From 1d95f81a9aa2f30581fe4f63be4e387f52d60885 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 19 Aug 2019 17:30:56 +0100
Subject: [PATCH] JAL-3364 align split frame sequence panels with wrapped view
 scale left

---
 src/jalview/gui/AlignmentPanel.java  |   10 +++++++---
 src/jalview/gui/FontChooser.java     |    5 -----
 src/jalview/gui/IdwidthAdjuster.java |    1 +
 src/jalview/gui/SeqPanel.java        |    2 --
 src/jalview/gui/SplitFrame.java      |   34 +++++++++++++++++++++-------------
 5 files changed, 29 insertions(+), 23 deletions(-)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index cd31bed..716c237 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -565,9 +565,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   /**
    * update alignment layout for viewport settings
-   * 
-   * @param wrap
-   *          DOCUMENT ME!
    */
   public void updateLayout()
   {
@@ -614,6 +611,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     idSpaceFillerPanel1.setVisible(!wrap);
 
+    AlignViewportI complement = av.getCodingComplement();
+    if (complement != null)
+    {
+      SplitFrame splitFrame = (SplitFrame) alignFrame
+              .getSplitViewContainer();
+      splitFrame.adjustLayout();
+    }
     repaint();
   }
 
diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java
index 92cc4c6..1b9ec1e 100755
--- a/src/jalview/gui/FontChooser.java
+++ b/src/jalview/gui/FontChooser.java
@@ -190,9 +190,7 @@ public class FontChooser extends GFontChooser
               .getCodingComplement()).antiAlias = ap.av.antiAlias;
       SplitFrame sv = (SplitFrame) ap.alignFrame.getSplitViewContainer();
       sv.adjustLayout();
-      sv.repaint();
     }
-
   }
 
   /**
@@ -251,7 +249,6 @@ public class FontChooser extends GFontChooser
         SplitFrame splitFrame = (SplitFrame) ap.alignFrame
                 .getSplitViewContainer();
         splitFrame.adjustLayout();
-        splitFrame.repaint();
       }
     }
 
@@ -346,7 +343,6 @@ public class FontChooser extends GFontChooser
         SplitFrame splitFrame = (SplitFrame) ap.alignFrame
                 .getSplitViewContainer();
         splitFrame.adjustLayout();
-        splitFrame.repaint();
       }
     }
 
@@ -430,7 +426,6 @@ public class FontChooser extends GFontChooser
     final SplitFrame splitFrame = (SplitFrame) ap.alignFrame
             .getSplitViewContainer();
     splitFrame.adjustLayout();
-    splitFrame.repaint();
   }
 
   /**
diff --git a/src/jalview/gui/IdwidthAdjuster.java b/src/jalview/gui/IdwidthAdjuster.java
index 0cffc3b..368b7b8 100755
--- a/src/jalview/gui/IdwidthAdjuster.java
+++ b/src/jalview/gui/IdwidthAdjuster.java
@@ -94,6 +94,7 @@ public class IdwidthAdjuster extends JPanel
     {
       viewport.getCodingComplement().setIdWidth(viewport.getIdWidth());
       SplitFrame sf = (SplitFrame) ap.alignFrame.getSplitViewContainer();
+      sf.adjustLayout();
       sf.repaint();
     }
 
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 1176df5..d64a034 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1253,7 +1253,6 @@ public class SeqPanel extends JPanel
             SplitFrame splitFrame = (SplitFrame) ap.alignFrame
                     .getSplitViewContainer();
             splitFrame.adjustLayout();
-            splitFrame.repaint();
           }
         }
       }
@@ -1287,7 +1286,6 @@ public class SeqPanel extends JPanel
             SplitFrame splitFrame = (SplitFrame) ap.alignFrame
                     .getSplitViewContainer();
             splitFrame.adjustLayout();
-            splitFrame.repaint();
           }
         }
       }
diff --git a/src/jalview/gui/SplitFrame.java b/src/jalview/gui/SplitFrame.java
index b1eb6b8..fd0ec63 100644
--- a/src/jalview/gui/SplitFrame.java
+++ b/src/jalview/gui/SplitFrame.java
@@ -161,26 +161,32 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
    */
   public void adjustLayout()
   {
+    final AlignViewport topViewport = ((AlignFrame) getTopFrame()).viewport;
+    final AlignViewport bottomViewport = ((AlignFrame) getBottomFrame()).viewport;
+
     /*
-     * Ensure sequence ids are the same width so sequences line up
+     * Ensure sequence ids are the same width so sequences line up;
+     * reduce the idwidth of a panel with a longer wrapped left scale
      */
-    int w1 = ((AlignFrame) getTopFrame()).getViewport().getIdWidth();
-    int w2 = ((AlignFrame) getBottomFrame()).getViewport().getIdWidth();
+    int w1 = topViewport.getIdWidth();
+    int w2 = bottomViewport.getIdWidth();
+    int topScaleLeft = topViewport.getWrapAlignment()
+            ? ((AlignFrame) getTopFrame()).alignPanel
+                    .getSeqPanel().seqCanvas.getLabelWidthWest()
+            : 0;
+    int bottomScaleLeft = bottomViewport.getWrapAlignment()
+            ? ((AlignFrame) getBottomFrame()).alignPanel
+                    .getSeqPanel().seqCanvas.getLabelWidthWest()
+            : 0;
     int w3 = Math.max(w1, w2);
-    if (w1 != w3)
-    {
-      ((AlignFrame) getTopFrame()).getViewport().setIdWidth(w3);
-    }
-    if (w2 != w3)
-    {
-      ((AlignFrame) getBottomFrame()).getViewport().setIdWidth(w3);
-    }
+    topViewport
+            .setIdWidth(w3 - Math.max(0, topScaleLeft - bottomScaleLeft));
+    bottomViewport
+            .setIdWidth(w3 - Math.max(0, bottomScaleLeft - topScaleLeft));
 
     /*
      * Scale protein to either 1 or 3 times character width of dna
      */
-    final AlignViewport topViewport = ((AlignFrame) getTopFrame()).viewport;
-    final AlignViewport bottomViewport = ((AlignFrame) getBottomFrame()).viewport;
     final AlignmentI topAlignment = topViewport.getAlignment();
     final AlignmentI bottomAlignment = bottomViewport.getAlignment();
     AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport
@@ -192,6 +198,8 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
       int scale = protein.isScaleProteinAsCdna() ? 3 : 1;
       protein.setCharWidth(scale * cdna.getViewStyle().getCharWidth());
     }
+
+    repaint();
   }
 
   /**
-- 
1.7.10.2