X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=bae4342276b8a701109efd851b0ca3593c14a3f7;hb=56e5bdc625697d50d7d3f422616f0f1b40ca2828;hp=3c18432c98864608f1d6c99b3e33e1ff4414e9d8;hpb=128c1c559ce7749ba5a39d30e6108f5ce8f4b99e;p=jalview.git

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 3c18432..bae4342 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,235 +1,411 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* 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 jalview.util.*;
 
 import java.io.*;
+
 import java.util.*;
 
-public class MSFfile extends AlignFile {
 
-  public MSFfile()
-  {}
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class MSFfile extends AlignFile
+{
 
-  public MSFfile(String inStr) {
-    super(inStr);
-  }
 
-  public MSFfile(String inFile, String type) throws IOException {
-    super(inFile,type);
-  }
+    /**
+     * Creates a new MSFfile object.
+     */
+    public MSFfile()
+    {
+    }
+
+    /**
+     * Creates a new MSFfile object.
+     *
+     * @param inStr DOCUMENT ME!
+     */
+    public MSFfile(String inStr)
+    {
+        super(inStr);
+    }
+
+    /**
+     * Creates a new MSFfile object.
+     *
+     * @param inFile DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public MSFfile(String inFile, String type) throws IOException
+    {
+        super(inFile, type);
+    }
 
-  private static com.stevesoft.pat.Regex gapre = new com.stevesoft.pat.Regex("\\~","-");
-  private static com.stevesoft.pat.Regex re2gap = new com.stevesoft.pat.Regex("["+jalview.util.Comparison.GapChars+"]","\\~");
+    /**
+     * DOCUMENT ME!
+     */
+    public void parse() throws IOException
+    {
+        int i = 0;
+        boolean seqFlag = false;
+        String key = new String();
+        Vector headers = new Vector();
+        Hashtable seqhash = new Hashtable();
+        String line;
+
+        try
+        {
+            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)
+        {
+            System.err.println("Exception parsing MSFFile " + e);
+            e.printStackTrace();
+        }
 
-  public void parse() {
-    int       i       = 0;
-    boolean   seqFlag = false;
-    String    key     = new String();
-    Vector    headers = new Vector();
-    Hashtable seqhash = new Hashtable();
-    String    line;
+        this.noSeqs = headers.size();
 
-    try {
-    while ((line = nextLine()) != null) {
+        //Add sequences to the hash
+        for (i = 0; i < headers.size(); i++)
+        {
+            if (seqhash.get(headers.elementAt(i)) != null)
+            {
+                String head = headers.elementAt(i).toString();
+                String seq = seqhash.get(head).toString();
 
-      StringTokenizer str = new StringTokenizer(line);
+                if (maxLength < head.length())
+                {
+                    maxLength = head.length();
+                }
 
-      while (str.hasMoreTokens()) {
+                // Replace ~ with a sensible gap character
+                seq = seq.replace('~', '-');
+                if (!isValidProteinSequence(seq))
+                {
+                    throw new IOException(AppletFormatAdapter.
+                                          INVALID_CHARACTERS
+                                          + " : " + head
+                                          + " : " + invalidCharacter);
+                }
 
-        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);
-        }
+                Sequence newSeq = parseId(head);
 
-        //if line has // set SeqFlag to 1 so we know sequences are coming
-        if (inStr.indexOf("//") != -1) {
-          seqFlag = true;
-        }
+                newSeq.setSequence(seq);
 
-        //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());
-          }
+                seqs.addElement(newSeq);
+            }
+            else
+            {
+                System.err.println("MSFFile Parser: Can't find sequence for " +
+                    headers.elementAt(i));
+            }
         }
-      }
-    }
-    } catch (IOException e) {
-      System.err.println("Exception parsing MSFFile " + e);
-      e.printStackTrace();
     }
 
-    this.noSeqs = headers.size();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int checkSum(String seq)
+    {
+        int check = 0;
+        String sequence = seq.toUpperCase();
+
+        for (int i = 0; i < sequence.length(); i++)
+        {
+            try
+            {
+
+                    int value = sequence.charAt(i);
+                    if (value!=-1)
+                    {
+                        check += (i % 57 +1) * value;
+                    }
+            }
+            catch (Exception e)
+            {
+                System.err.println("Exception during MSF Checksum calculation");
+                e.printStackTrace();
+            }
+        }
 
