From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 8 Nov 2019 09:37:12 +0000 (+0000)
Subject: JAL-3081 restore annotation ordering from project (work in progress)
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=23d8036c19be1f358742c213d0251163e0ab67a0;p=jalview.git

JAL-3081 restore annotation ordering from project (work in progress)
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e3c42a7..092cf47 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -5442,7 +5442,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Sorts annotations and repaints the alignment
    */
   @Override
-  protected void sortAnnotations()
+  public void sortAnnotations()
   {
     alignPanel.sortAnnotations();
     alignPanel.paintAlignment(false, false);
@@ -5673,13 +5673,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   }
 
+  /**
+   * Sets the flag for whether auto-calculated annotations should be shown above
+   * other annotations. If the given value is the same as the current setting,
+   * simply returns false. Otherwise updates the setting, and returns true. If
+   * annotation sort order is currently set to 'Custom', this is changed to
+   * 'None', because 'Custom' ordering ignores all sort options.
+   */
   @Override
-  protected boolean setShowAutoCalculatedAbove(
-          boolean showAutoCalculatedAbove)
+  public boolean setShowAutoCalculatedAbove(boolean b)
   {
-    if (viewport.isShowAutocalculatedAbove() != showAutoCalculatedAbove)
+    if (viewport.isShowAutocalculatedAbove() != b)
     {
-      viewport.setShowAutocalculatedAbove(showAutoCalculatedAbove);
+      viewport.setShowAutocalculatedAbove(b);
 
       /*
        * change CUSTOM annotation ordering to NONE 
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 502ab9d..c606b9f 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.analysis.AnnotationSorter;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
@@ -821,14 +822,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * Sorts annotations according to currently selected preference
+   * Sorts annotations according to currently selected preferences. Does nothing
+   * if currently set to 'Custom' (manual) ordering.
    */
   void sortAnnotations()
   {
-    final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
-            av.isShowAutocalculatedAbove());
-    sorter.sort(getAlignment().getAlignmentAnnotation(),
-            av.getSortAnnotationsBy());
+    SequenceAnnotationOrder sortBy = av.getSortAnnotationsBy();
+    if (sortBy != SequenceAnnotationOrder.CUSTOM)
+    {
+      final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+              av.isShowAutocalculatedAbove());
+      sorter.sort(getAlignment().getAlignmentAnnotation(), sortBy);
+    }
   }
 
   /**
diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 02b405e..e15bb1a 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -24,6 +24,7 @@ import static jalview.math.RotatableMatrix.Axis.X;
 import static jalview.math.RotatableMatrix.Axis.Y;
 import static jalview.math.RotatableMatrix.Axis.Z;
 
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.analysis.PCA;
 import jalview.analysis.scoremodels.ScoreModels;
@@ -1479,6 +1480,8 @@ public class Jalview2XML
       view.setRenderGaps(av.isRenderGaps());
       view.setShowAnnotation(av.isShowAnnotation());
       view.setShowBoxes(av.getShowBoxes());
+      view.setShowAutocalcAbove(av.isShowAutocalculatedAbove());
+      view.setSortAnnotationsBy(av.getSortAnnotationsBy().name());
       view.setShowColourText(av.getColourText());
       view.setShowFullId(av.getShowJVSuffix());
       view.setRightAlignIds(av.isRightAlignIds());
@@ -4916,9 +4919,8 @@ public class Jalview2XML
 
     viewport.setColourText(safeBoolean(view.isShowColourText()));
 
-    viewport
-            .setConservationSelected(
-                    safeBoolean(view.isConservationSelected()));
+    viewport.setConservationSelected(
+            safeBoolean(view.isConservationSelected()));
     viewport.setIncrement(safeInt(view.getConsThreshold()));
     viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
     viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
@@ -4934,10 +4936,27 @@ public class Jalview2XML
     viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment()));
     viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation()));
 
-    viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
+    Boolean autocalcFirst = view.isShowAutocalcAbove();
+    if (autocalcFirst != null)
+    {
+      af.setShowAutoCalculatedAbove(autocalcFirst.booleanValue());
+    }
+    String sortBy = view.getSortAnnotationsBy();
+    if (sortBy != null)
+    {
+      try
+      {
+        viewport.setSortAnnotationsBy(
+                SequenceAnnotationOrder.valueOf(sortBy));
+      } catch (IllegalArgumentException e)
+      {
+        Cache.log.error(
+                "Invalid annotation sort specifier in project: " + sortBy);
+      }
+    }
 
+    viewport.setShowBoxes(safeBoolean(view.isShowBoxes()));
     viewport.setShowText(safeBoolean(view.isShowText()));
-
     viewport.setTextColour(new Color(safeInt(view.getTextCol1())));
     viewport.setTextColour2(new Color(safeInt(view.getTextCol2())));
     viewport.setThresholdTextColour(safeInt(view.getTextColThreshold()));
@@ -5177,6 +5196,7 @@ public class Jalview2XML
       // recompute any autoannotation
       af.alignPanel.updateAnnotation(false, true);
       reorderAutoannotation(af, al, autoAlan);
+      af.sortAnnotations();
       af.alignPanel.alignmentChanged();
     }
     else