From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 16 Sep 2024 15:50:49 +0000 (+0100)
Subject: JAL-4392 autohide the secondary structure consensus annotation by setting AlignmentAn... 
X-Git-Tag: Release_2_11_4_0~5^2~4^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9e2fa8ea576657fb12aed3ad639b221c4354b000;p=jalview.git

JAL-4392 autohide the secondary structure consensus annotation by setting AlignmentAnnotation.hasData to false so it is not displayed in view
---

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 0fa80b3..dd5cb91 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -189,7 +189,7 @@ public class AAFrequency
 
       result[column] = profile;
     }
-    return new Profiles(result);
+    return new Profiles(seqCount,  result);
     // long elapsed = System.currentTimeMillis() - now;
     // jalview.bin.Console.outPrintln(elapsed);
   }
@@ -234,7 +234,7 @@ public class AAFrequency
     int seqCount = sequences.length;
 
     ProfileI[] result = new ProfileI[width];
-
+    int maxSSannotcount=0;
     for (int column = start; column < end; column++)
     {
 
@@ -290,8 +290,9 @@ public class AAFrequency
       }
 
       result[column] = profile;
+      maxSSannotcount=Math.max(maxSSannotcount, ssCount);
     }
-    return new Profiles(result);
+    return new Profiles(maxSSannotcount,result);
   }
 
   /**
@@ -405,7 +406,7 @@ public class AAFrequency
       */
       return;
     }
-
+    
     for (int i = startCol; i < endCol; i++)
     {
       ProfileI profile = profiles.get(i);
diff --git a/src/jalview/analysis/AlignmentAnnotationUtils.java b/src/jalview/analysis/AlignmentAnnotationUtils.java
index f5626ce..ac1bda0 100644
--- a/src/jalview/analysis/AlignmentAnnotationUtils.java
+++ b/src/jalview/analysis/AlignmentAnnotationUtils.java
@@ -131,7 +131,7 @@ public class AlignmentAnnotationUtils
          */
         {
           String rememberAs = calcId + "!" + displayLabel;
-          if (aa.visible && !addedToShown.contains(rememberAs))
+          if (aa.isForDisplay() && !addedToShown.contains(rememberAs)) // exclude noData annotations
           {
             if (!shownTypes.containsKey(calcId))
             {
@@ -214,7 +214,7 @@ public class AlignmentAnnotationUtils
     BitSet result = new BitSet();
     for (AlignmentAnnotation ann : annotations)
     {
-      if (ann.graph == AlignmentAnnotation.LINE_GRAPH && ann.visible)
+      if (ann.graph == AlignmentAnnotation.LINE_GRAPH && ann.visible) 
       {
         int gg = ann.graphGroup;
         if (gg > -1)
diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index ba74f67..0a3ce71 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -3072,7 +3072,7 @@ public class AlignmentUtils
 
         for (AlignmentAnnotation annot : aa)
         {
-          if (annot.visible)
+          if (annot.isForDisplay())
           {
             return annot;
           }
diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index aa71eb7..9a99b69 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -316,7 +316,7 @@ public class Dna
          * protein we need a smarter way to 'translate' without generating
          * invalid (unbalanced) structure annotation.
          */
-        if (annotation.autoCalculated || !annotation.visible
+        if (annotation.autoCalculated || !annotation.isForDisplay()
                 || annotation.isRNA())
         {
           continue;
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index d85c3d8..e31f292 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -289,6 +289,14 @@ public class AlignmentAnnotation
 
   /** is the row visible */
   public boolean visible = true;
+  
+  /**
+   * is there data for this annotation row to display ? if not then hide it!
+   * For rows that are only shown when data is present (default true)
+   */
+  public boolean hasData=true;
+
+
 
   public int graphGroup = -1;
 
@@ -764,6 +772,7 @@ public class AlignmentAnnotation
     this.label = annotation.label;
     this.padGaps = annotation.padGaps;
     this.visible = annotation.visible;
+    this.hasData = annotation.hasData;
     this.centreColLabels = annotation.centreColLabels;
     this.scaleColLabel = annotation.scaleColLabel;
     this.showAllColLabels = annotation.showAllColLabels;
@@ -1577,6 +1586,14 @@ public class AlignmentAnnotation
   {
     return graphMin < graphMax;
   }
+  
+  /**
+   * @return true if hasData and visible are true
+   */
+  public boolean isForDisplay()
+  {
+    return hasData && visible;
+  }
 
   /**
    * delete any columns in alignmentAnnotation that are hidden (including
diff --git a/src/jalview/datamodel/Profiles.java b/src/jalview/datamodel/Profiles.java
index 14eae51..0d28e69 100644
--- a/src/jalview/datamodel/Profiles.java
+++ b/src/jalview/datamodel/Profiles.java
@@ -22,11 +22,13 @@ package jalview.datamodel;
 
 public class Profiles implements ProfilesI
 {
-
+  int sourceCount;
+  
   private ProfileI[] profiles;
 
-  public Profiles(ProfileI[] p)
+  public Profiles(int sourceCount, ProfileI[] p)
   {
+    this.sourceCount=sourceCount;
     profiles = p;
   }
 
@@ -61,4 +63,9 @@ public class Profiles implements ProfilesI
     return profiles == null ? 0 : profiles.length - 1;
   }
 
+  @Override
+  public int getCount()
+  {
+    return sourceCount;
+  }
 }
diff --git a/src/jalview/datamodel/ProfilesI.java b/src/jalview/datamodel/ProfilesI.java
index 82398d9..29108c2 100644
--- a/src/jalview/datamodel/ProfilesI.java
+++ b/src/jalview/datamodel/ProfilesI.java
@@ -28,5 +28,11 @@ public interface ProfilesI
   int getStartColumn();
 
   int getEndColumn();
+  
+  /**
+   * 
+   * @return number of contributing sequences/annotation rows
+   */
+  int getCount();
 
