JAL-2195 JAL-2262 house keeping

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

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 5ecd644..6bdffe1 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -20,12 +20,15 @@
  */
 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.ProfileI;
+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 +50,8 @@ 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'
    */
@@ -72,13 +65,13 @@ public class AAFrequency
     }
   }
 
-  public static final Profile[] calculate(List<SequenceI> list,
+  public static final ProfileI[] calculate(List<SequenceI> list,
           int start, int end)
   {
     return calculate(list, start, end, false);
   }
 
-  public static final Profile[] calculate(List<SequenceI> sequences,
+  public static final ProfileI[] calculate(List<SequenceI> sequences,
           int start, int end, boolean profile)
   {
     SequenceI[] seqs = new SequenceI[sequences.size()];
@@ -94,7 +87,7 @@ public class AAFrequency
         }
       }
 
-      Profile[] reply = new Profile[width];
+      ProfileI[] reply = new ProfileI[width];
 
       if (end >= width)
       {
@@ -111,14 +104,16 @@ 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
    *          if true, store all symbol counts
    */
   public static final void calculate(final SequenceI[] sequences,
-          int start, int end, Profile[] result, boolean saveFullProfile)
+          int start, int end, ProfileI[] result, boolean saveFullProfile)
   {
     // long now = System.currentTimeMillis();
     int seqCount = sequences.length;
@@ -169,8 +164,7 @@ 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();
         }
@@ -179,7 +173,7 @@ public class AAFrequency
       int maxCount = residueCounts.getModalCount();
       String maxResidue = residueCounts.getResiduesForCount(maxCount);
       int gapCount = residueCounts.getGapCount();
-      Profile profile = new Profile(seqCount, gapCount, maxCount,
+      ProfileI profile = new Profile(seqCount, gapCount, maxCount,
               maxResidue);
 
       if (saveFullProfile)
@@ -220,8 +214,8 @@ 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
@@ -240,7 +234,7 @@ public class AAFrequency
    *          number of sequences
    */
   public static void completeConsensus(AlignmentAnnotation consensus,
-          Profile[] profiles, int iStart, int width, boolean ignoreGaps,
+          ProfileI[] profiles, int iStart, int width, boolean ignoreGaps,
           boolean showSequenceLogo, long nseq)
   {
     // long now = System.currentTimeMillis();
@@ -258,7 +252,7 @@ public class AAFrequency
 
     for (int i = iStart; i < width; i++)
     {
-      Profile profile;
+      ProfileI profile;
       if (i >= profiles.length || ((profile = profiles[i]) == null))
       {
         /*
@@ -274,7 +268,16 @@ 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;
@@ -299,7 +302,7 @@ public class AAFrequency
    *          the number of decimal places to format percentages to
    * @return
    */
-  static String getTooltip(Profile profile, float pid,
+  static String getTooltip(ProfileI profile, float pid,
           boolean showSequenceLogo, boolean ignoreGaps, int dp)
   {
     ResidueCount counts = profile.getCounts();
@@ -317,15 +320,18 @@ 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;
@@ -347,7 +353,7 @@ public class AAFrequency
    *          calculations
    * @return
    */
-  public static int[] extractProfile(Profile profile,
+  public static int[] extractProfile(ProfileI profile,
           boolean ignoreGaps)
   {
     int[] rtnval = new int[64];