X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAlignFile.java;h=1bea24b80a163d46fb96906ed75c1eefdd54c6cf;hb=115a611d005faab33f978a469578bcacbcecc112;hp=497f0a580836af85016458f6f32c3ecd97adc9a3;hpb=6fd29e7e2753c9066fa31b76ab71827f96d471ff;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 497f0a5..1bea24b 100755
--- 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 +27,14 @@ 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;
+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(
@@ -192,6 +207,11 @@ public abstract class AlignFile extends FileParse
     }
     parseCalled = true;
     parse();
+    if (closeData && !dataClosed)
+    {
+      dataIn.close();
+      dataClosed = true;
+    }
   }
 
   /**
@@ -359,7 +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), "");
@@ -413,12 +433,24 @@ public abstract class AlignFile extends FileParse
     newickStrings.addElement(new String[] { treeName, newickString });
   }
 
-  protected int getTreeCount()
+  @Override
+  public int getTreeCount()
   {
     return newickStrings == null ? 0 : newickStrings.size();
   }
 
   @Override
+  public boolean hasTrees()
+  {
+    return getTreeCount()>0;
+  }
+  
+  @Override
+  public List<String[]> getNewickTrees()
+  {
+    return newickStrings;
+  }
+  @Override
   public void addGroups(AlignmentI al)
   {