Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

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

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 6bdffe1..17874e6 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -26,9 +26,11 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.Profile;
 import jalview.datamodel.ProfileI;
+import jalview.datamodel.Profiles;
+import jalview.datamodel.ProfilesI;
 import jalview.datamodel.ResidueCount;
-import jalview.datamodel.SequenceI;
 import jalview.datamodel.ResidueCount.SymbolCounts;
+import jalview.datamodel.SequenceI;
 import jalview.ext.android.SparseIntArray;
 import jalview.util.Comparison;
 import jalview.util.Format;
@@ -65,13 +67,13 @@ public class AAFrequency
     }
   }
 
-  public static final ProfileI[] calculate(List<SequenceI> list,
+  public static final ProfilesI calculate(List<SequenceI> list,
           int start, int end)
   {
     return calculate(list, start, end, false);
   }
 
-  public static final ProfileI[] calculate(List<SequenceI> sequences,
+  public static final ProfilesI calculate(List<SequenceI> sequences,
           int start, int end, boolean profile)
   {
     SequenceI[] seqs = new SequenceI[sequences.size()];
@@ -81,20 +83,19 @@ public class AAFrequency
       for (int i = 0; i < sequences.size(); i++)
       {
         seqs[i] = sequences.get(i);
-        if (seqs[i].getLength() > width)
+        int length = seqs[i].getLength();
+        if (length > width)
         {
-          width = seqs[i].getLength();
+          width = length;
         }
       }
 
-      ProfileI[] reply = new ProfileI[width];
-
       if (end >= width)
       {
         end = width;
       }
 
-      calculate(seqs, start, end, reply, profile);
+      ProfilesI reply = calculate(seqs, width, start, end, profile);
       return reply;
     }
   }
@@ -103,17 +104,17 @@ public class AAFrequency
    * Calculate the consensus symbol(s) for each column in the given range.
    * 
    * @param sequences
+   * @param width
+   *          the full width of the alignment
    * @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, ProfileI[] result, boolean saveFullProfile)
+  public static final ProfilesI calculate(final SequenceI[] sequences,
+          int width, int start, int end, boolean saveFullProfile)
   {
     // long now = System.currentTimeMillis();
     int seqCount = sequences.length;
@@ -121,6 +122,8 @@ public class AAFrequency
     int nucleotideCount = 0;
     int peptideCount = 0;
 
+    ProfileI[] result = new ProfileI[width];
+
     for (int column = start; column < end; column++)
     {
       /*
@@ -183,6 +186,7 @@ public class AAFrequency
 
       result[column] = profile;
     }
+    return new Profiles(result);
     // long elapsed = System.currentTimeMillis() - now;
     // System.out.println(elapsed);
   }
@@ -221,10 +225,10 @@ public class AAFrequency
    *          the annotation row to add annotations to
    * @param profiles
    *          the source consensus data
-   * @param iStart
-   *          start column
-   * @param width
-   *          end column
+   * @param startCol
+   *          start column (inclusive)
+   * @param endCol
+   *          end column (exclusive)
    * @param ignoreGaps
    *          if true, normalise residue percentages ignoring gaps
    * @param showSequenceLogo
@@ -234,12 +238,12 @@ public class AAFrequency
    *          number of sequences
    */
   public static void completeConsensus(AlignmentAnnotation consensus,
-          ProfileI[] profiles, int iStart, int width, boolean ignoreGaps,
+          ProfilesI profiles, int startCol, int endCol, boolean ignoreGaps,
           boolean showSequenceLogo, long nseq)
   {
     // long now = System.currentTimeMillis();
     if (consensus == null || consensus.annotations == null
-            || consensus.annotations.length < width)
+            || consensus.annotations.length < endCol)
     {
       /*
        * called with a bad alignment annotation row 
@@ -248,21 +252,21 @@ public class AAFrequency
       return;
     }
 
-    final int dp = getPercentageDp(nseq);
-
-    for (int i = iStart; i < width; i++)
+    for (int i = startCol; i < endCol; i++)
     {
-      ProfileI profile;
-      if (i >= profiles.length || ((profile = profiles[i]) == null))
+      ProfileI profile = profiles.get(i);
+      if (profile == null)
       {
         /*
          * happens if sequences calculated over were 
          * shorter than alignment width
          */
         consensus.annotations[i] = null;
-        continue;
+        return;
       }
 
+      final int dp = getPercentageDp(nseq);
+
       float value = profile.getPercentageIdentity(ignoreGaps);
 
       String description = getTooltip(profile, value, showSequenceLogo,
@@ -277,8 +281,8 @@ public class AAFrequency
       {
         modalResidue = "+";
       }
-      consensus.annotations[i] = new Annotation(modalResidue,
-              description, ' ', value);
+      consensus.annotations[i] = new Annotation(modalResidue, description,
+              ' ', value);
     }
     // long elapsed = System.currentTimeMillis() - now;
     // System.out.println(-elapsed);