patch fixes JAL-1558

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

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 656cdcb..d028ade 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
 
@@ -91,7 +92,7 @@ public class AAFrequency
     Hashtable residueHash;
     int maxCount, nongap, i, j, v, jSize = sequences.length;
     String maxResidue;
-    char c;
+    char c='-';
     float percentage;
 
     int[] values = new int[255];
@@ -105,7 +106,7 @@ public class AAFrequency
       maxResidue = "";
       nongap = 0;
       values = new int[255];
-
+      
       for (j = 0; j < jSize; j++)
       {
         if (sequences[j] == null)
@@ -143,8 +144,11 @@ public class AAFrequency
           values['-']++;
         }
       }
-
-      for (v = 'A'; v < 'Z'; v++)
+      if (jSize==1)
+      {
+        maxResidue = String.valueOf(c);
+        maxCount=1;
+      } else {for (v = 'A'; v < 'Z'; v++)
       {
         if (values[v] < 2 || values[v] < maxCount)
         {
@@ -161,7 +165,7 @@ public class AAFrequency
         }
         maxCount = values[v];
       }
-
+      }
       if (maxResidue.length() == 0)
       {
         maxResidue = "-";
@@ -178,8 +182,12 @@ public class AAFrequency
       percentage = ((float) maxCount * 100) / jSize;
       residueHash.put(PID_GAPS, new Float(percentage));
 
-      percentage = ((float) maxCount * 100) / nongap;
+      if (nongap>0) {
+        // calculate for non-gapped too
+        percentage = ((float) maxCount * 100) / nongap;
+      }
       residueHash.put(PID_NOGAPS, new Float(percentage));
+      
       result[i] = residueHash;
     }
   }
@@ -222,16 +230,22 @@ public class AAFrequency
       return;
     }
     String fmtstr="%3.1f";
-    int precision=2;
-    while (nseq>100) {
+    int precision=0;
+    while (nseq>=10) {
       precision++;
       nseq/=10;
     }
-    if (precision>2)
+    final Format fmt;
+    if (precision>1)
     {
-      fmtstr = "%"+(2+precision)+"."+precision+"f";
+      //if (precision>2)
+      {
+        fmtstr = "%"+(2+precision)+"."+(precision)+"f";
+      }
+      fmt = new Format(fmtstr);
+    } else {
+      fmt = null;
     }
-    Format fmt = new Format(fmtstr);
     for (int i = iStart; i < width; i++)
     {
       Hashtable hci;
@@ -277,7 +291,7 @@ public class AAFrequency
             tval = profile[0][alphabet[c]] * 100f
                     / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
             mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
-                    + fmt.form(tval) + "%";
+                    + ((fmt!=null) ? fmt.form(tval) : ((int) tval)) + "%";
           }
         }
         else
@@ -300,7 +314,7 @@ public class AAFrequency
                       * 100f
                       / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
               mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
-                      + " " + fmt.form(tval) + "%";
+                      + " " + ((fmt!=null) ? fmt.form(tval) : ((int) tval)) + "%";
               p++;
 
             }
@@ -310,7 +324,7 @@ public class AAFrequency
       }
       else
       {
-        mouseOver += (fmt.form(value) + "%");
+        mouseOver += ((fmt!=null) ? fmt.form(value) : ((int) value)) + "%";
       }
       consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
               value);