X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=7a469dd8b49ae67d5cfea66d7ac3612277cb118d;hb=dd645839efa022cd15c6247398692412b7c2ceaa;hp=ae8e0d0e0a0d292bfc7a36bdc9f13a67c41b48e2;hpb=4fe43371b9524afd658c97c8767cf7e6dc84459e;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index ae8e0d0e..7a469dd 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -25,19 +25,35 @@ import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public abstract class AlignFile
-    extends FileParse
+public abstract class AlignFile extends FileParse
 {
   int noSeqs = 0;
+
   int maxLength = 0;
+
+  /**
+   * Sequences to be added to form a new alignment.
+   */
   protected Vector seqs;
+
+  /**
+   * annotation to be added to generated alignment object
+   */
   protected Vector annotations;
+
+  /**
+   * Properties to be added to generated alignment object
+   */
+  protected Hashtable properties;
+
   long start;
+
   long end;
+
   boolean jvSuffix = true;
 
   /**
@@ -49,11 +65,13 @@ public abstract class AlignFile
 
   /**
    * Constructor which parses the data from a file of some specified type.
-   * @param inFile Filename to read from.
-   * @param type   What type of file to read from (File, URL)
+   * 
+   * @param inFile
+   *                Filename to read from.
+   * @param type
+   *                What type of file to read from (File, URL)
    */
-  public AlignFile(String inFile, String type)
-      throws IOException
+  public AlignFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
 
@@ -63,6 +81,20 @@ public abstract class AlignFile
   }
 
   /**
+   * Attempt to read from the position where some other parsing process left
+   * off.
+   * 
+   * @param source
+   * @throws IOException
+   */
+  public AlignFile(FileParse source) throws IOException
+  {
+    super(source);
+    initData();
+    parse();
+  }
+
+  /**
    * Return the seqs Vector
    */
   public Vector getSeqs()
@@ -85,15 +117,77 @@ public abstract class AlignFile
     return s;
   }
 
+  /**
+   * called by AppletFormatAdapter to generate an annotated alignment, rather
+   * than bare sequences.
+   * 
+   * @param al
+   */
   public void addAnnotations(Alignment al)
   {
+    addProperties(al);
     for (int i = 0; i < annotations.size(); i++)
     {
-      al.addAnnotation(
-          (AlignmentAnnotation) annotations.elementAt(i)
-          );
+      al.addAnnotation((AlignmentAnnotation) annotations.elementAt(i));
+    }
+
+  }
+
+  /**
+   * Add any additional information extracted from the file to the alignment
+   * properties.
+   * 
+   * @note implicitly called by addAnnotations()
+   * @param al
+   */
+  public void addProperties(Alignment al)
+  {
+    if (properties != null && properties.size() > 0)
+    {
+      Enumeration keys = properties.keys();
+      Enumeration vals = properties.elements();
+      while (keys.hasMoreElements())
+      {
+        al.setProperty(keys.nextElement(), vals.nextElement());
+      }
     }
+  }
 
+  /**
+   * Store a non-null key-value pair in a hashtable used to set alignment
+   * properties note: null keys will raise an error, null values will result in
+   * the key/value pair being silently ignored.
+   * 
+   * @param key -
+   *                non-null key object
+   * @param value -
+   *                non-null value
+   */
+  protected void setAlignmentProperty(Object key, Object value)
+  {
+    if (key == null)
+    {
+      throw new Error(
+              "Implementation error: Cannot have null alignment property key.");
+    }
+    if (value == null)
+    {
+      return; // null properties are ignored.
+    }
+    if (properties == null)
+    {
+      properties = new Hashtable();
+    }
+    properties.put(key, value);
+  }
+
+  protected Object getAlignmentProperty(Object key)
+  {
+    if (properties != null && key != null)
+    {
+      return properties.get(key);
+    }
+    return null;
   }
 
   /**
@@ -107,8 +201,9 @@ public abstract class AlignFile
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
    */
   protected void setSeqs(SequenceI[] s)
   {
@@ -123,8 +218,7 @@ public abstract class AlignFile
   /**
    * This method must be implemented to parse the contents of the file.
    */
-  public abstract void parse()
-      throws IOException;
+  public abstract void parse() throws IOException;
 
   /**
    * Print out in alignment file format the Sequences in the seqs Vector.
@@ -138,7 +232,7 @@ public abstract class AlignFile
 
   /**
    * A general parser for ids.
-   *
+   * 
    * @String id Id to be parsed
    */
   Sequence parseId(String id)
@@ -160,10 +254,9 @@ public abstract class AlignFile
   }
 
   /**
-   * Creates the output id.
-   * Adds prefix Uniprot format source|id
-   * And suffix Jalview /start-end
-   *
+   * Creates the output id. Adds prefix Uniprot format source|id And suffix
+   * Jalview /start-end
+   * 
    * @String id Id to be parsed
    */
   String printId(SequenceI seq)
@@ -171,4 +264,28 @@ public abstract class AlignFile
     return seq.getDisplayId(jvSuffix);
   }
 
+  /**
+   * vector of String[] treeName, newickString pairs
+   */
+  Vector newickStrings = null;
+
+  protected void addNewickTree(String treeName, String newickString)
+  {
+    if (newickStrings == null)
+    {
+      newickStrings = new Vector();
+    }
+    newickStrings.addElement(new String[]
+    { treeName, newickString });
+  }
+
+  protected int getTreeCount()
+  {
+    if (newickStrings == null)
+    {
+      return 0;
+    }
+    return newickStrings.size();
+  }
+
 }