X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=b9a14bafa245ca5a21f06350a7d85401d1808c77;hb=49cc4c921eac8fd966dfe4fa4b86d00655ea2f67;hp=63827a17a0a4a1ef6f8703ff5853233e2f0e581b;hpb=f960a9572b838aa32b8618324a12e9e4767f98cf;p=jalview.git

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 63827a1..b9a14ba 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,78 +1,127 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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 {
+import jalview.datamodel.*;
+import jalview.util.*;
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class MSFfile
+    extends AlignFile
+{
+
+  /**
+   * Creates a new MSFfile object.
+   */
   public MSFfile()
-  {}
-
-  public MSFfile(String inStr) {
-    super(inStr);
+  {
   }
 
-  public MSFfile(String inFile, String type) throws IOException {
-    super(inFile,type);
+  /**
+   * 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+"]","\\~");
-
-  public void parse() {
-    int       i       = 0;
-    boolean   seqFlag = false;
-    String    key     = new String();
-    Vector    headers = new Vector();
+  /**
+   * 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);
+    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);
+          }
 
-      while (str.hasMoreTokens()) {
+          //if line has // set SeqFlag to 1 so we know sequences are coming
+          if (inStr.indexOf("//") != -1)
+          {
+            seqFlag = true;
+          }
 
-        String inStr = str.nextToken();
+          //Process lines as sequence lines if seqFlag is set
+          if ( (inStr.indexOf("//") == -1) && (seqFlag == true))
+          {
+            //seqeunce id is the first field
+            key = inStr;
 
-        //If line has header information add to the headers vector
-        if (inStr.indexOf("Name:") != -1) {
-          key = str.nextToken();
-          headers.addElement(key);
-        }
+            StringBuffer tempseq;
 
-        //if line has // set SeqFlag to 1 so we know sequences are coming
-        if (inStr.indexOf("//") != -1) {
-          seqFlag = true;
-        }
+            //Get sequence from hash if it exists
+            if (seqhash.containsKey(key))
+            {
+              tempseq = (StringBuffer) seqhash.get(key);
+            }
+            else
+            {
+              tempseq = new StringBuffer();
+              seqhash.put(key, tempseq);
+            }
 
-        //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());
+            //loop through the rest of the words
+            while (str.hasMoreTokens())
+            {
+              //append the word to the sequence
+              tempseq.append(str.nextToken());
+            }
           }
         }
       }
     }
-    } catch (IOException e) {
+    catch (IOException e)
+    {
       System.err.println("Exception parsing MSFFile " + e);
       e.printStackTrace();
     }
@@ -80,175 +129,271 @@ public class MSFfile extends AlignFile {
     this.noSeqs = headers.size();
 
     //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();
-
-        int start = 1;
-        int end = seq.length();
-
-        if (maxLength <  head.length() ) {
-          maxLength =  head.length();
+    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();
+
+        if (maxLength < head.length())
+        {
+          maxLength = head.length();
         }
 
-        if (head.indexOf("/") > 0 ) {
+        // Replace ~ with a sensible gap character
+        seq = seq.replace('~', '-');
 
-          StringTokenizer st = new StringTokenizer(head,"/");
+        Sequence newSeq = parseId(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();
-            }
-          }
-        }
-        // Replace ~ with a sensible gap character
-        seq = gapre.replaceAll(seq);
-        Sequence newSeq = new Sequence(head,seq,start,end);
+        newSeq.setSequence(seq);
 
         seqs.addElement(newSeq);
-
-      } else {
-        System.err.println("MSFFile Parser: Can't find sequence for " + headers.elementAt(i));
+      }
+      else
+      {
+        System.err.println("MSFFile Parser: Can't find sequence for " +
+                           headers.elementAt(i));
       }
     }
-
   }
 
-  public static int checkSum(String seq) {
-    //String chars =  "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";
+  /**
+   * DOCUMENT ME!
+   *
+   * @param seq DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int checkSum(String seq)
+  {
     int check = 0;
+    String sequence = seq.toUpperCase();
 
-    String index =  "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";
-    index += "--------------------------------------------------------------------------------------------------------------------------------";
+    for (int i = 0; i < sequence.length(); i++)
+    {
+      try
+      {
 
-    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;
-          }
+        int value = sequence.charAt(i);
+        if (value != -1)
+        {
+          check += (i % 57 + 1) * value;
         }
-      } catch (Exception e) {
+      }
+      catch (Exception e)
+      {
         System.err.println("Exception during MSF Checksum calculation");
         e.printStackTrace();
       }
     }
+
     return check % 10000;
   }
 
-  public static String print(SequenceI[] s) {
-    return print(s, false);
-  }
-  public static String print(SequenceI[] s, boolean is_NA) {
-    StringBuffer out = new StringBuffer("!!"+(is_NA ? "NA":"AA")+"_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param is_NA DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String print(SequenceI[] seqs)
+  {
+
+    boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);
+
+    SequenceI[] s = new SequenceI[seqs.length];
+
+    StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +
+                                        "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.
 
     int max = 0;
     int maxid = 0;
     int i = 0;
-    String big = "";
 
