X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignmentProperties.java;h=f2a6150dc69dd4254ba9da1f59c6e12dff91368a;hb=1f029391e9e263b132a62eaefcc2fe68badacfd6;hp=45d46d86a4e036097e171ab9f87fee6bcd4438f5;hpb=6c889c6524f1ba8f56dbea5211b44753846a1bdf;p=jalview.git

diff --git a/src/jalview/io/AlignmentProperties.java b/src/jalview/io/AlignmentProperties.java
index 45d46d8..f2a6150 100644
--- a/src/jalview/io/AlignmentProperties.java
+++ b/src/jalview/io/AlignmentProperties.java
@@ -1,20 +1,38 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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++)
@@ -42,27 +61,31 @@ public class AlignmentProperties
               - alignment.getSequenceAt(i).getStart();
       avg += size;
       if (size > max)
+      {
         max = size;
+      }
       if (size < min)
+      {
         min = size;
+      }
     }
-    avg = avg / (float) alignment.getHeight();
-    pw.append(nl);
-    pw.append("Sequences: " + alignment.getHeight());
-    pw.append(nl);
-    pw.append("Minimum Sequence Length: " + min);
-    pw.append(nl);
-    pw.append("Maximum Sequence Length: " + max);
-    pw.append(nl);
-    pw.append("Average Length: " + (int) avg);
+    avg = avg / alignment.getHeight();
+    pw.print(nl);
+    pw.print("Sequences: " + alignment.getHeight());
+    pw.print(nl);
+    pw.print("Minimum Sequence Length: " + min);
+    pw.print(nl);
+    pw.print("Maximum Sequence Length: " + max);
+    pw.print(nl);
+    pw.print("Average Length: " + (int) avg);
 
     if (((Alignment) alignment).alignmentProperties != null)
     {
-      pw.append(nl);
-      pw.append(nl);
+      pw.print(nl);
+      pw.print(nl);
       if (html)
       {
-        pw.append("<table border=\"1\">");
+        pw.print("<table border=\"1\">");
       }
       Hashtable props = ((Alignment) alignment).alignmentProperties;
       Enumeration en = props.keys();
@@ -89,16 +112,16 @@ public class AlignmentProperties
             }
             pos = npos + 1;
           } while (npos != -1);
-          pw.append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
+          pw.print("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
         }
         else
         {
-          pw.append("\n" + key + "\t" + vals);
+          pw.print(nl + key + "\t" + vals);
         }
       }
       if (html)
       {
-        pw.append("</table>");
+        pw.print("</table>");
       }
     }
   }