JAL-958 JAL-966 refactor group/alignment associated conservation, consensus and logo...

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 54a1d6f..61b2950 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -117,4 +117,14 @@ public interface AlignViewportI
   void setHiddenRepSequences(
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
 
+  /**
+   * hides or shows dynamic annotation rows based on groups and group and alignment associated auto-annotation state flags
+   * apply the current group/autoannotation settings to the alignment view. 
+   * Usually you should call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to ensure the annotation panel bounds are set correctly.
+   * @param applyGlobalSettings - apply to all autoannotation rows or just the ones associated with the current visible region
+   * @param preserveNewGroupSettings - don't apply global settings to groups which don't already have group associated annotation
+   */
+  void updateGroupAnnotationSettings(boolean applyGlobalSettings,
+          boolean preserveNewGroupSettings);
+
 }

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index ba6d873..fffe55a 100644 (file)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -906,65 +906,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, Alignme
 
   public void updateAnnotation(boolean applyGlobalSettings)
   {
-    // TODO: this should be merged with other annotation update stuff - that
-    // sits on AlignViewport
-    boolean updateCalcs = false;
-    boolean conv = av.isShowGroupConservation();
-    boolean cons = av.isShowGroupConsensus();
-    boolean showprf = av.isShowSequenceLogo();
-    boolean showConsHist = av.isShowConsensusHistogram();
-
-    boolean sortg = true;
-
-    // remove old automatic annotation
-    // add any new annotation
-
-    ; // OrderedBy(av.alignment.getSequencesArray());
-    // intersect alignment annotation with alignment groups
-
-    AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation();
-    Hashtable oldrfs = new Hashtable();
-    if (aan != null)
-    {
-      for (int an = 0; an < aan.length; an++)
-      {
-        if (aan[an].autoCalculated && aan[an].groupRef != null)
-        {
-          oldrfs.put(aan[an].groupRef, aan[an].groupRef);
-          av.getAlignment().deleteAnnotation(aan[an]);
-          aan[an] = null;
-        }
-      }
-    }
-    if (av.getAlignment().getGroups()!= null)
-    {
-      for (SequenceGroup sg:av.getAlignment().getGroups())
-      {
-        updateCalcs = false;
-        if (applyGlobalSettings || !oldrfs.containsKey(sg))
-        {
-          // set defaults for this group's conservation/consensus
-          sg.setshowSequenceLogo(showprf);
-          sg.setShowConsensusHistogram(showConsHist);
-        }
-        if (conv)
-        {
-          updateCalcs = true;
-          av.getAlignment().addAnnotation(sg.getConservationRow(), 0);
-        }
-        if (cons)
-        {
-          updateCalcs = true;
-          av.getAlignment().addAnnotation(sg.getConsensus(), 0);
-        }
-        // refresh the annotation rows
-        if (updateCalcs)
-        {
-          sg.recalcConservation();
-        }
-      }
-    }
-    oldrfs.clear();
+    updateAnnotation(applyGlobalSettings, false);
+  }
+  public void updateAnnotation(boolean applyGlobalSettings, boolean preserveNewGroupSettings)
+  {
+    av.updateGroupAnnotationSettings(applyGlobalSettings, preserveNewGroupSettings);
     adjustAnnotationHeight();
   }
 

