Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 338c4b2..b2cf262 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 +80,10 @@ public abstract class AlignFile extends FileParse
 
   private boolean parseImmediately = true;
 
+  private boolean dataClosed = false;
+
+  private boolean doXferSettings = true;
+
   /**
    * @return if doParse() was called at construction time
    */
@@ -112,7 +117,7 @@ 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 +135,10 @@ 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)
@@ -148,6 +154,12 @@ public abstract class AlignFile extends FileParse
    * @param source
    * @throws IOException
    */
+  public AlignFile(FileParse source, boolean doXferSettings)
+          throws IOException
+  {
+    this(true, source, true, doXferSettings);
+  }
+
   public AlignFile(FileParse source) throws IOException
   {
     this(true, source);
@@ -164,16 +176,29 @@ 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
+  {
+    this(parseImmediately, source, closeData, true);
+  }
+
+  public AlignFile(boolean parseImmediately, FileParse source,
+          boolean closeData, boolean doXferSettings) throws IOException
+  {
     super(source);
     initData();
 
     // stash flag in case parse needs to know if it has to autoconfigure or was
     // configured after construction
     this.parseImmediately = parseImmediately;
+    this.doXferSettings = doXferSettings;
 
     if (parseImmediately)
     {
-      doParse();
+      doParse(closeData);
     }
   }
 
@@ -184,6 +209,11 @@ 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(
@@ -191,8 +221,12 @@ public abstract class AlignFile extends FileParse
                       + "Need to call initData() again before parsing can be reattempted.");
     }
     parseCalled = true;
-    parse();
-    dataIn.close();
+    parse(this.doXferSettings);
+    if (closeData && !dataClosed)
+    {
+      dataIn.close();
+      dataClosed = true;
+    }
   }
 
   /**
@@ -352,6 +386,18 @@ public abstract class AlignFile extends FileParse
   public abstract void parse() throws IOException;
 
   /**
+   * This method is only overridden by JmolParser because of its use in
+   * StructureFile to parse annotations
+   * 
+   * @param doXferSettings
+   * @throws IOException
+   */
+  public void parse(boolean doXferSettings) throws IOException
+  {
+    parse();
+  }
+
+  /**
    * A general parser for ids.
    * 
    * @String id Id to be parsed
@@ -360,7 +406,7 @@ 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), "");
@@ -433,4 +479,14 @@ public abstract class AlignFile extends FileParse
   {
     seqs.add(seq);
   }
+
+  public void setDoXferSettings(boolean b)
+  {
+    doXferSettings = b;
+  }
+
+  public boolean getDoXferSettings()
+  {
+    return doXferSettings;
+  }
 }