X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=0a0520ab3d9bff4d7180b71b4dac2901591c1197;hb=c932f0e85a8852824cdd8ce790af68682732c85c;hp=9036eb4844aa13c46db3daca972d404ae81bd5ca;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 9036eb4..0a0520a 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,8 @@
  */
 package jalview.io;
 
+import java.util.Locale;
+
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
@@ -58,7 +60,7 @@ public class MSFfile extends AlignFile
    * @throws IOException
    *           DOCUMENT ME!
    */
-  public MSFfile(String inFile, String type) throws IOException
+  public MSFfile(String inFile, DataSourceType type) throws IOException
   {
     super(inFile, type);
   }
@@ -134,7 +136,7 @@ public class MSFfile extends AlignFile
       }
     } catch (IOException e)
     {
-      System.err.println("Exception parsing MSFFile " + e);
+      jalview.bin.Console.errPrintln("Exception parsing MSFFile " + e);
       e.printStackTrace();
     }
 
@@ -167,7 +169,7 @@ public class MSFfile extends AlignFile
       }
       else
       {
-        System.err.println("MSFFile Parser: Can't find sequence for "
+        jalview.bin.Console.errPrintln("MSFFile Parser: Can't find sequence for "
                 + headers.get(i));
       }
     }
@@ -184,7 +186,7 @@ public class MSFfile extends AlignFile
   public int checkSum(String seq)
   {
     int check = 0;
-    String sequence = seq.toUpperCase();
+    String sequence = seq.toUpperCase(Locale.ROOT);
 
     for (int i = 0; i < sequence.length(); i++)
     {
@@ -198,7 +200,7 @@ public class MSFfile extends AlignFile
         }
       } catch (Exception e)
       {
-        System.err.println("Exception during MSF Checksum calculation");
+        jalview.bin.Console.errPrintln("Exception during MSF Checksum calculation");
         e.printStackTrace();
       }
     }
@@ -216,7 +218,8 @@ public class MSFfile extends AlignFile
    * 
    * @return DOCUMENT ME!
    */
-  public String print(SequenceI[] sqs)
+  @Override
+  public String print(SequenceI[] sqs, boolean jvSuffix)
   {
 
     boolean is_NA = Comparison.isNucleotide(sqs);
@@ -277,10 +280,10 @@ public class MSFfile extends AlignFile
       i++;
     }
 
-    Format maxLenpad = new Format("%" + (new String("" + max)).length()
-            + "d");
-    Format maxChkpad = new Format("%" + (new String("1" + max)).length()
-            + "d");
+    Format maxLenpad = new Format(
+            "%" + (new String("" + max)).length() + "d");
+    Format maxChkpad = new Format(
+            "%" + (new String("1" + max)).length() + "d");
     i = 0;
 
     int bigChecksum = 0;
@@ -293,7 +296,7 @@ public class MSFfile extends AlignFile
     }
 
     long maxNB = 0;
-    out.append("   MSF: " + s[0].getSequence().length + "   Type: "
+    out.append("   MSF: " + s[0].getLength() + "   Type: "
             + (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum % 10000)
             + "   ..");
     out.append(newline);
@@ -307,11 +310,11 @@ public class MSFfile extends AlignFile
     while ((i < s.length) && (s[i] != null))
     {
 
-      nameBlock[i] = new String("  Name: " + printId(s[i]) + " ");
+      nameBlock[i] = new String("  Name: " + printId(s[i], jvSuffix) + " ");
 
-      idBlock[i] = new String("Len: "
-              + maxLenpad.form(s[i].getSequence().length) + "  Check: "
-              + maxChkpad.form(checksums[i]) + "  Weight: 1.00" + newline);
+      idBlock[i] = new String("Len: " + maxLenpad.form(s[i].getLength())
+              + "  Check: " + maxChkpad.form(checksums[i])
+              + "  Weight: 1.00" + newline);
 
       if (s[i].getName().length() > maxid)
       {
@@ -359,7 +362,7 @@ public class MSFfile extends AlignFile
 
       while ((j < s.length) && (s[j] != null))
       {
-        String name = printId(s[j]);
+        String name = printId(s[j], jvSuffix);
 
         out.append(new Format("%-" + maxid + "s").form(name + " "));
 
@@ -368,8 +371,8 @@ public class MSFfile extends AlignFile
           int start = (i * 50) + (k * 10);
           int end = start + 10;
 
-          if ((end < s[j].getSequence().length)
-                  && (start < s[j].getSequence().length))
+          int length = s[j].getLength();
+          if ((end < length) && (start < length))
           {
             out.append(s[j].getSequence(start, end));
 
@@ -384,7 +387,7 @@ public class MSFfile extends AlignFile
           }
           else
           {
-            if (start < s[j].getSequence().length)
+            if (start < length)
             {
               out.append(s[j].getSequenceAsString().substring(start));
               out.append(newline);
@@ -407,15 +410,4 @@ public class MSFfile extends AlignFile
 
     return out.toString();
   }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  @Override
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
 }