X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAlignFile.java;h=4de510a332ad20c063d28914f5d80cada9732afe;hb=66170487efac01381b97cda847c4a381a8c731ab;hp=57922e7f240dc3eca69189a5473a300089e1062e;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 57922e7..4de510a 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -40,7 +40,7 @@ import java.util.Vector;
  * @author $author$
  * @version $Revision$
  */
-public abstract class AlignFile extends FileParse
+public abstract class AlignFile extends FileParse implements AlignmentFileI
 {
   int noSeqs = 0;
 
@@ -65,14 +65,12 @@ public abstract class AlignFile extends FileParse
   /**
    * Properties to be added to generated alignment object
    */
-  protected Hashtable properties;
+  private Hashtable properties;
 
   long start;
 
   long end;
 
-  boolean jvSuffix = true;
-
   private boolean parseCalled;
 
   /**
@@ -86,17 +84,24 @@ public abstract class AlignFile extends FileParse
     initData();
   }
 
+  public AlignFile(SequenceI[] seqs)
+  {
+    this();
+    setSeqs(seqs);
+  }
+
   /**
    * Constructor which parses the data from a file of some specified type.
    * 
    * @param dataObject
    *          Filename, URL or Pasted String to read from.
-   * @param type
+   * @param sourceType
    *          What type of file to read from (File, URL, Pasted String)
    */
-  public AlignFile(String dataObject, String type) throws IOException
+  public AlignFile(String dataObject, DataSourceType sourceType)
+          throws IOException
   {
-    this(true, dataObject, type);
+    this(true, dataObject, sourceType);
   }
 
   /**
@@ -107,14 +112,15 @@ public abstract class AlignFile extends FileParse
    *          if false, need to call 'doParse()' to begin parsing data
    * @param dataObject
    *          Filename, URL or Pasted String to read from.
-   * @param type
+   * @param sourceType
    *          What type of file to read from (File, URL)
    * @throws IOException
    */
-  public AlignFile(boolean parseImmediately, String dataObject, String type)
+  public AlignFile(boolean parseImmediately, String dataObject,
+          DataSourceType sourceType)
           throws IOException
   {
-    super(dataObject, type);
+    super(dataObject, sourceType);
     initData();
     if (parseImmediately)
     {
@@ -191,6 +197,7 @@ public abstract class AlignFile extends FileParse
   /**
    * Return the Sequences in the seqs Vector as an array of Sequences
    */
+  @Override
   public SequenceI[] getSeqsAsArray()
   {
     SequenceI[] s = new SequenceI[seqs.size()];
@@ -209,6 +216,7 @@ public abstract class AlignFile extends FileParse
    * 
    * @param al
    */
+  @Override
   public void addAnnotations(AlignmentI al)
   {
     addProperties(al);
@@ -314,7 +322,8 @@ public abstract class AlignFile extends FileParse
    * @param s
    *          DOCUMENT ME!
    */
-  protected void setSeqs(SequenceI[] s)
+  @Override
+  public void setSeqs(SequenceI[] s)
   {
     seqs = new Vector<SequenceI>();
 
@@ -330,16 +339,6 @@ public abstract class AlignFile extends FileParse
   public abstract void parse() throws IOException;
 
   /**
-   * Print out in alignment file format the Sequences in the seqs Vector.
-   */
-  public abstract String print();
-
-  public void addJVSuffix(boolean b)
-  {
-    jvSuffix = b;
-  }
-
-  /**
    * A general parser for ids.
    * 
    * @String id Id to be parsed
@@ -371,14 +370,21 @@ public abstract class AlignFile extends FileParse
   }
 
   /**
-   * 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 optionally
+   * suffix Jalview /start-end
+   * 
+   * @param jvsuffix
    * 
    * @String id Id to be parsed
    */
+  String printId(SequenceI seq, boolean jvsuffix)
+  {
+    return seq.getDisplayId(jvsuffix);
+  }
+
   String printId(SequenceI seq)
   {
-    return seq.getDisplayId(jvSuffix);
+    return printId(seq, true);
   }
 
   /**
@@ -400,6 +406,7 @@ public abstract class AlignFile extends FileParse
     return newickStrings == null ? 0 : newickStrings.size();
   }
 
+  @Override
   public void addGroups(AlignmentI al)
   {