merge

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

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index b810050..007d538 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -755,6 +755,7 @@ public class AlignmentSorter
               MessageManager
                       .getString("error.implementation_error_sortbyfeature"));
     }
+
     boolean ignoreScore = method != FEATURE_SCORE;
     StringBuffer scoreLabel = new StringBuffer();
     scoreLabel.append(start + stop + method);
@@ -769,6 +770,21 @@ public class AlignmentSorter
     {
       scoreLabel.append(groupLabels[i] == null ? "null" : groupLabels[i]);
     }
+
+    /*
+     * if resorting the same feature, toggle sort order
+     */
+    if (lastSortByFeatureScore == null
+            || !scoreLabel.toString().equals(lastSortByFeatureScore))
+    {
+      sortByFeatureScoreAscending = true;
+    }
+    else
+    {
+      sortByFeatureScoreAscending = !sortByFeatureScoreAscending;
+    }
+    lastSortByFeatureScore = scoreLabel.toString();
+
     SequenceI[] seqs = alignment.getSequencesArray();
 
     boolean[] hasScore = new boolean[seqs.length]; // per sequence score
@@ -855,7 +871,7 @@ public class AlignmentSorter
             labs[l] = (fs[l].getDescription() != null ? fs[l]
                     .getDescription() : fs[l].getType());
           }
-          jalview.util.QuickSort.sort(labs, ((Object[]) feats[i]));
+          QuickSort.sort(labs, ((Object[]) feats[i]));
         }
       }
       if (hasScore[i])
@@ -898,32 +914,27 @@ public class AlignmentSorter
           }
           else
           {
-            int nf = (feats[i] == null) ? 0
-                    : ((SequenceFeature[]) feats[i]).length;
-            // System.err.println("Sorting on Score: seq "+seqs[i].getName()+
-            // " Feats: "+nf+" Score : "+scores[i]);
+            // int nf = (feats[i] == null) ? 0
+            // : ((SequenceFeature[]) feats[i]).length;
+            // // System.err.println("Sorting on Score: seq " +
+            // seqs[i].getName()
+            // + " Feats: " + nf + " Score : " + scores[i]);
           }
         }
       }
-
-      jalview.util.QuickSort.sort(scores, seqs);
+      QuickSort.sortByDouble(scores, seqs, sortByFeatureScoreAscending);
     }
     else if (method == FEATURE_DENSITY)
     {
-
-      // break ties between equivalent numbers for adjacent sequences by adding
-      // 1/Nseq*i on the original order
-      double fr = 0.9 / (1.0 * seqs.length);
       for (int i = 0; i < seqs.length; i++)
       {
-        double nf;
-        scores[i] = (0.05 + fr * i)
-                + (nf = ((feats[i] == null) ? 0.0
-                        : 1.0 * ((SequenceFeature[]) feats[i]).length));
+        int featureCount = feats[i] == null ? 0
+                : ((SequenceFeature[]) feats[i]).length;
+        scores[i] = featureCount;
         // System.err.println("Sorting on Density: seq "+seqs[i].getName()+
-        // " Feats: "+nf+" Score : "+scores[i]);
+        // " Feats: "+featureCount+" Score : "+scores[i]);
       }
-      jalview.util.QuickSort.sort(scores, seqs);
+      QuickSort.sortByDouble(scores, seqs, sortByFeatureScoreAscending);
     }
     else
     {
@@ -933,24 +944,8 @@ public class AlignmentSorter
                 MessageManager.getString("error.not_yet_implemented"));
       }
     }
-    if (lastSortByFeatureScore == null
-            || !scoreLabel.toString().equals(lastSortByFeatureScore))
-    {
-      sortByFeatureScoreAscending = true;
-    }
-    else
-    {
-      sortByFeatureScoreAscending = !sortByFeatureScoreAscending;
-    }
-    if (sortByFeatureScoreAscending)
-    {
-      setOrder(alignment, seqs);
-    }
-    else
-    {
-      setReverseOrder(alignment, seqs);
-    }
-    lastSortByFeatureScore = scoreLabel.toString();
+
+    setOrder(alignment, seqs);
   }
 
 }