JAL-98 Profile and ResidueCount moved from analysis to datamodel

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

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 8b42a01..30d5373 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -20,12 +20,14 @@
  */
 package jalview.analysis;
 
-import jalview.analysis.ResidueCount.SymbolCounts;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.Profile;
+import jalview.datamodel.ResidueCount;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.ResidueCount.SymbolCounts;
 import jalview.ext.android.SparseIntArray;
 import jalview.util.Comparison;
 import jalview.util.Format;
@@ -47,18 +49,8 @@ import java.util.List;
  */
 public class AAFrequency
 {
-  public static final String MAXCOUNT = "C";
-
-  public static final String MAXRESIDUE = "R";
-
-  public static final String PID_GAPS = "G";
-
-  public static final String PID_NOGAPS = "N";
-
   public static final String PROFILE = "P";
 
-  public static final String ENCODED_CHARS = "E";
-
   /*
    * Quick look-up of String value of char 'A' to 'Z'
    */
@@ -111,7 +103,9 @@ public class AAFrequency
    * 
    * @param sequences
    * @param start
+   *          start column (inclusive, base zero)
    * @param end
+   *          end column (exclusive)
    * @param result
    *          array in which to store profile per column
    * @param saveFullProfile
@@ -169,8 +163,7 @@ public class AAFrequency
         else
         {
           /*
-           * here we count a gap if the sequence doesn't
-           * reach this column (is that correct?)
+           * count a gap if the sequence doesn't reach this column
            */
           residueCounts.addGap();
         }
@@ -220,8 +213,8 @@ public class AAFrequency
   /**
    * Derive the consensus annotations to be added to the alignment for display.
    * This does not recompute the raw data, but may be called on a change in
-   * display options, such as 'show logo', which may in turn result in a change
-   * in the derived values.
+   * display options, such as 'ignore gaps', which may in turn result in a
+   * change in the derived values.
    * 
    * @param consensus
    *          the annotation row to add annotations to
@@ -274,7 +267,16 @@ public class AAFrequency
       String description = getTooltip(profile, value, showSequenceLogo,
               ignoreGaps, dp);
 
-      consensus.annotations[i] = new Annotation(profile.getModalResidue(),
+      String modalResidue = profile.getModalResidue();
+      if ("".equals(modalResidue))
+      {
+        modalResidue = "-";
+      }
+      else if (modalResidue.length() > 1)
+      {
+        modalResidue = "+";
+      }
+      consensus.annotations[i] = new Annotation(modalResidue,
               description, ' ', value);
     }
     // long elapsed = System.currentTimeMillis() - now;
@@ -317,15 +319,18 @@ public class AAFrequency
       String maxRes = profile.getModalResidue();
       if (maxRes.length() > 1)
       {
-        sb.append("[").append(maxRes).append("] ");
-        maxRes = "+";
+        sb.append("[").append(maxRes).append("]");
       }
       else
       {
-        sb.append(maxRes).append(" ");
+        sb.append(maxRes);
+      }
+      if (maxRes.length() > 0)
+      {
+        sb.append(" ");
+        Format.appendPercentage(sb, pid, dp);
+        sb.append("%");
       }
-      Format.appendPercentage(sb, pid, dp);
-      sb.append("%");
       description = sb.toString();
     }
     return description;
@@ -363,7 +368,6 @@ public class AAFrequency
     QuickSort.sort(values, symbols);
     int nextArrayPos = 2;
     int totalPercentage = 0;
-    // FIXME what if all gapped (divisor is zero)?
     final int divisor = ignoreGaps ? profile.getNonGapped() : profile
             .getHeight();