JAL-958 store/recover normalised flag

[jalview.git] / src / jalview / io / AlignmentProperties.java

diff --git a/src/jalview/io/AlignmentProperties.java b/src/jalview/io/AlignmentProperties.java
index 45d46d8..14cc9c4 100644 (file)
--- a/src/jalview/io/AlignmentProperties.java
+++ b/src/jalview/io/AlignmentProperties.java
@@ -1,5 +1,19 @@
-/**
+/*
+ * 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
+ * 
+ * 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/>.
  */
 package jalview.io;
 
@@ -33,7 +47,7 @@ public class AlignmentProperties
    */
   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++)
@@ -47,22 +61,22 @@ public class AlignmentProperties
         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);
+    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 +103,16 @@ 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>");
       }
     }
   }