JAL-629 stash some TFType and PAEFile info into a PDBEntry

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 338c4b2..1233940 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -33,6 +33,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
+import jalview.util.StringUtils;
 
 /**
  * DOCUMENT ME!
@@ -79,6 +80,8 @@ public abstract class AlignFile extends FileParse
 
   private boolean parseImmediately = true;
 
+  private boolean dataClosed = false;
+
   /**
    * @return if doParse() was called at construction time
    */
@@ -112,7 +115,7 @@ public abstract class AlignFile extends FileParse
    * @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);
@@ -130,9 +133,10 @@ public abstract class AlignFile extends FileParse
    *          What type of file to read from (File, URL)
    * @throws IOException
    */
-  public AlignFile(boolean parseImmediately, String dataObject,
+  public AlignFile(boolean parseImmediately, Object dataObject,
           DataSourceType sourceType) throws IOException
   {
+    // BH allows File or String
     super(dataObject, sourceType);
     initData();
     if (parseImmediately)
@@ -164,6 +168,12 @@ 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();
 
@@ -173,7 +183,7 @@ public abstract class AlignFile extends FileParse
 
     if (parseImmediately)
     {
-      doParse();
+      doParse(closeData);
     }
   }
 
@@ -184,6 +194,11 @@ 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(
@@ -192,7 +207,11 @@ public abstract class AlignFile extends FileParse
     }
     parseCalled = true;
     parse();
-    dataIn.close();
+    if (closeData && !dataClosed)
+    {
+      dataIn.close();
+      dataClosed = true;
+    }
   }
 
   /**
@@ -360,7 +379,7 @@ public abstract class AlignFile extends FileParse
   {
     Sequence seq = null;
     id = id.trim();
-    int space = id.indexOf(" ");
+    int space = StringUtils.indexOfFirstWhitespace(id);
     if (space > -1)
     {
       seq = new Sequence(id.substring(0, space), "");