X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=b2f8b2b47f838b0eb40f207acb6d9a06e64fa676;hb=a40bbc57a85658544e2e5d7cc2a7596b762566dc;hp=ad834be8c071b4ffda0f1dc6103aee5a9b4cf8f4;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index ad834be..b2f8b2b 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,26 +1,39 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * 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.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
-import java.io.*;
-import java.util.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+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;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -37,12 +50,17 @@ 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
    */
-  protected Vector annotations;
+  protected Vector<AlignmentAnnotation> annotations;
+
+  /**
+   * SequenceGroups to be added to the alignment object
+   */
+  protected List<SequenceGroup> seqGroups;
 
   /**
    * Properties to be added to generated alignment object
@@ -55,11 +73,17 @@ public abstract class AlignFile extends FileParse
 
   boolean jvSuffix = true;
 
+  private boolean parseCalled;
+
   /**
    * Creates a new AlignFile object.
    */
   public AlignFile()
   {
+    // Shouldn't we init data structures (JBPNote: not sure - initData is for
+    // initialising the structures used for reading from a datasource, and the
+    // bare constructor hasn't got any datasource)
+    initData();
   }
 
   /**
@@ -72,13 +96,28 @@ public abstract class AlignFile extends FileParse
    */
   public AlignFile(String inFile, String type) throws IOException
   {
+    this(true, inFile, 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
+   * @param inFile
+   *          Filename to read from.
+   * @param type
+   *          What type of file to read from (File, URL)
+   * @throws IOException
+   */
+  public AlignFile(boolean parseImmediately, String inFile, String type) throws IOException
+  {
     super(inFile, type);
-
     initData();
-
-    parse();
+    if (parseImmediately) {
+      doParse();
+    }
   }
-
   /**
    * Attempt to read from the position where some other parsing process left
    * off.
@@ -88,19 +127,58 @@ public abstract class AlignFile extends FileParse
    */
   public AlignFile(FileParse source) throws IOException
   {
+    this(true,source);
+  }
+  /**
+   * 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
+  {
     super(source);
     initData();
+    if (parseImmediately) {
+      doParse();
+    }
+  }
+  /**
+   * called if parsing was delayed till after parser was constructed
+   * @throws IOException
+   */
+  public void doParse() throws IOException
+  {
+    if (parseCalled)
+    {
+      throw new IOException(
+              "Implementation error: Parser called twice for same data.\n"
+                      + "Need to call initData() again before parsing can be reattempted.");
+    }
+    parseCalled=true;
     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;
   }
 
+  public List<SequenceGroup> getSeqGroups()
+  {
+    return seqGroups;
+  }
+
   /**
    * Return the Sequences in the seqs Vector as an array of Sequences
    */
@@ -127,11 +205,27 @@ 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);
     }
 
   }
 
+  public void addSeqGroups(AlignmentI al)
+  {
+    this.seqGroups = al.getGroups();
+
+  }
+
   /**
    * Add any additional information extracted from the file to the alignment
    * properties.
@@ -166,8 +260,7 @@ public abstract class AlignFile extends FileParse
   {
     if (key == null)
     {
-      throw new Error(
-              "Implementation error: Cannot have null alignment property key.");
+      throw new Error(MessageManager.getString("error.implementation_error_cannot_have_null_alignment"));
     }
     if (value == null)
     {
@@ -196,6 +289,8 @@ public abstract class AlignFile extends FileParse
   {
     seqs = new Vector();
     annotations = new Vector();
+    seqGroups = new ArrayList<SequenceGroup>();
+    parseCalled=false;
   }
 
   /**