X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=69d32cb3efd05661837c3472816d5c38fc4b2e69;hb=d305e02d8b425bb501141ad32142aeb8572adc57;hp=f7ad5f6db537420408f4ce683b0c95a6c972d6bf;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index f7ad5f6..69d32cb 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,24 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
  * This file is part of Jalview.
- *
+ * 
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * 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/>.
+ * 
+ * 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;
 
 import java.util.*;
 
+import jalview.util.Format;
 import jalview.datamodel.*;
 
 /**
@@ -90,7 +94,7 @@ 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];
@@ -142,25 +146,31 @@ public class AAFrequency
           values['-']++;
         }
       }
-
-      for (v = 'A'; v < 'Z'; v++)
+      if (jSize == 1)
       {
-        if (values[v] < 2 || values[v] < maxCount)
+        maxResidue = String.valueOf(c);
+        maxCount = 1;
+      }
+      else
+      {
+        for (v = 'A'; v < 'Z'; v++)
         {
-          continue;
-        }
+          if (values[v] < 2 || values[v] < maxCount)
+          {
+            continue;
+          }
 
-        if (values[v] > maxCount)
-        {
-          maxResidue = String.valueOf((char) v);
-        }
-        else if (values[v] == maxCount)
-        {
-          maxResidue += String.valueOf((char) v);
+          if (values[v] > maxCount)
+          {
+            maxResidue = String.valueOf((char) v);
+          }
+          else if (values[v] == maxCount)
+          {
+            maxResidue += String.valueOf((char) v);
+          }
+          maxCount = values[v];
         }
-        maxCount = values[v];
       }
-
       if (maxResidue.length() == 0)
       {
         maxResidue = "-";
@@ -177,8 +187,13 @@ 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;
     }
   }
@@ -194,22 +209,24 @@ public class AAFrequency
    * @param width
    * @param ignoreGapsInConsensusCalculation
    * @param includeAllConsSymbols
+   * @param nseq
    */
   public static void completeConsensus(AlignmentAnnotation consensus,
           Hashtable[] hconsensus, int iStart, int width,
           boolean ignoreGapsInConsensusCalculation,
-          boolean includeAllConsSymbols)
+          boolean includeAllConsSymbols, long nseq)
   {
     completeConsensus(consensus, hconsensus, iStart, width,
-            ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // new
-                                                                            // char[]
+            ignoreGapsInConsensusCalculation, includeAllConsSymbols, null,
+            nseq); // new
+    // char[]
     // { 'A', 'C', 'G', 'T', 'U' });
   }
 
   public static void completeConsensus(AlignmentAnnotation consensus,
           Hashtable[] hconsensus, int iStart, int width,
           boolean ignoreGapsInConsensusCalculation,
-          boolean includeAllConsSymbols, char[] alphabet)
+          boolean includeAllConsSymbols, char[] alphabet, long nseq)
   {
     float tval, value;
     if (consensus == null || consensus.annotations == null
@@ -219,6 +236,26 @@ public class AAFrequency
       // initialised properly
       return;
     }
+    String fmtstr = "%3.1f";
+    int precision = 0;
+    while (nseq >= 10)
+    {
+      precision++;
+      nseq /= 10;
+    }
+    final Format fmt;
+    if (precision > 1)
+    {
+      // if (precision>2)
+      {
+        fmtstr = "%" + (2 + precision) + "." + (precision) + "f";
+      }
+      fmt = new Format(fmtstr);
+    }
+    else
+    {
+      fmt = null;
+    }
     for (int i = iStart; i < width; i++)
     {
       Hashtable hci;
@@ -229,7 +266,6 @@ public class AAFrequency
         consensus.annotations[i] = null;
         continue;
       }
-
       value = 0;
       Float fv;
       if (ignoreGapsInConsensusCalculation)
@@ -265,7 +301,7 @@ public class AAFrequency
             tval = profile[0][alphabet[c]] * 100f
                     / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
             mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
-                    + ((int) tval) + "%";
+                    + ((fmt != null) ? fmt.form(tval) : ((int) tval)) + "%";
           }
         }
         else
@@ -288,7 +324,9 @@ public class AAFrequency
                       * 100f
                       / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
               mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
-                      + " " + ((int) tval) + "%";
+                      + " "
+                      + ((fmt != null) ? fmt.form(tval) : ((int) tval))
+                      + "%";
               p++;
 
             }
@@ -298,7 +336,8 @@ public class AAFrequency
       }
       else
       {
-        mouseOver += ((int) value + "%");
+        mouseOver += ((fmt != null) ? fmt.form(value) : ((int) value))
+                + "%";
       }
       consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
               value);