Merge branch 'develop' into feature/r2_11_2/JAL-3808_gff2_exonerate

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index cea2870..3202ac9 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -20,13 +20,6 @@
  */
 package jalview.io;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Enumeration;
@@ -34,6 +27,13 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
 /**
  * DOCUMENT ME!
  * 
@@ -79,6 +79,8 @@ public abstract class AlignFile extends FileParse
 
   private boolean parseImmediately = true;
 
+  private boolean dataClosed = false;
+
   /**
    * @return if doParse() was called at construction time
    */
@@ -165,6 +167,12 @@ public abstract class AlignFile extends FileParse
   public AlignFile(boolean parseImmediately, FileParse source)
           throws IOException
   {
+    this(parseImmediately, source, true);
+  }
+
+  public AlignFile(boolean parseImmediately, FileParse source,
+          boolean closeData) throws IOException
+  {
     super(source);
     initData();
 
@@ -174,7 +182,7 @@ public abstract class AlignFile extends FileParse
 
     if (parseImmediately)
     {
-      doParse();
+      doParse(closeData);
     }
   }
 
@@ -185,6 +193,11 @@ public abstract class AlignFile extends FileParse
    */
   public void doParse() throws IOException
   {
+    doParse(true);
+  }
+
+  public void doParse(boolean closeData) throws IOException
+  {
     if (parseCalled)
     {
       throw new IOException(
@@ -193,6 +206,11 @@ public abstract class AlignFile extends FileParse
     }
     parseCalled = true;
     parse();
+    if (closeData && !dataClosed)
+    {
+      dataIn.close();
+      dataClosed = true;
+    }
   }
 
   /**