-    //Add sequences to the hash
-    for (i = 0; i < headers.size(); i++ ) {
+        return check % 10000;
+    }
 
-      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();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param is_NA DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String print(SequenceI[] seqs)
+    {
 
-        if (maxLength <  head.length() ) {
-          maxLength =  head.length();
-        }
+      boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);
 
-        if (head.indexOf("/") > 0 ) {
+      SequenceI [] s = new SequenceI[seqs.length];
 
-          StringTokenizer st = new StringTokenizer(head,"/");
+        StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +
+                "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
 
-          if (st.countTokens() == 2) {
+        int max = 0;
+        int maxid = 0;
+        int i = 0;
 
-            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();
+        while ((i < seqs.length) && (seqs[i] != null))
+        {
+          // Replace all internal gaps with . and external spaces with ~
+          s[i] =new Sequence(seqs[i].getName(),seqs[i].getSequence().replace('-', '.'));
+
+          StringBuffer sb = new StringBuffer(s[i].getSequence());
+          for (int ii = 0; ii < sb.length(); ii++)
+          {
+            if (sb.charAt(ii) == '.')
+            {
+              sb.setCharAt(ii, '~');
             }
+            else
+              break;
           }
-        }
-        // Replace ~ with a sensible gap character
-        seq = gapre.replaceAll(seq);
-        Sequence newSeq = new Sequence(head,seq,start,end);
-
-        seqs.addElement(newSeq);
 
-      } else {
-        System.err.println("MSFFile Parser: Can't find sequence for " + headers.elementAt(i));
-      }
-    }
+          for (int ii = sb.length() - 1; ii > 0; ii--)
+          {
+            if (sb.charAt(ii) == '.')
+            {
+              sb.setCharAt(ii,'~');
+            }
+            else
+              break;
+          }
 
-  }
+            s[i].setSequence(sb.toString());
 
-  public static int checkSum(String seq) {
-    //String chars =  "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";
-    int check = 0;
+            if (s[i].getSequence().length() > max)
+            {
+                max = s[i].getSequence().length();
+            }
 
-    String index =  "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";
-    index += "--------------------------------------------------------------------------------------------------------------------------------";
+            i++;
+        }
 
-    for(int i = 0; i < seq.length(); i++) {
-      try {
-        if (i <seq.length()) {
-          int pos = index.indexOf(seq.substring(i,i+1));
-          if (!index.substring(pos,pos+1).equals("_")) {
-            check += ((i % 57) + 1) * pos;
-          }
+        Format maxLenpad = new Format("%" + (new String("" + max)).length() +
+                "d");
+        Format maxChkpad = new Format("%" + (new String("1" + max)).length() +
+                "d");
+        i = 0;
+
+        int bigChecksum = 0;
+        int [] checksums = new int[s.length];
+        while ( i < s.length )
+        {
+          checksums[i] = checkSum(s[i].getSequence());
+          bigChecksum += checksums[i];
+          i++;
         }
-      } catch (Exception e) {
-        System.err.println("Exception during MSF Checksum calculation");
-        e.printStackTrace();
-      }
-    }
-    return check % 10000;
-  }
 
-  public static String print(SequenceI[] s) {
-    StringBuffer out = new StringBuffer("PileUp\n\n");
+        long maxNB = 0;
+        out.append("   MSF: " + s[0].getSequence().length() + "   Type: " +
+            (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum%10000) + "   ..\n\n\n");
 
-    int max = 0;
-    int maxid = 0;
+        String[] nameBlock = new String[s.length];
+        String[] idBlock = new String[s.length];
 
