JAL-1933 show occupancy in tooltip for row

[jalview.git] / src / jalview / analysis / AAFrequency.java

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index b5dab6f..b806355 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -37,6 +37,7 @@ import jalview.util.Format;
 import jalview.util.MappingUtils;
 import jalview.util.QuickSort;
 
+import java.awt.Color;
 import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.List;
@@ -67,8 +68,8 @@ public class AAFrequency
     }
   }
 
-  public static final ProfilesI calculate(List<SequenceI> list,
-          int start, int end)
+  public static final ProfilesI calculate(List<SequenceI> list, int start,
+          int end)
   {
     return calculate(list, start, end, false);
   }
@@ -291,7 +292,7 @@ public class AAFrequency
   /**
    * Derive the gap count annotation row.
    * 
-   * @param consensus
+   * @param gaprow
    *          the annotation row to add annotations to
    * @param profiles
    *          the source consensus data
@@ -300,12 +301,11 @@ public class AAFrequency
    * @param endCol
    *          end column (exclusive)
    */
-  public static void completeGapAnnot(AlignmentAnnotation consensus,
+  public static void completeGapAnnot(AlignmentAnnotation gaprow,
           ProfilesI profiles, int startCol, int endCol, long nseq)
   {
-    // long now = System.currentTimeMillis();
-    if (consensus == null || consensus.annotations == null
-            || consensus.annotations.length < endCol)
+    if (gaprow == null || gaprow.annotations == null
+            || gaprow.annotations.length < endCol)
     {
       /*
        * called with a bad alignment annotation row 
@@ -313,7 +313,10 @@ public class AAFrequency
        */
       return;
     }
-
+    // always set ranges again
+    gaprow.graphMax = nseq;
+    gaprow.graphMin = 0;
+    double scale = 0.8/nseq;
     for (int i = startCol; i < endCol; i++)
     {
       ProfileI profile = profiles.get(i);
@@ -323,18 +326,18 @@ public class AAFrequency
          * happens if sequences calculated over were 
          * shorter than alignment width
          */
-        consensus.annotations[i] = null;
+        gaprow.annotations[i] = null;
         return;
       }
 
-      final int gapped = profile.getGapped();
+      final int gapped = profile.getNonGapped();
 
       String description = "" + gapped;
 
-      consensus.annotations[i] = new Annotation(gapped);
+      gaprow.annotations[i] = new Annotation("", description,
+              '\0', gapped, jalview.util.ColorUtils.bleachColour(
+                      Color.DARK_GRAY, (float) scale * gapped));
     }
-    // long elapsed = System.currentTimeMillis() - now;
-    // System.out.println(-elapsed);
   }
 
   /**
@@ -406,8 +409,7 @@ public class AAFrequency
    *          calculations
    * @return
    */
-  public static int[] extractProfile(ProfileI profile,
-          boolean ignoreGaps)
+  public static int[] extractProfile(ProfileI profile, boolean ignoreGaps)
   {
     int[] rtnval = new int[64];
     ResidueCount counts = profile.getCounts();