From 948228d480dcd77e194de69b393dfe5f29f51bb3 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 2 Sep 2013 18:09:08 +0100
Subject: [PATCH] JAL-1373 generate percentages with appropriate precision

---
 src/jalview/analysis/AAFrequency.java        |   19 +++++++++++++++----
 src/jalview/analysis/StructureFrequency.java |   17 +++++++++++++++--
 2 files changed, 30 insertions(+), 6 deletions(-)

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 33660b5..656cdcb 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -19,6 +19,7 @@ package jalview.analysis;
 
 import java.util.*;
 
+import jalview.util.Format;
 import jalview.datamodel.*;
 
 /**
@@ -220,6 +221,17 @@ public class AAFrequency
       // initialised properly
       return;
     }
+    String fmtstr="%3.1f";
+    int precision=2;
+    while (nseq>100) {
+      precision++;
+      nseq/=10;
+    }
+    if (precision>2)
+    {
+      fmtstr = "%"+(2+precision)+"."+precision+"f";
+    }
+    Format fmt = new Format(fmtstr);
     for (int i = iStart; i < width; i++)
     {
       Hashtable hci;
@@ -230,7 +242,6 @@ public class AAFrequency
         consensus.annotations[i] = null;
         continue;
       }
-
       value = 0;
       Float fv;
       if (ignoreGapsInConsensusCalculation)
@@ -266,7 +277,7 @@ public class AAFrequency
             tval = profile[0][alphabet[c]] * 100f
                     / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
             mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
-                    + ((int) tval) + "%";
+                    + fmt.form(tval) + "%";
           }
         }
         else
@@ -289,7 +300,7 @@ public class AAFrequency
                       * 100f
                       / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
               mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
-                      + " " + ((int) tval) + "%";
+                      + " " + fmt.form(tval) + "%";
               p++;
 
             }
@@ -299,7 +310,7 @@ public class AAFrequency
       }
       else
       {
-        mouseOver += ((int) value + "%");
+        mouseOver += (fmt.form(value) + "%");
       }
       consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
               value);
diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index fe022c0..948bdc1 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -21,6 +21,7 @@ package jalview.analysis;
 
 import java.util.*;
 
+import jalview.util.Format;
 import jalview.datamodel.*;
 
 /**
@@ -309,6 +310,18 @@ public class StructureFrequency
       // initialised properly
       return;
     }
+    String fmtstr="%3.1f";
+    int precision=2;
+    while (nseq>100) {
+      precision++;
+      nseq/=10;
+    }
+    if (precision>2)
+    {
+      fmtstr = "%"+(2+precision)+"."+precision+"f";
+    }
+    Format fmt = new Format(fmtstr);
+    
     for (int i = iStart; i < width; i++)
     {
       Hashtable hci;
@@ -385,7 +398,7 @@ public class StructureFrequency
             tval = (vl[c] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
                     : 0]);
             mouseOver += ((p == 0) ? "" : "; ") + (char) ((int[]) ca[c])[0]
-                    + (char) ((int[]) ca[c])[1] + " " + ((int) tval) + "%";
+                    + (char) ((int[]) ca[c])[1] + " " + fmt.form(tval) + "%";
             p++;
 
           }
@@ -395,7 +408,7 @@ public class StructureFrequency
       }
       else
       {
-        mouseOver += ((int) value + "%");
+        mouseOver += (fmt.form(value) + "%");
       }
       consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
               value);
-- 
1.7.10.2