Merge branch 'develop' into features/JAL-2094_colourInterface

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 984eff6..5760fbe 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -89,14 +89,14 @@ public abstract class AlignFile extends FileParse
   /**
    * Constructor which parses the data from a file of some specified type.
    * 
-   * @param inFile
-   *          Filename to read from.
+   * @param dataObject
+   *          Filename, URL or Pasted String to read from.
    * @param type
-   *          What type of file to read from (File, URL)
+   *          What type of file to read from (File, URL, Pasted String)
    */
-  public AlignFile(String inFile, String type) throws IOException
+  public AlignFile(String dataObject, String type) throws IOException
   {
-    this(true, inFile, type);
+    this(true, dataObject, type);
   }
 
   /**
@@ -105,16 +105,16 @@ public abstract class AlignFile extends FileParse
    * 
    * @param parseImmediately
    *          if false, need to call 'doParse()' to begin parsing data
-   * @param inFile
-   *          Filename to read from.
+   * @param dataObject
+   *          Filename, URL or Pasted String to read from.
    * @param type
    *          What type of file to read from (File, URL)
    * @throws IOException
    */
-  public AlignFile(boolean parseImmediately, String inFile, String type)
+  public AlignFile(boolean parseImmediately, String dataObject, String type)
           throws IOException
   {
-    super(inFile, type);
+    super(dataObject, type);
     initData();
     if (parseImmediately)
     {