-    while (i < s.length && s[i] != null) {
-      String sq;
-      big += (sq=s[i].getSequence());
-      if (sq.length() > max) {
-        max = sq.length();
+    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].getSequenceAsString().replace('-', '.'));
+
+      StringBuffer sb = new StringBuffer();
+      sb.append(s[i].getSequence());
+
+      for (int ii = 0; ii < sb.length(); ii++)
+      {
+        if (sb.charAt(ii) == '.')
+        {
+          sb.setCharAt(ii, '~');
+        }
+        else
+        {
+          break;
+        }
       }
+
+      for (int ii = sb.length() - 1; ii > 0; ii--)
+      {
+        if (sb.charAt(ii) == '.')
+        {
+          sb.setCharAt(ii, '~');
+        }
+        else
+        {
+          break;
+        }
+      }
+
+      s[i].setSequence(sb.toString());
+
+      if (s[i].getSequence().length > max)
+      {
+        max = s[i].getSequence().length;
+      }
+
       i++;
     }
-    Format maxLenpad = new Format("%"+(new String(""+max)).length()+"d");
-    Format maxChkpad = new Format("%"+(new String("1"+max)).length()+"d");
+
+    Format maxLenpad = new Format("%" + (new String("" + max)).length() +
+                                  "d");
+    Format maxChkpad = new Format("%" + (new String("1" + max)).length() +
+                                  "d");
     i = 0;
-    long bigcheck = checkSum(big);
-    long maxNB=0;
-    out.append("   MSF: " + s[0].getSequence().length() + "   Type: "+(is_NA?"N":"P")+"    Check:  " + bigcheck + "   ..\n\n\n");
-    String nameBlock[] = new String[s.length];
-    String idBlock[] = new String[s.length];
-    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());
-      nameBlock[i]=new String("  Name: "+name+" ");
-      idBlock[i] = new String("Len: " + maxLenpad.form(s[i].getSequence().length()) + "  Check:" + maxChkpad.form(check) + "  Weight: 1.00\n");
-
-      if (name.length() > maxid) {
-        maxid = name.length();
+
+    int bigChecksum = 0;
+    int[] checksums = new int[s.length];
+    while (i < s.length)
+    {
+      checksums[i] = checkSum(s[i].getSequenceAsString());
+      bigChecksum += checksums[i];
+      i++;
+    }
+
+    long maxNB = 0;
+    out.append("   MSF: " + s[0].getSequence().length + "   Type: " +
+               (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum % 10000) +
+               "   ..\n\n\n");
+
+    String[] nameBlock = new String[s.length];
+    String[] idBlock = new String[s.length];
+
+    i = 0;
+    while ( (i < s.length) && (s[i] != null))
+    {
+
+      nameBlock[i] = new String("  Name: " + printId(s[i]) + " ");
+
+      idBlock[i] = new String("Len: " +
+                              maxLenpad.form(s[i].getSequence().length) +
+                              "  Check: " +
+                              maxChkpad.form(checksums[i]) + "  Weight: 1.00\n");
+
+      if (s[i].getName().length() > maxid)
+      {
+        maxid = s[i].getName().length();
       }
-      if (nameBlock[i].length()>maxNB) {
-        maxNB=nameBlock[i].length();
+
+      if (nameBlock[i].length() > maxNB)
+      {
+        maxNB = nameBlock[i].length();
       }
 
       i++;
     }
-    if (maxid < 10) {
+
+    if (maxid < 10)
+    {
       maxid = 10;
     }
-    if (maxNB<15) {
-      maxNB=15;
+
+    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]);
+
+    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");
+    out.append("\n\n//\n\n");
 
     int len = 50;
 
-    int nochunks =  max / len + 1;
-    if (max%len == 0) {
+    int nochunks = (max / len) + 1;
+
+    if ( (max % len) == 0)
+    {
       nochunks--;
     }
-    for (i = 0; i < nochunks; i++) {
+
+    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;
+      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(re2gap.replaceAll(s[j].getSequence().substring(start,end)));
-            if (k < 4) {
-              // out.append(" ");
-            } else {
+          if ( (end < s[j].getSequence().length) &&
+              (start < s[j].getSequence().length))
+          {
+            out.append(s[j].getSequence(start, end));
+
+            if (k < 4)
+            {
+              out.append(" ");
+            }
+            else
+            {
               out.append("\n");
             }
-          } else {
-            if (start < s[j].getSequence().length()) {
-              out.append(re2gap.replaceAll(s[j].getSequence().substring(start)));
+          }
+          else
+          {
+            if (start < s[j].getSequence().length)
+            {
+              out.append(s[j].getSequenceAsString().substring(start));
               out.append("\n");
-            } else {
-              if (k == 0) {
+            }
+            else
+            {
+              if (k == 0)
+              {
                 out.append("\n");
               }
             }
           }
         }
+
         j++;
       }
-      out.append("\n");
 
+      out.append("\n");
     }
+
     return out.toString();
   }
-  public String print() {
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String print()
+  {
     return print(getSeqsAsArray());
   }
 }
-
-
-
-
-
-
-