 }
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 0f5a9e8..83bd980 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -405,7 +405,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         for (i = 0; i < al.getAlignmentAnnotation().length; i++)
         {
           AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
-          if (visibleOnly && !aa.visible)
+          if (visibleOnly && !aa.isForDisplay())
           {
             continue;
           }
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 27417f0..32298ca 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -192,7 +192,7 @@ public class AnnotationLabels extends JPanel
       for (int i = 0; i < aa.length; i++)
       {
         selectedRow = -1;
-        if (!aa[i].visible)
+        if (!aa[i].isForDisplay())
         {
           continue;
         }
@@ -1379,7 +1379,7 @@ public class AnnotationLabels extends JPanel
       for (int i = 0; i < aa.length; i++)
       {
         visible = true;
-        if (!aa[i].visible && !includeHidden)
+        if (!aa[i].isForDisplay() && !includeHidden)
         {
           hasHiddenRows = true;
           continue;
@@ -1387,7 +1387,7 @@ public class AnnotationLabels extends JPanel
         olY = y;
         // look ahead to next annotation
         for (nexAA = i + 1; nexAA < aa.length
-                && (!aa[nexAA].visible && includeHidden); nexAA++)
+                && (!aa[nexAA].isForDisplay() && includeHidden); nexAA++)
           ;
         y += aa[i].height;
         if (clip)
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index ea32684..747eac3 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -564,7 +564,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     for (int i = 0; i < aa.length; i++)
     {
-      if (aa[i].visible)
+      if (aa[i].isForDisplay())
       {
         height += aa[i].height;
       }
@@ -1231,7 +1231,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     int height = 0, lheight = 0;
     for (int i = 0; i < aa.length; i++)
     {
-      if (aa[i].visible)
+      if (aa[i].isForDisplay())
       {
         lheight = height;
         height += aa[i].height;
diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 9e9329a..2f5b919 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -565,7 +565,7 @@ public class AnnotationRenderer
       }
 
       Annotation[] row_annotations = row.annotations;
-      if (!row.visible)
+      if (!row.isForDisplay())
       {
         continue;
       }
diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 62b4579..7a53b1a 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -109,7 +109,7 @@ public class RNAHelicesColour extends ResidueColourScheme
     {
 
       // is this a sensible way of determining type of annotation?
-      if (annotations[i].visible && annotations[i].isRNA()
+      if (annotations[i].isForDisplay() && annotations[i].isRNA()
               && annotations[i].isValidStruc())
       {
         annotation = annotations[i];
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index f4201c1..a48616c 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -2213,7 +2213,7 @@ public abstract class AlignmentViewport
           jalview.bin.Console.errPrintln("Null annotation row: ignoring.");
           continue;
         }
-        if (!aa.visible)
+        if (!aa.isForDisplay())
         {
           continue;
         }
diff --git a/src/jalview/workers/SecondaryStructureConsensusThread.java b/src/jalview/workers/SecondaryStructureConsensusThread.java
index 945d99b..1263133 100644
--- a/src/jalview/workers/SecondaryStructureConsensusThread.java
+++ b/src/jalview/workers/SecondaryStructureConsensusThread.java
@@ -206,6 +206,8 @@ public class SecondaryStructureConsensusThread extends AlignCalcWorker
       {
         deriveGap(gap, hSSConsensus);
       }
+      
+      ssConsensus.hasData=hSSConsensus.getCount()>0;
     }
   }
 
diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 61ec3d0..94c9771 100644
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -98,7 +98,7 @@ public class StrucConsensusThread extends AlignCalcWorker
       {
         for (int i = 0; i < aa.length; i++)
         {
-          if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
+          if (aa[i].isForDisplay() && aa[i].isRNA() && aa[i].isValidStruc())
           {
             rnaStruc = aa[i];
             break;
diff --git a/test/jalview/datamodel/SequenceGroupTest.java b/test/jalview/datamodel/SequenceGroupTest.java
index 622ebb9..a99509a 100644
--- a/test/jalview/datamodel/SequenceGroupTest.java
+++ b/test/jalview/datamodel/SequenceGroupTest.java
@@ -260,7 +260,7 @@ public class SequenceGroupTest
             Collections.<SequenceI> emptyList(), 3, 12);
     PA.setValue(cons, "consSequence", new Sequence("s", "abc"));
     sg.getGroupColourScheme().setConservation(cons);
-    sg.getGroupColourScheme().setConsensus(new Profiles(null));
+    sg.getGroupColourScheme().setConsensus(new Profiles(0,null));
     sg.setDisplayBoxes(false);
     sg.setDisplayText(false);
     sg.setColourText(true);
diff --git a/test/jalview/renderer/ResidueShaderTest.java b/test/jalview/renderer/ResidueShaderTest.java
index 528abed..d5384d6 100644
--- a/test/jalview/renderer/ResidueShaderTest.java
+++ b/test/jalview/renderer/ResidueShaderTest.java
@@ -63,7 +63,7 @@ public class ResidueShaderTest
     profiles[2] = new Profile(4, 4, 0, "");
     profiles[3] = new Profile(4, 1, 2, "T");
     ResidueShader ccs = new ResidueShader(new PIDColourScheme());
-    ccs.setConsensus(new Profiles(profiles));
+    ccs.setConsensus(new Profiles(3,profiles));
 
     /*
      * no threshold
@@ -389,6 +389,13 @@ public class ResidueShaderTest
       {
         return 0;
       }
+      
+      @Override
+      public int getCount()
+      {
+        // TODO Auto-generated method stub
+        return 0;
+      }
 
     };
     return consensus;