X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=cea28705553b083dd7ab5ea083ec4c3e53d34048;hb=7a1b05d3e521e5d532ad03b23a33ab21675ebd1f;hp=73330754a18bd558f774aa4c502f3ddcc6cd894f;hpb=35ce4609cc8a776b1d85a1f2c2c70aaa106c1a3b;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 7333075..cea2870 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -40,8 +40,8 @@ import java.util.Vector;
  * @author $author$
  * @version $Revision$
  */
-public abstract class AlignFile extends FileParse implements
-        AlignmentFileReaderI, AlignmentFileWriterI
+public abstract class AlignFile extends FileParse
+        implements AlignmentFileReaderI, AlignmentFileWriterI
 {
   int noSeqs = 0;
 
@@ -72,7 +72,20 @@ public abstract class AlignFile extends FileParse implements
 
   long end;
 
-  private boolean parseCalled;
+  /**
+   * true if parse() has been called
+   */
+  private boolean parseCalled = false;
+
+  private boolean parseImmediately = true;
+
+  /**
+   * @return if doParse() was called at construction time
+   */
+  protected boolean isParseImmediately()
+  {
+    return parseImmediately;
+  }
 
   /**
    * Creates a new AlignFile object.
@@ -99,7 +112,7 @@ public abstract class AlignFile extends FileParse implements
    * @param sourceType
    *          What type of file to read from (File, URL, Pasted String)
    */
-  public AlignFile(String dataObject, DataSourceType sourceType)
+  public AlignFile(Object dataObject, DataSourceType sourceType)
           throws IOException
   {
     this(true, dataObject, sourceType);
@@ -117,10 +130,10 @@ public abstract class AlignFile extends FileParse implements
    *          What type of file to read from (File, URL)
    * @throws IOException
    */
-  public AlignFile(boolean parseImmediately, String dataObject,
-          DataSourceType sourceType)
-          throws IOException
+  public AlignFile(boolean parseImmediately, Object dataObject,
+          DataSourceType sourceType) throws IOException
   {
+    // BH allows File or String
     super(dataObject, sourceType);
     initData();
     if (parseImmediately)
@@ -154,6 +167,11 @@ public abstract class AlignFile extends FileParse implements
   {
     super(source);
     initData();
+
+    // stash flag in case parse needs to know if it has to autoconfigure or was
+    // configured after construction
+    this.parseImmediately = parseImmediately;
+
     if (parseImmediately)
     {
       doParse();
@@ -175,11 +193,6 @@ public abstract class AlignFile extends FileParse implements
     }
     parseCalled = true;
     parse();
-    // sets the index of each sequence in the alignment
-    for (int i = 0, c = seqs.size(); i < c; i++)
-    {
-      seqs.get(i).setIndex(i);
-    }
   }
 
   /**
@@ -282,9 +295,8 @@ public abstract class AlignFile extends FileParse implements
   {
     if (key == null)
     {
-      throw new Error(
-              MessageManager
-                      .getString("error.implementation_error_cannot_have_null_alignment"));
+      throw new Error(MessageManager.getString(
+              "error.implementation_error_cannot_have_null_alignment"));
     }
     if (value == null)
     {