight();
+    total = (total*total-total)/2;
     this.scoreMatrix = scoreMatrix;
     if (run)
     {
@@ -196,11 +199,11 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     float[][] alignmentScores = new float[seqs.length][seqs.length];
     double totscore = 0D;
     int count = seqs.length;
-
+    int fracprogress=0;
     boolean first = true;
     long time=System.currentTimeMillis();
-    progress = 0;
-    firePropertyChange(TOTAL, 0, total);
+    long fprogress = 0;
+    firePropertyChange(TOTAL, 0, 500);
 
     for (int i = 1; i < count; i++)
     {
@@ -261,12 +264,20 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
           sequences.add(as.getAlignedSeq1());
           sequences.add(as.getAlignedSeq2());
         }
-        firePropertyChange(PROGRESS, progress, ++progress);
+        ++fprogress;
       }
       if (i<count)
       {
-        // remaining time in minutes ~ is (elapsed time)/ 0.5*(n*n)
-        etime = 0.0001*(total-progress)*(System.currentTimeMillis()-time)/progress;
+        int newfracprogress=(int) Math.floor((500.0*(double)fprogress)/((double)total));
+        // need to fake a different starting value until we have an ETA calculated
+        firePropertyChange(PROGRESS, fracprogress, newfracprogress);
+        fracprogress = newfracprogress;
+        progress=fprogress;
+        // remaining time in minutes ~ is remaining*(elapsed time)/progress;
+        double lasteta=etime;
+        double rate = ((double)(System.currentTimeMillis()-time))/(double)progress;
+        etime = rate*(total-progress)/60000;
+        firePropertyChange(ETA, 0,etime);
       }
     }
     alignmentScores[count - 1][count - 1] = Float.NaN;
@@ -284,7 +295,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
   
   public boolean hasEta()
   {
-    return !Double.isNaN(etime);
+    return etime>0;
   }
   public double getEta()
   {
-- 
1.7.10.2