X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=3ca2563b1e80d83ce47c28a1e0fb1510090c406c;hb=7897c6cb08b496285bcb5fa9ed2d9f7d887d0068;hp=c38fad33fe774b19f2c11db38d6a5b0a9d3a163f;hpb=49685e6426d5ac136dce4907196751680c667670;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index c38fad3..3ca2563 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -25,29 +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;
 
   /**
@@ -59,11 +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);
 
@@ -71,8 +79,11 @@ public abstract class AlignFile
 
     parse();
   }
+
   /**
-   * Attempt to read from the position where some other parsing process left off.
+   * Attempt to read from the position where some other parsing process left
+   * off.
+   * 
    * @param source
    * @throws IOException
    */
@@ -82,6 +93,7 @@ public abstract class AlignFile
     initData();
     parse();
   }
+
   /**
    * Return the seqs Vector
    */
@@ -104,10 +116,11 @@ public abstract class AlignFile
 
     return s;
   }
+
   /**
-   * called by AppletFormatAdapter to generate
-   * an annotated alignment, rather than bare
-   * sequences.
+   * called by AppletFormatAdapter to generate an annotated alignment, rather
+   * than bare sequences.
+   * 
    * @param al
    */
   public void addAnnotations(Alignment al)
@@ -115,21 +128,21 @@ public abstract class AlignFile
     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.
+   * 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)
+    if (properties != null && properties.size() > 0)
     {
       Enumeration keys = properties.keys();
       Enumeration vals = properties.elements();
@@ -139,36 +152,44 @@ public abstract class AlignFile
       }
     }
   }
+
   /**
-   * 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
+   * 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)
+    if (key == null)
     {
-      throw new Error("Implementation error: Cannot have null alignment property key.");
+      throw new Error(
+              "Implementation error: Cannot have null alignment property key.");
     }
-    if (value==null)
+    if (value == null)
     {
       return; // null properties are ignored.
     }
-    if (properties==null)
+    if (properties == null)
     {
       properties = new Hashtable();
     }
     properties.put(key, value);
   }
+
   protected Object getAlignmentProperty(Object key)
   {
-    if (properties!=null && key!=null)
+    if (properties != null && key != null)
     {
       return properties.get(key);
     }
     return null;
   }
+
   /**
    * Initialise objects to store sequence data in.
    */
@@ -180,8 +201,9 @@ public abstract class AlignFile
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
    */
   protected void setSeqs(SequenceI[] s)
   {
@@ -196,8 +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.
@@ -211,7 +232,7 @@ public abstract class AlignFile
 
   /**
    * A general parser for ids.
-   *
+   * 
    * @String id Id to be parsed
    */
   Sequence parseId(String id)
@@ -233,20 +254,20 @@ 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)
   {
     return seq.getDisplayId(jvSuffix);
   }
+
   /**
    * vector of String[] treeName, newickString pairs
    */
-  Vector newickStrings=null;
+  Vector newickStrings = null;
 
   protected void addNewickTree(String treeName, String newickString)
   {
@@ -254,12 +275,13 @@ public abstract class AlignFile
     {
       newickStrings = new Vector();
     }
-    newickStrings.addElement(new String[] { treeName, newickString});
+    newickStrings.addElement(new String[]
+    { treeName, newickString });
   }
 
   protected int getTreeCount()
   {
-    if (newickStrings==null)
+    if (newickStrings == null)
     {
       return 0;
     }