X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=1dafb91284fc1592011b00d86502cb85f28e05eb;hb=292a54416608154f37e53241c9f6edcd05e62f5d;hp=0dfef6a12b30ee2cf4a087c3b3c11ced4c3aabc6;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 0dfef6a..1dafb91 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -16,102 +16,164 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package jalview.io;
 
 import jalview.datamodel.*;
 
 import java.io.*;
+
 import java.util.*;
 
-public abstract class AlignFile extends FileParse {
-  int noSeqs    = 0;
-  int maxLength = 0;
 
-  Vector    seqs;
-  Vector    headers;
+/**
+ * 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;
+
+    /**
+     * Creates a new AlignFile object.
+     */
+    public AlignFile()
+    {
+    }
 
-  long start;
-  long end;
 
-  public 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)
+     */
+    public AlignFile(String inFile, String type) throws IOException
+    {
+        super(inFile, type);
 
-  public AlignFile(String inStr) {
-    initData();
-System.out.println("is this ever called??");
-    try{
-      parse();
-    }catch(Exception ex){}
-  }
+        initData();
 
-/**
- * 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)
- */
-  public AlignFile(String inFile, String type) throws IOException {
-    super(inFile,type);
+        parse();
+    }
 
-    initData();
+    /**
+     * Return the seqs Vector
+     */
+    public Vector getSeqs()
+    {
+        return seqs;
+    }
 
-    parse();
+    /**
+     * Return the Sequences in the seqs Vector as an array of Sequences
+     */
+    public SequenceI[] getSeqsAsArray()
+    {
+        SequenceI[] s = new SequenceI[seqs.size()];
 
-  }
+        for (int i = 0; i < seqs.size(); i++)
+        {
+            s[i] = (SequenceI) seqs.elementAt(i);
+        }
 
-/**
- * Return the seqs Vector
- */
-  public Vector getSeqs() {
-    return seqs;
-  }
+        return s;
+    }
 
-/**
- * Return the Sequences in the seqs Vector as an array of Sequences
- */
-  public SequenceI [] getSeqsAsArray() {
-    SequenceI [] s = new SequenceI[seqs.size()];
-    for (int i=0;i < seqs.size();i++) {
-      s[i] = (SequenceI)seqs.elementAt(i);
+    /**
+     * Initialise objects to store sequence data in.
+     */
+    protected void initData()
+    {
+        seqs = new Vector();
+        headers = new Vector();
     }
-    return s;
-  }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     */
+    protected void setSeqs(SequenceI[] s)
+    {
+        seqs = new Vector();
+
+        for (int i = 0; i < s.length; i++)
+        {
+            seqs.addElement(s[i]);
+        }
+    }
 
-/**
- * Initialise objects to store sequence data in.
- */
-  protected void initData() {
-    seqs    = new Vector();
-    headers = new Vector();
-  }
-
-  protected void setSeqs(SequenceI [] s) {
-    seqs = new Vector();
-    for (int i=0; i<s.length; i++) {
-      seqs.addElement(s[i]);
+    // Checks whether sequence is valid aa characters
+    protected boolean isValidProteinSequence(String sequence)
+    {
+        for (int i = 0; i < sequence.length(); i++)
+            if (!jalview.schemes.ResidueProperties.aaHash.containsKey(
+                        String.valueOf(sequence.charAt(i))))
+            {
+                invalidCharacter = sequence.charAt(i);
+                return false;
+            }
+
+        return true;
     }
-  }
 
-  // Checks whether sequence is valid aa characters
-  protected boolean isValidProteinSequence(String sequence)
-  {
-    for (int i = 0; i < sequence.length(); i++)
-      if (!jalview.schemes.ResidueProperties.aaHash.containsKey(String.valueOf(sequence.charAt(i))))
-        return false;
+    char invalidCharacter;
 
-    return true;
-  }
+    /**
+     * This method must be implemented to parse the contents of the file.
+     */
+    public abstract void parse() throws IOException;
 
+    /**
+     * Print out in alignment file format the Sequences in the seqs Vector.
+     */
+    public abstract String print();
 
-/**
- * This method must be implemented to parse the contents of the file.
- */
-  public abstract void parse() throws IOException;
+    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);
+    }
 
-/**
- * Print out in alignment file format the Sequences in the seqs Vector.
- */
-  public abstract String print();
 }