-    int i = 0;
-    String big = "";
-    while (i < s.length && s[i] != null) {
-      big += s[i].getSequence();
-      i++;
-    }
-    i = 0;
-    int bigcheck = checkSum(big);
-
-    out.append("   MSF: " + s[0].getSequence().length() + "   Type: P    Check:  " + bigcheck + "   ..\n\n\n");
-
-    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 + "  Weight:  1.00\n");
-      if (seq.length() > max) {
-        max = seq.length();
-      }
-      if (name.length() > maxid) {
-        maxid = name.length();
-      }
-      i++;
-    }
+        i=0;
+        while ((i < s.length) && (s[i] != null))
+        {
 
-    if (maxid < 10) {
-      maxid = 10;
-    }
-    maxid++;
-    out.append( "\n\n//\n\n");
+            nameBlock[i] = new String("  Name: " + printId(s[i])+" ");
 
-    int len = 50;
+            idBlock[i] = new String("Len: " +
+                    maxLenpad.form(s[i].getSequence().length()) + "  Check: " +
+                    maxChkpad.form(checksums[i]) + "  Weight: 1.00\n");
 
-    int nochunks =  max / len + 1;
-    if (max%len == 0) {
-      nochunks--;
-    }
-    for (i = 0; i < nochunks; i++) {
-      int j = 0;
-      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()) + " ");
-        for (int k = 0; k < 5; k++) {
-
-          int start = i*50 + k*10;
-          int end = start + 10;
-
-          if (end < s[j].getSequence().length() && start < s[j].getSequence().length() ) {
-            out.append(re2gap.replaceAll(s[j].getSequence().substring(start,end)));
-            if (k < 4) {
-              // out.append(" ");
-            } else {
-              out.append("\n");
+            if (s[i].getName().length() > maxid)
+            {
+                maxid = s[i].getName().length();
             }
-          } else {
-            if (start < s[j].getSequence().length()) {
-              out.append(re2gap.replaceAll(s[j].getSequence().substring(start)));
-              out.append("\n");
-            } else {
-              if (k == 0) {
-                out.append("\n");
-              }
+
+            if (nameBlock[i].length() > maxNB)
+            {
+                maxNB = nameBlock[i].length();
             }
-          }
+
+            i++;
         }
-        j++;
-      }
-      out.append("\n");
 
-    }
-    return out.toString();
-  }
-  public String print() {
-    return print(getSeqsAsArray());
-  }
-}
+        if (maxid < 10)
+        {
+            maxid = 10;
+        }
+
+        if (maxNB < 15)
+        {
+            maxNB = 15;
+        }
 
+        Format nbFormat = new Format("%-" + maxNB + "s");
 
+        for (i = 0; (i < s.length) && (s[i] != null); i++)
+        {
+            out.append(nbFormat.form(nameBlock[i]) + idBlock[i]);
+        }
 
+        maxid++;
+        out.append("\n\n//\n\n");
 
+        int len = 50;
 
+        int nochunks = (max / len) + 1;
 
+        if ((max % len) == 0)
+        {
+            nochunks--;
+        }
+
+        for (i = 0; i < nochunks; i++)
+        {
+            int j = 0;
+
+            while ((j < s.length) && (s[j] != null))
+            {
+                String name = printId( s[j] );
+
+                out.append(new Format("%-" + maxid + "s").form(name+" "));
+
+
+                for (int k = 0; k < 5; k++)
+                {
+                    int start = (i * 50) + (k * 10);
+                    int end = start + 10;
+
+                    if ((end < s[j].getSequence().length()) &&
+                            (start < s[j].getSequence().length()))
+                    {
+                        out.append(s[j].getSequence().substring(start, end));
+
+                        if (k < 4)
+                        {
+                             out.append(" ");
+                        }
+                        else
+                        {
+                            out.append("\n");
+                        }
+                    }
+                    else
+                    {
+                        if (start < s[j].getSequence().length())
+                        {
+                            out.append(s[j].getSequence().substring(start));
+                            out.append("\n");
+                        }
+                        else
+                        {
+                            if (k == 0)
+                            {
+                                out.append("\n");
+                            }
+                        }
+                    }
+                }
+
+                j++;
+            }
 
+            out.append("\n");
+        }
+
+        return out.toString();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String print()
+    {
+        return print(getSeqsAsArray());
+    }
+}