X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPileUpfile.java;h=c945fd561cefa0a657d1ed408633509a078cd8e7;hb=ca05d2959da096c30276df437bc24fcf9dc5adb6;hp=c200c5e8105b77df29fde1237968b5fd0a037e7f;hpb=13b2b876b5bc46693d881b4551842279158311f5;p=jalview.git

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index c200c5e..c945fd5 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -30,181 +30,53 @@ package jalview.io;
  *
  **/
 import java.io.*;
-import java.util.*;
 
 import jalview.datamodel.*;
 import jalview.util.*;
 
-public class PileUpfile
-    extends AlignFile
+public class PileUpfile  extends MSFfile
 {
-  public PileUpfile()
-  {
-  }
-
-  public PileUpfile(String inStr)
-  {
-    super(inStr);
-  }
-
-  public PileUpfile(String inFile, String type)
-      throws IOException
-  {
-    super(inFile, type);
-  }
-
-  public void parse()
-  {
-    int i = 0;
-    boolean seqFlag = false;
-    String key = new String();
-    Vector headers = new Vector();
-    Hashtable seqhash = new Hashtable();
-    String line;
 
-    try
+    /**
+     * Creates a new MSFfile object.
+     */
+    public PileUpfile()
     {
-      while ( (line = nextLine()) != null)
-      {
-        StringTokenizer str = new StringTokenizer(line);
-
-        while (str.hasMoreTokens())
-        {
-          String inStr = str.nextToken();
-
-          //If line has header information add to the headers vector
-          if (inStr.indexOf("Name:") != -1)
-          {
-            key = str.nextToken();
-            headers.addElement(key);
-          }
-
-          //if line has // set SeqFlag to 1 so we know sequences are coming
-          if (inStr.indexOf("//") != -1)
-          {
-            seqFlag = true;
-          }
-
-          //Process lines as sequence lines if seqFlag is set
-          if ( (inStr.indexOf("//") == -1) && (seqFlag == true))
-          {
-            //seqeunce id is the first field
-            key = inStr;
-
-            StringBuffer tempseq;
-
-            //Get sequence from hash if it exists
-            if (seqhash.containsKey(key))
-            {
-              tempseq = (StringBuffer) seqhash.get(key);
-            }
-            else
-            {
-              tempseq = new StringBuffer();
-              seqhash.put(key, tempseq);
-            }
-
-            //loop through the rest of the words
-            while (str.hasMoreTokens())
-            {
-              //append the word to the sequence
-              tempseq.append(str.nextToken());
-            }
-          }
-        }
-      }
     }
-    catch (IOException e)
+    /**
+     * Creates a new MSFfile object.
+     *
+     * @param inStr DOCUMENT ME!
+     */
+    public PileUpfile(String inStr)
     {
-      System.err.println("Exception parsing PileUpfile " + e);
-      e.printStackTrace();
+        super(inStr);
     }
 
-    this.noSeqs = headers.size();
-
-    //Add sequences to the hash
-    for (i = 0; i < headers.size(); i++)
+    /**
+     * Creates a new MSFfile object.
+     *
+     * @param inFile DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public PileUpfile(String inFile, String type) throws IOException
     {
-      if (seqhash.get(headers.elementAt(i)) != null)
-      {
-        String head = headers.elementAt(i).toString();
-        String seq = seqhash.get(head).toString();
-
-        int start = 1;
-        int end = seq.length();
-
-        if (maxLength < head.length())
-        {
-          maxLength = head.length();
-        }
-
-        if (head.indexOf("/") > 0)
-        {
-          StringTokenizer st = new StringTokenizer(head, "/");
-
-          if (st.countTokens() == 2)
-          {
-            head = st.nextToken();
-
-            String tmp = st.nextToken();
-            st = new StringTokenizer(tmp, "-");
-
-            if (st.countTokens() == 2)
-            {
-              start = Integer.valueOf(st.nextToken()).intValue();
-              end = Integer.valueOf(st.nextToken()).intValue();
-            }
-          }
-        }
-
-        Sequence newSeq = new Sequence(head, seq, start, end);
-
-        seqs.addElement(newSeq);
-      }
-      else
-      {
-        System.err.println(
-            "PileUpfile Parser: Can't find sequence for " +
-            headers.elementAt(i));
-      }
+        super(inFile, type);
     }
-  }
-
-  public static int checkSum(String seq)
+   /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String print()
   {
-    //String chars =  "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";
-    int check = 0;
-
-    String sequence = seq.toUpperCase();
-
-    String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";
-    index += "--------------------------------------------------------------------------------------------------------------------------------";
-
-    for (int i = 0; i < sequence.length(); i++)
-    {
-      try
-      {
-        if (i < sequence.length())
-        {
-          int pos = index.indexOf(sequence.charAt(i));
-
-          if (index.charAt(pos)!='_')
-          {
-            check += ( ( (i % 57) + 1) * pos);
-          }
-        }
-      }
-      catch (Exception e)
-      {
-        System.err.println("Exception during MSF Checksum calculation");
-        e.printStackTrace();
-      }
-    }
-
-    return check % 10000;
+      return print(getSeqsAsArray());
   }
 
-  public static String print(SequenceI[] s)
+
+  public  String print(SequenceI[] s)
   {
     StringBuffer out = new StringBuffer("PileUp\n\n");
 
@@ -212,29 +84,25 @@ public class PileUpfile
     int maxid = 0;
 
     int i = 0;
-    String big = "";
-
-    while ( (i < s.length) && (s[i] != null))
+    int bigChecksum = 0;
+    int[] checksums = new int[s.length];
+    while (i < s.length)
     {
-      big += s[i].getSequence();
+      checksums[i] = checkSum(s[i].getSequence());
+      bigChecksum += checksums[i];
       i++;
     }
 
-    i = 0;
-
-    int bigcheck = checkSum(big);
-
     out.append("   MSF: " + s[0].getSequence().length() +
-               "   Type: P    Check:  " + bigcheck + "   ..\n\n\n");
+               "   Type: P    Check:  " + bigChecksum%10000 + "   ..\n\n\n");
 
+    i=0;
     while ( (i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequence();
-      String name = s[i].getName() + "/" + s[i].getStart() + "-" +
-          s[i].getEnd();
-      int check = checkSum(s[i].getSequence());
-      out.append(" Name: " + name + " oo  Len:  " +
-                 s[i].getSequence().length() + "  Check:  " + check +
+      out.append(" Name: " + printId(s[i]) +
+                 " oo  Len:  " +
+                 s[i].getSequence().length() + "  Check:  " + checksums[i] +
                  "  Weight:  1.00\n");
 
       if (seq.length() > max)
@@ -242,9 +110,9 @@ public class PileUpfile
         max = seq.length();
       }
 
-      if (name.length() > maxid)
+      if (s[i].getName().length() > maxid)
       {
-        maxid = name.length();
+        maxid = s[i].getName().length();
       }
 
       i++;
@@ -273,9 +141,9 @@ public class PileUpfile
 
       while ( (j < s.length) && (s[j] != null))
       {
-        String name = s[j].getName();
-        out.append(new Format("%-" + maxid + "s").form(name + "/" +
-            s[j].getStart() + "-" + s[j].getEnd()) + " ");
+        String name = printId(s[j]);
+
+         out.append(new Format("%-" + maxid + "s").form(name + " "));
 
         for (int k = 0; k < 5; k++)
         {
@@ -321,9 +189,4 @@ public class PileUpfile
 
     return out.toString();
   }
-
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
 }