JAL-1347 RNA Structure consensus follows the alignment viewport consensus rendering...

[jalview.git] / src / jalview / renderer / AnnotationRenderer.java

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index fcdd77d..09152d6 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -42,10 +42,22 @@ import com.stevesoft.pat.Regex;
 
 public class AnnotationRenderer
 {
+  /**
+   * flag indicating if timing and redraw parameter info should be output
+   */
+  private final boolean debugRedraw;
 
   public AnnotationRenderer()
   {
-    // TODO Auto-generated constructor stub
+    this(false);
+  }
+  /**
+   * Create a new annotation Renderer
+   * @param debugRedraw flag indicating if timing and redraw parameter info should be output
+   */
+  public AnnotationRenderer(boolean debugRedraw)
+  {
+    this.debugRedraw=debugRedraw;
   }
 
   public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
@@ -153,11 +165,12 @@ public class AnnotationRenderer
   /**
    * indicate if the renderer should only render the visible portion of the annotation given the current view settings
    */
-  private boolean useClip=false;
+  private boolean useClip=true;
   /**
    * master flag indicating if renderer should ever try to clip. not enabled for jalview 2.8.1 
    */
   private boolean canClip=false;
+  
   // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
   // av)
   public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
@@ -227,7 +240,7 @@ public class AnnotationRenderer
       }
       // TODO extend annotation row to enable dynamic and static profile data to
       // be stored
-      if (aa.groupRef == null && aa.sequenceRef == null && av_renderProfile)
+      if (aa.groupRef == null && aa.sequenceRef == null)
       {
         return AAFrequency.extractProfile(hconsensus[column],
                 av_ignoreGapsConsensus);
@@ -249,7 +262,7 @@ public class AnnotationRenderer
         // to
         // be stored
         if (aa.groupRef == null && aa.sequenceRef == null
-                && av_renderProfile && hStrucConsensus != null
+                && hStrucConsensus != null
                 && hStrucConsensus.length > column)
         {
           return StructureFrequency.extractProfile(hStrucConsensus[column],
@@ -282,6 +295,7 @@ public class AnnotationRenderer
           AlignViewportI av, Graphics g, int activeRow, int startRes,
           int endRes)
   {
+    long stime=System.currentTimeMillis();
     boolean usedFaded = false;
     // NOTES:
     // AnnotationPanel needs to implement: ImageObserver, access to
@@ -304,6 +318,8 @@ public class AnnotationRenderer
     boolean centreColLabels, centreColLabelsDef = av
             .getCentreColumnLabels();
     boolean scaleColLabel = false;
+    AlignmentAnnotation consensusAnnot=av.getAlignmentConsensusAnnotation(),structConsensusAnnot=av.getAlignmentStrucConsensusAnnotation();
+    boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
 
     BitSet graphGroupDrawn = new BitSet();
     int charOffset = 0; // offset for a label
@@ -317,6 +333,26 @@ public class AnnotationRenderer
     for (int i = 0; i < aa.length; i++)
     {
       AlignmentAnnotation row = aa[i];
+      {
+        // check if this is a consensus annotation row and set the display settings appropriately
+        // TODO: generalise this to have render styles for consensus/profile
+        // data
+        if (row.groupRef != null && row == row.groupRef.getConsensus())
+        {
+          renderHistogram = row.groupRef.isShowConsensusHistogram();
+          renderProfile = row.groupRef.isShowSequenceLogo();
+          normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
+        }
+        else if (row == consensusAnnot || row == structConsensusAnnot)
+        {
+          renderHistogram = av_renderHistogram;
+          renderProfile = av_renderProfile;
+          normaliseProfile = av_normaliseProfile;
+        } else {
+          renderHistogram = true;
+          // don't need to set render/normaliseProfile since they are not currently used in any other annotation track renderer
+        }
+      }
       Annotation[] row_annotations = row.annotations;
       if (!row.visible)
       {
@@ -617,6 +653,7 @@ public class AnnotationRenderer
         {
           if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
           {
+            // TODO: JAL-1291 revise rendering model so the graphGroup map is computed efficiently for all visible labels
             float groupmax = -999999, groupmin = 9999999;
             for (int gg = 0; gg < aa.length; gg++)
             {
@@ -659,7 +696,7 @@ public class AnnotationRenderer
         else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
         {
           drawBarGraph(g, row, row_annotations, startRes, endRes,
-                  row.graphMin, row.graphMax, y);
+                  row.graphMin, row.graphMax, y, renderHistogram,renderProfile,normaliseProfile);
         }
       }
     } else {
@@ -678,20 +715,27 @@ public class AnnotationRenderer
         y += aa[i].height;
       }
     }
-    if (canClip)
+    if (debugRedraw)
     {
-      if (clipst)
-      {
-        System.err.println("Start clip at : " + yfrom + " (index " + f_i
-                + ")");
-      }
-      if (clipend)
+      if (canClip)
       {
-        System.err
-                .println("End clip at : " + yto + " (index " + f_to + ")");
+        if (clipst)
+        {
+          System.err.println("Start clip at : " + yfrom + " (index " + f_i
+                  + ")");
+        }
+        if (clipend)
+        {
+          System.err.println("End clip at : " + yto + " (index " + f_to
+                  + ")");
+        }
       }
+      ;
+      System.err.println("Annotation Rendering time:"
+              + (System.currentTimeMillis() - stime));
     }
     ;
+
     return !usedFaded;
   }
 
@@ -888,7 +932,7 @@ public class AnnotationRenderer
 
   public void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
           Annotation[] aa_annotations, int sRes, int eRes, float min,
-          float max, int y)
+          float max, int y, boolean renderHistogram,boolean renderProfile,boolean normaliseProfile)
   {
     if (sRes > aa_annotations.length)
     {
@@ -912,23 +956,6 @@ public class AnnotationRenderer
 
     int column;
     int aaMax = aa_annotations.length - 1;
-    boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
-    // if (aa.autoCalculated && aa.label.startsWith("Consensus"))
-    {
-      // TODO: generalise this to have render styles for consensus/profile data
-      if (_aa.groupRef != null)
-      {
-        renderHistogram = _aa.groupRef.isShowConsensusHistogram();
-        renderProfile = _aa.groupRef.isShowSequenceLogo();
-        normaliseProfile = _aa.groupRef.isNormaliseSequenceLogo();
-      }
-      else
-      {
-        renderHistogram = av_renderHistogram;
-        renderProfile = av_renderProfile;
-        normaliseProfile = av_normaliseProfile;
-      }
-    }
     while (x < eRes - sRes)
     {
       column = sRes + x;