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index bcdd620..ad7b995 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1402,66 +1402,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
   public void updateAnnotation(boolean applyGlobalSettings, boolean preserveNewGroupSettings)
   {
-    // TODO: this should be merged with other annotation update stuff - that
-    // sits on AlignViewport
-    boolean updateCalcs = false;
-    boolean conv = av.isShowGroupConservation();
-    boolean cons = av.isShowGroupConsensus();
-    boolean showprf = av.isShowSequenceLogo();
-    boolean showConsHist = av.isShowConsensusHistogram();
-    boolean normLogo = av.isNormaliseSequenceLogo();
-
-    boolean sortg = true;
-
-    // remove old automatic annotation
-    // add any new annotation
-
-    // intersect alignment annotation with alignment groups
-
-    AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation();
-    Hashtable oldrfs = new Hashtable();
-    if (aan != null)
-    {
-      for (int an = 0; an < aan.length; an++)
-      {
-        if (aan[an].autoCalculated && aan[an].groupRef != null)
-        {
-          oldrfs.put(aan[an].groupRef, aan[an].groupRef);
-          av.getAlignment().deleteAnnotation(aan[an]);
-          aan[an] = null;
-        }
-      }
-    }
-    if (av.getAlignment().getGroups()!=null)
-    {
-      for (SequenceGroup sg:av.getAlignment().getGroups())
-      {
-        updateCalcs = false;
-        if (applyGlobalSettings || (!preserveNewGroupSettings && !oldrfs.containsKey(sg)))
-        {
-          // set defaults for this group's conservation/consensus
-          sg.setshowSequenceLogo(showprf);
-          sg.setShowConsensusHistogram(showConsHist);
-          sg.setNormaliseSequenceLogo(normLogo);
-        }
-        if (conv)
-        {
-          updateCalcs = true;
-          av.getAlignment().addAnnotation(sg.getConservationRow(), 0);
-        }
-        if (cons)
-        {
-          updateCalcs = true;
-          av.getAlignment().addAnnotation(sg.getConsensus(), 0);
-        }
-        // refresh the annotation rows
-        if (updateCalcs)
-        {
-          sg.recalcConservation();
-        }
-      }
-    }
-    oldrfs.clear();
+    av.updateGroupAnnotationSettings(applyGlobalSettings, preserveNewGroupSettings);
     adjustAnnotationHeight();
   }
 

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 27af11e..4ea4656 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -40,6 +40,7 @@ import jalview.workers.AlignCalcManager;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
+import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -1445,4 +1446,73 @@ public abstract class AlignmentViewport implements AlignViewportI
     }
     return height;
   }
+
+  @Override
+  public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
+          boolean preserveNewGroupSettings)
+  {
+    boolean updateCalcs = false;
+    boolean conv = isShowGroupConservation();
+    boolean cons = isShowGroupConsensus();
+    boolean showprf = isShowSequenceLogo();
+    boolean showConsHist = isShowConsensusHistogram();
+    boolean normLogo = isNormaliseSequenceLogo();
+
+    /**
+     * TODO reorder the annotation rows according to group/sequence ordering on alignment
+     */
+    boolean sortg = true;
+
+    // remove old automatic annotation
+    // add any new annotation
+
+    // intersect alignment annotation with alignment groups
+
+    AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
+    List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
+    if (aan != null)
+    {
+      for (int an = 0; an < aan.length; an++)
+      {
+        if (aan[an].autoCalculated && aan[an].groupRef != null)
+        {
+          oldrfs.add(aan[an].groupRef);
+          alignment.deleteAnnotation(aan[an]);
+          aan[an] = null;
+        }
+      }
+    }
+    if (alignment.getGroups() != null)
+    {
+      for (SequenceGroup sg : alignment.getGroups())
+      {
+        updateCalcs = false;
+        if (applyGlobalSettings
+                || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
+        {
+          // set defaults for this group's conservation/consensus
+          sg.setshowSequenceLogo(showprf);
+          sg.setShowConsensusHistogram(showConsHist);
+          sg.setNormaliseSequenceLogo(normLogo);
+        }
+        if (conv)
+        {
+          updateCalcs = true;
+          alignment.addAnnotation(sg.getConservationRow(), 0);
+        }
+        if (cons)
+        {
+          updateCalcs = true;
+          alignment.addAnnotation(sg.getConsensus(), 0);
+        }
+        // refresh the annotation rows
+        if (updateCalcs)
+        {
+          sg.recalcConservation();
+        }
+      }
+    }
+    oldrfs.clear();
+  }
+
 }