Fix bug in zoom calculation. (#1426)

Fixing a rounding error  in calculateZoom.  Instead of rounding to the closest integer zoom level I believe
we should be rounding up to the nearest zoom level which can contain the given window.

This fixes a display issue with the ZoomSliderPanel.  I'm not 100% sure I understand the potential consequences
of changing thhis for other code that relies on it, so it would be good to have a second pair of eyes on it.
It seems intuitively to be correct now but it's possible the use case of "zoom level which is closest to the width of the given window"
was really what was wanted.  I haven't found any obvious issues with some manual testing of this change.

src/main/java/org/broad/igv/ui/panel/ReferenceFrame.java

@@ -29,7 +29,6 @@
  */
 package org.broad.igv.ui.panel;
 
-import org.broad.igv.logging.*;
 import org.broad.igv.Globals;
 import org.broad.igv.event.IGVEventBus;
 import org.broad.igv.event.ViewChange;
@@ -38,10 +37,11 @@
 import org.broad.igv.feature.Range;
 import org.broad.igv.feature.genome.Genome;
 import org.broad.igv.feature.genome.GenomeManager;
+import org.broad.igv.logging.LogManager;
+import org.broad.igv.logging.Logger;
 import org.broad.igv.prefs.Constants;
 import org.broad.igv.prefs.IGVPreferences;
 import org.broad.igv.prefs.PreferencesManager;
-import org.broad.igv.sam.InsertionManager;
 import org.broad.igv.sam.InsertionMarker;
 import org.broad.igv.ui.IGV;
 import org.broad.igv.ui.util.MessageUtils;
@@ -54,7 +54,7 @@
  */
 public class ReferenceFrame {
 
-    private static Logger log = LogManager.getLogger(ReferenceFrame.class);
+    private static final Logger log = LogManager.getLogger(ReferenceFrame.class);
 
     IGVEventBus eventBus;
 
@@ -712,7 +712,7 @@ private void beforeScaleZoom(Locus locus) {
     }
 
     /**
-     * Calculate the zoom level given start/end in bp.
+     * Calculate the minimum zoom level which can completely contain the given start/end in bp.
      * Doesn't change anything
      *
      * @param start
@@ -721,10 +721,14 @@ private void beforeScaleZoom(Locus locus) {
      */
     public int calculateZoom(double start, double end) {
         final double windowLength = Math.min(end - start, getChromosomeLength());
-        return (int) Math.round(Globals.log2((getChromosomeLength() / windowLength) * (((double) widthInPixels) / binsPerTile)));
+        final double exactZoom = Globals.log2((getChromosomeLength() / windowLength) * (((double) widthInPixels) / binsPerTile));
+        //round up so that you get a zoom level which contains the given window
+        return (int) Math.ceil(exactZoom);
     }
 
 
+
+
     private static int getChromosomeLength(String chrName) {
         Genome genome = getGenome();
 

src/main/java/org/broad/igv/ui/panel/ZoomSliderPanel.java

@@ -214,7 +214,7 @@ private void paintVisibilityThresholds(final Graphics2D transGraphics) {
                     .sorted()
                     .distinct()
                     .map(threshold -> this.getReferenceFrame().calculateZoom(0, threshold))
-                    .collect(Collectors.toList());
+                    .toList();
 
             transGraphics.setColor(TRANSPARENT_BLUE);
             Rectangle maxZoom = zoomLevelRects[zoomLevelRects.length - 1];