JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 5d8a297..e5c8e04 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,14 +20,6 @@
  */
 package jalview.io;
 
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
@@ -35,6 +27,13 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
 /**
  * DOCUMENT ME!
  * 
@@ -98,9 +97,10 @@ public abstract class AlignFile extends FileParse
   {
     this(true, inFile, type);
   }
-  
+
   /**
-   * Constructor which (optionally delays) parsing of data from a file of some specified type.
+   * Constructor which (optionally delays) parsing of data from a file of some
+   * specified type.
    * 
    * @param parseImmediately
    *          if false, need to call 'doParse()' to begin parsing data
@@ -110,14 +110,17 @@ public abstract class AlignFile extends FileParse
    *          What type of file to read from (File, URL)
    * @throws IOException
    */
-  public AlignFile(boolean parseImmediately, String inFile, String type) throws IOException
+  public AlignFile(boolean parseImmediately, String inFile, String type)
+          throws IOException
   {
     super(inFile, type);
     initData();
-    if (parseImmediately) {
+    if (parseImmediately)
+    {
       doParse();
     }
   }
+
   /**
    * Attempt to read from the position where some other parsing process left
    * off.
@@ -127,25 +130,31 @@ public abstract class AlignFile extends FileParse
    */
   public AlignFile(FileParse source) throws IOException
   {
-    this(true,source);
+    this(true, source);
   }
+
   /**
-   * Construct a new parser to read from the position where some other parsing process left
+   * Construct a new parser to read from the position where some other parsing
+   * process left
    * 
    * @param parseImmediately
    *          if false, need to call 'doParse()' to begin parsing data
    * @param source
    */
-  public AlignFile(boolean parseImmediately, FileParse source) throws IOException
+  public AlignFile(boolean parseImmediately, FileParse source)
+          throws IOException
   {
     super(source);
     initData();
-    if (parseImmediately) {
+    if (parseImmediately)
+    {
       doParse();
     }
   }
+
   /**
    * called if parsing was delayed till after parser was constructed
+   * 
    * @throws IOException
    */
   public void doParse() throws IOException
@@ -156,7 +165,7 @@ public abstract class AlignFile extends FileParse
               "Implementation error: Parser called twice for same data.\n"
                       + "Need to call initData() again before parsing can be reattempted.");
     }
-    parseCalled=true;
+    parseCalled = true;
     parse();
     // sets the index of each sequence in the alignment
     for (int i = 0, c = seqs.size(); i < c; i++)
@@ -165,7 +174,6 @@ public abstract class AlignFile extends FileParse
     }
   }
 
-
   /**
    * Return the seqs Vector
    */
@@ -200,7 +208,7 @@ public abstract class AlignFile extends FileParse
    * 
    * @param al
    */
-  public void addAnnotations(Alignment al)
+  public void addAnnotations(AlignmentI al)
   {
     addProperties(al);
     for (int i = 0; i < annotations.size(); i++)
@@ -212,14 +220,18 @@ public abstract class AlignFile extends FileParse
        * Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i));
        * Rna.HelixMap(pairArray);
        */
-      AlignmentAnnotation an = annotations
-              .elementAt(i);
+      AlignmentAnnotation an = annotations.elementAt(i);
       an.validateRangeAndDisplay();
       al.addAnnotation(an);
     }
 
   }
 
+  /**
+   * register sequence groups on the alignment for **output**
+   * 
+   * @param al
+   */
   public void addSeqGroups(AlignmentI al)
   {
     this.seqGroups = al.getGroups();
@@ -233,7 +245,7 @@ public abstract class AlignFile extends FileParse
    * @note implicitly called by addAnnotations()
    * @param al
    */
-  public void addProperties(Alignment al)
+  public void addProperties(AlignmentI al)
   {
     if (properties != null && properties.size() > 0)
     {
@@ -260,7 +272,9 @@ public abstract class AlignFile extends FileParse
   {
     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)
     {
@@ -290,7 +304,7 @@ public abstract class AlignFile extends FileParse
     seqs = new Vector<SequenceI>();
     annotations = new Vector<AlignmentAnnotation>();
     seqGroups = new ArrayList<SequenceGroup>();
-    parseCalled=false;
+    parseCalled = false;
   }
 
   /**
@@ -369,8 +383,7 @@ public abstract class AlignFile extends FileParse
     {
       newickStrings = new Vector<String[]>();
     }
-    newickStrings.addElement(new String[]
-    { treeName, newickString });
+    newickStrings.addElement(new String[] { treeName, newickString });
   }
 
   protected int getTreeCount()
@@ -378,4 +391,13 @@ public abstract class AlignFile extends FileParse
     return newickStrings == null ? 0 : newickStrings.size();
   }
 
+  public void addGroups(AlignmentI al)
+  {
+
+    for (SequenceGroup sg : getSeqGroups())
+    {
+      al.addGroup(sg);
+    }
+  }
+
 }