X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=3ef721003a82c83babb5a951563de6ff79ff3c2a;hb=d904a499f1863e96cd699e0c5f7f0f81710e8ad9;hp=7a469dd8b49ae67d5cfea66d7ac3612277cb118d;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 7a469dd..3ef7210 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,27 +1,31 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 file is part of Jalview.
  * 
- * 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.
+ * Jalview 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 3 of the License, or (at your option) any later version.
  * 
- * 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
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.io;
 
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -38,7 +42,7 @@ public abstract class AlignFile extends FileParse
   /**
    * Sequences to be added to form a new alignment.
    */
-  protected Vector seqs;
+  protected Vector<SequenceI> seqs;
 
   /**
    * annotation to be added to generated alignment object
@@ -67,17 +71,19 @@ public abstract class AlignFile extends FileParse
    * Constructor which parses the data from a file of some specified type.
    * 
    * @param inFile
-   *                Filename to read from.
+   *          Filename to read from.
    * @param type
-   *                What type of file to read from (File, URL)
+   *          What type of file to read from (File, URL)
    */
   public AlignFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
-
     initData();
-
     parse();
+    // sets the index of each sequence in the alignment
+    for( int i=0,c=seqs.size(); i<c; i++ ) {  
+    	seqs.get(i).setIndex(i);  
+    }
   }
 
   /**
@@ -92,12 +98,16 @@ public abstract class AlignFile extends FileParse
     super(source);
     initData();
     parse();
+    // sets the index of each sequence in the alignment
+    for( int i=0,c=seqs.size(); i<c; i++ ) {  
+    	seqs.get(i).setIndex(i);  
+    }
   }
 
   /**
    * Return the seqs Vector
    */
-  public Vector getSeqs()
+  public Vector<SequenceI> getSeqs()
   {
     return seqs;
   }
@@ -128,7 +138,17 @@ public abstract class AlignFile extends FileParse
     addProperties(al);
     for (int i = 0; i < annotations.size(); i++)
     {
-      al.addAnnotation((AlignmentAnnotation) annotations.elementAt(i));
+      // detect if annotations.elementAt(i) rna secondary structure
+      // if so then do:
+      /*
+       * SequenceFeature[] pairArray =
+       * Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i));
+       * Rna.HelixMap(pairArray);
+       */
+      AlignmentAnnotation an = (AlignmentAnnotation) annotations
+              .elementAt(i);
+      an.validateRangeAndDisplay();
+      al.addAnnotation(an);
     }
 
   }
@@ -158,10 +178,10 @@ public abstract class AlignFile extends FileParse
    * 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
+   * @param key
+   *          - non-null key object
+   * @param value
+   *          - non-null value
    */
   protected void setAlignmentProperty(Object key, Object value)
   {
@@ -203,7 +223,7 @@ public abstract class AlignFile extends FileParse
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void setSeqs(SequenceI[] s)
   {