Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

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

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index ec1c82e..da925e4 100755 (executable)
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -55,15 +55,16 @@ public class FastaFile extends AlignFile
    * 
    * @param inFile
    *          DOCUMENT ME!
-   * @param type
+   * @param sourceType
    *          DOCUMENT ME!
    * 
    * @throws IOException
    *           DOCUMENT ME!
    */
-  public FastaFile(String inFile, String type) throws IOException
+  public FastaFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public FastaFile(FileParse source) throws IOException
@@ -71,6 +72,11 @@ public class FastaFile extends AlignFile
     super(source);
   }
 
+  public FastaFile(SequenceI[] seqs)
+  {
+    super(seqs);
+  }
+
   /**
    * DOCUMENT ME!
    * 
@@ -180,28 +186,15 @@ public class FastaFile extends AlignFile
     }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param s
-   *          DOCUMENT ME!
-   * @param len
-   *          DOCUMENT ME!
-   * @param gaps
-   *          DOCUMENT ME!
-   * @param displayId
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public String print(SequenceI[] s)
+  @Override
+  public String print(SequenceI[] s, boolean jvsuffix)
   {
     out = new StringBuffer();
     int i = 0;
 
     while ((i < s.length) && (s[i] != null))
     {
-      out.append(">" + printId(s[i]));
+      out.append(">" + printId(s[i], jvsuffix));
       if (s[i].getDescription() != null)
       {
         out.append(" " + s[i].getDescription());
@@ -233,15 +226,4 @@ public class FastaFile extends AlignFile
 
     return out.toString();
   }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  @Override
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
 }