X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=73330754a18bd558f774aa4c502f3ddcc6cd894f;hb=b8cd52fe7bed59130e5b080acfd42c3ef2effdbb;hp=7e0cabd07b58c1345ce4c6297d732bf2639638f5;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 7e0cabd..7333075 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -40,14 +40,16 @@ import java.util.Vector;
  * @author $author$
  * @version $Revision$
  */
-public abstract class AlignFile extends FileParse
+public abstract class AlignFile extends FileParse implements
+        AlignmentFileReaderI, AlignmentFileWriterI
 {
   int noSeqs = 0;
 
   int maxLength = 0;
 
   /**
-   * Sequences to be added to form a new alignment.
+   * Sequences to be added to form a new alignment. TODO: remove vector in this
+   * class
    */
   protected Vector<SequenceI> seqs;
 
@@ -64,14 +66,12 @@ 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;
 
   /**
@@ -85,17 +85,24 @@ 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 inFile
-   *          Filename to read from.
-   * @param type
-   *          What type of file to read from (File, URL)
+   * @param dataObject
+   *          Filename, URL or Pasted String to read from.
+   * @param sourceType
+   *          What type of file to read from (File, URL, Pasted String)
    */
-  public AlignFile(String inFile, String type) throws IOException
+  public AlignFile(String dataObject, DataSourceType sourceType)
+          throws IOException
   {
-    this(true, inFile, type);
+    this(true, dataObject, sourceType);
   }
 
   /**
@@ -104,16 +111,17 @@ public abstract class AlignFile extends FileParse
    * 
    * @param parseImmediately
    *          if false, need to call 'doParse()' to begin parsing data
-   * @param inFile
-   *          Filename to read from.
-   * @param type
+   * @param dataObject
+   *          Filename, URL or Pasted String to read from.
+   * @param sourceType
    *          What type of file to read from (File, URL)
    * @throws IOException
    */
-  public AlignFile(boolean parseImmediately, String inFile, String type)
+  public AlignFile(boolean parseImmediately, String dataObject,
+          DataSourceType sourceType)
           throws IOException
   {
-    super(inFile, type);
+    super(dataObject, sourceType);
     initData();
     if (parseImmediately)
     {
@@ -190,6 +198,7 @@ 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()];
@@ -208,6 +217,7 @@ public abstract class AlignFile extends FileParse
    * 
    * @param al
    */
+  @Override
   public void addAnnotations(AlignmentI al)
   {
     addProperties(al);
@@ -313,7 +323,8 @@ 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>();
 
@@ -329,16 +340,6 @@ 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
@@ -351,7 +352,15 @@ public abstract class AlignFile extends FileParse
     if (space > -1)
     {
       seq = new Sequence(id.substring(0, space), "");
-      seq.setDescription(id.substring(space + 1));
+      String desc = id.substring(space + 1);
+      seq.setDescription(desc);
+
+      /*
+       * it is tempting to parse Ensembl style gene description e.g.
+       * chromosome:GRCh38:7:140696688:140721955:1 and set the
+       * start position of the sequence, but this causes much confusion
+       * for reverse strand feature locations
+       */
     }
     else
     {
@@ -362,14 +371,21 @@ 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);
   }
 
   /**
@@ -391,6 +407,7 @@ public abstract class AlignFile extends FileParse
     return newickStrings == null ? 0 : newickStrings.size();
   }
 
+  @Override
   public void addGroups(AlignmentI al)
   {
 
@@ -400,4 +417,8 @@ public abstract class AlignFile extends FileParse
     }
   }
 
+  protected void addSequence(SequenceI seq)
+  {
+    seqs.add(seq);
+  }
 }