X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=73d0f0f6fa5dca4d1cad9dab68e4b5301d8dfea0;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=63827a17a0a4a1ef6f8703ff5853233e2f0e581b;hpb=f960a9572b838aa32b8618324a12e9e4767f98cf;p=jalview.git

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 63827a1..73d0f0f 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,254 +1,409 @@
-package jalview.io;
-
-import jalview.datamodel.*;
-import jalview.util.*;
-
-import java.io.*;
-import java.util.*;
-
-public class MSFfile extends AlignFile {
-
-  public MSFfile()
-  {}
-
-  public MSFfile(String inStr) {
-    super(inStr);
-  }
-
-  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();
-    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();
-    }
-
-    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();
-        }
-
-        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();
-            }
-          }
-        }
-        // 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));
-      }
-    }
-
-  }
-
-  public static int checkSum(String seq) {
-    //String chars =  "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";
-    int check = 0;
-
-    String index =  "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";
-    index += "--------------------------------------------------------------------------------------------------------------------------------";
-
-    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;
-          }
-        }
-      } 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.
-
-    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();
-      }
-      i++;
-    }
-    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();
-      }
-      if (nameBlock[i].length()>maxNB) {
-        maxNB=nameBlock[i].length();
-      }
-
-      i++;
-    }
-    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 =  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");
-            }
-          } 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");
-              }
-            }
-          }
-        }
-        j++;
-      }
-      out.append("\n");
-
-    }
-    return out.toString();
-  }
-  public String print() {
-    return print(getSeqsAsArray());
-  }
-}
-
-
-
-
-
-
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 java.io.*;
+import java.util.*;
+
+import jalview.datamodel.*;
+import jalview.util.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class MSFfile extends AlignFile
+{
+
+  /**
+   * Creates a new MSFfile object.
+   */
+  public MSFfile()
+  {
+  }
+
+  /**
+   * 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);
+  }
+
+  public MSFfile(FileParse source) throws IOException
+  {
+    super(source);
+  }
+
+  {
+    // TODO Auto-generated constructor stub
+  }
+
+  /**
+   * 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();
+    }
+
+    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();
+
+        if (maxLength < head.length())
+        {
+          maxLength = head.length();
+        }
+
+        // Replace ~ with a sensible gap character
+        seq = seq.replace('~', '-');
+
+        Sequence newSeq = parseId(head);
+
+        newSeq.setSequence(seq);
+
+        seqs.addElement(newSeq);
+      }
+      else
+      {
+        System.err.println("MSFFile Parser: Can't find sequence for "
+                + headers.elementAt(i));
+      }
+    }
+  }
+
+  /**
+   * 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();
+      }
+    }
+
+    return check % 10000;
+  }
+
+  /**
+   * 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;
+
+    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");
+    i = 0;
+
+    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();
+      }
+
+      i++;
+    }
+
+    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(start, end));
+
+            if (k < 4)
+            {
+              out.append(" ");
+            }
+            else
+            {
+              out.append("\n");
+            }
+          }
+          else
+          {
+            if (start < s[j].getSequence().length)
+            {
+              out.append(s[j].getSequenceAsString().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());
+  }
+}