X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignmentProperties.java;h=a7dcba05e1d0706487f9fb99c3cf80ccc516e208;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=fc6d525e037de7ce3c527ad6a6c43fd0be190e91;hpb=5a81ff332d527628562ff29ffe37c4a5e8eb1a61;p=jalview.git

diff --git a/src/jalview/io/AlignmentProperties.java b/src/jalview/io/AlignmentProperties.java
index fc6d525..a7dcba0 100644
--- a/src/jalview/io/AlignmentProperties.java
+++ b/src/jalview/io/AlignmentProperties.java
@@ -1,20 +1,38 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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 
+ * 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.io;
 
-import java.io.IOException;
-import java.io.StringWriter;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+
 import java.io.PrintWriter;
+import java.io.StringWriter;
 import java.util.Enumeration;
 import java.util.Hashtable;
 
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-
 /**
- * Render associated attributes of an alignment. The heart of this code was refactored from jalview.gui.AlignFrame and jalview.appletgui.AlignFrame 
- * TODO: consider extending the html renderer to annotate elements with CSS ids enabling finer output format control.
+ * Render associated attributes of an alignment. The heart of this code was
+ * refactored from jalview.gui.AlignFrame and jalview.appletgui.AlignFrame TODO:
+ * consider extending the html renderer to annotate elements with CSS ids
+ * enabling finer output format control.
  * 
  */
 public class AlignmentProperties
@@ -28,12 +46,13 @@ public class AlignmentProperties
 
   /**
    * render the alignment's properties report as text or an HTML fragment
+   * 
    * @param pw
    * @param html
    */
   public void writeProperties(PrintWriter pw, boolean html)
   {
-    final String nl = html ? "<br>" : "\n";
+    final String nl = html ? "<br>" : System.getProperty("line.separator");
     float avg = 0;
     int min = Integer.MAX_VALUE, max = 0;
     for (int i = 0; i < alignment.getHeight(); i++)
@@ -42,11 +61,15 @@ public class AlignmentProperties
               - alignment.getSequenceAt(i).getStart();
       avg += size;
       if (size > max)
+      {
         max = size;
+      }
       if (size < min)
+      {
         min = size;
+      }
     }
-    avg = avg / (float) alignment.getHeight();
+    avg = avg / alignment.getHeight();
     pw.print(nl);
     pw.print("Sequences: " + alignment.getHeight());
     pw.print(nl);
@@ -62,7 +85,7 @@ public class AlignmentProperties
       pw.print(nl);
       if (html)
       {
-        pw.append("<table border=\"1\">");
+        pw.print("<table border=\"1\">");
       }
       Hashtable props = ((Alignment) alignment).alignmentProperties;
       Enumeration en = props.keys();
@@ -93,7 +116,7 @@ public class AlignmentProperties
         }
         else
         {
-          pw.print("\n" + key + "\t" + vals);
+          pw.print(nl + key + "\t" + vals);
         }
       }
       if (html)