X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=f933961b3c6886330bcdc2f2520aa195913cd66f;hb=58e82de6951f919828899de75b908cd1114d8511;hp=04ddff3fe9599a277032650e50a69df81312db6c;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 04ddff3..f933961 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -25,24 +25,45 @@ import java.io.*;
 import java.util.*;
 
 
-public abstract class AlignFile extends FileParse {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public abstract class AlignFile extends FileParse
+{
     int noSeqs = 0;
     int maxLength = 0;
     Vector seqs;
     Vector headers;
     long start;
     long end;
+    boolean jvSuffix = true;
 
-    public AlignFile() {
+    /**
+     * Creates a new AlignFile object.
+     */
+    public AlignFile()
+    {
     }
 
-    public AlignFile(String inStr) {
+    /**
+     * Creates a new AlignFile object.
+     *
+     * @param inStr DOCUMENT ME!
+     */
+    public AlignFile(String inStr)
+    {
         initData();
         System.out.println("is this ever called??");
 
-        try {
+        try
+        {
             parse();
-        } catch (Exception ex) {
+        }
+        catch (Exception ex)
+        {
         }
     }
 
@@ -51,7 +72,8 @@ public abstract class AlignFile extends FileParse {
      * @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);
 
         initData();
@@ -62,17 +84,20 @@ public abstract class AlignFile extends FileParse {
     /**
      * Return the seqs Vector
      */
-    public Vector getSeqs() {
+    public Vector getSeqs()
+    {
         return seqs;
     }
 
     /**
      * Return the Sequences in the seqs Vector as an array of Sequences
      */
-    public SequenceI[] getSeqsAsArray() {
+    public SequenceI[] getSeqsAsArray()
+    {
         SequenceI[] s = new SequenceI[seqs.size()];
 
-        for (int i = 0; i < seqs.size(); i++) {
+        for (int i = 0; i < seqs.size(); i++)
+        {
             s[i] = (SequenceI) seqs.elementAt(i);
         }
 
@@ -82,24 +107,34 @@ public abstract class AlignFile extends FileParse {
     /**
      * Initialise objects to store sequence data in.
      */
-    protected void initData() {
+    protected void initData()
+    {
         seqs = new Vector();
         headers = new Vector();
     }
 
-    protected void setSeqs(SequenceI[] s) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     */
+    protected void setSeqs(SequenceI[] s)
+    {
         seqs = new Vector();
 
-        for (int i = 0; i < s.length; i++) {
+        for (int i = 0; i < s.length; i++)
+        {
             seqs.addElement(s[i]);
         }
     }
 
     // Checks whether sequence is valid aa characters
-    protected boolean isValidProteinSequence(String sequence) {
+    protected boolean isValidProteinSequence(String sequence)
+    {
         for (int i = 0; i < sequence.length(); i++)
             if (!jalview.schemes.ResidueProperties.aaHash.containsKey(
-                        String.valueOf(sequence.charAt(i)))) {
+                        String.valueOf(sequence.charAt(i))))
+            {
                 return false;
             }
 
@@ -115,4 +150,45 @@ public abstract class AlignFile extends FileParse {
      * 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
+     */
+    Sequence parseId(String id)
+    {
+      Sequence seq = null;
+      id = id.trim();
+      int space = id.indexOf(" ");
+      if(space>-1)
+      {
+        seq = new Sequence(id.substring(0, space),"");
+        seq.setDescription(id.substring(space+1));
+      }
+      else
+      {
+        seq = new Sequence(id, "");
+      }
+
+      return seq;
+    }
+
+    /**
+     * 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);
+    }
+
 }