JAL-1517 fix copyright for 2.8.2

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

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index de65412..0f53882 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,25 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.
+ * 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.*;
 
 /**
@@ -91,7 +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];
@@ -105,7 +108,7 @@ public class AAFrequency
       maxResidue = "";
       nongap = 0;
       values = new int[255];
-
+      
       for (j = 0; j < jSize; j++)
       {
         if (sequences[j] == null)
@@ -143,8 +146,11 @@ 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 +167,7 @@ public class AAFrequency
         }
         maxCount = values[v];
       }
-
+      }
       if (maxResidue.length() == 0)
       {
         maxResidue = "-";
@@ -178,8 +184,12 @@ 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;
     }
   }
@@ -195,14 +205,15 @@ 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
+            ignoreGapsInConsensusCalculation, includeAllConsSymbols, null, nseq); // new
                                                                             // char[]
     // { 'A', 'C', 'G', 'T', 'U' });
   }
@@ -210,7 +221,7 @@ public class AAFrequency
   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
@@ -220,6 +231,23 @@ 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;
@@ -230,7 +258,6 @@ public class AAFrequency
         consensus.annotations[i] = null;
         continue;
       }
-
       value = 0;
       Float fv;
       if (ignoreGapsInConsensusCalculation)
@@ -266,7 +293,7 @@ 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
@@ -289,7 +316,7 @@ 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++;
 
             }
@@ -299,7 +326,7 @@ public class AAFrequency
       }
       else
       {
-        mouseOver += ((int) value + "%");
+        mouseOver += ((fmt!=null) ? fmt.form(value) : ((int) value)) + "%";
       }
       consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
               value);