X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=661857f2d8b389e8cb637cc989a7c0bad6db879b;hb=f4b7a6009254c29ca4bc4a2b73de173b12b752c7;hp=e77a0d3025771df08ea09b60b5a37b23ab2f73d2;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index e77a0d3..661857f 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -16,528 +16,796 @@
 * 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.analysis;
 
-import jalview.schemes.*;
 import jalview.datamodel.SequenceI;
+
+import jalview.schemes.*;
+
 import jalview.util.*;
-import jalview.io.*;
 
-import java.util.*;
-import java.io.*;
 import java.awt.*;
 
-public class AlignSeq {
+import java.util.*;
 
-  int[][] score;
-  int[][] E;
-  int[][] F;
-  int[][] traceback;
-
-  int[] seq1;
-  int[] seq2;
 
-  SequenceI s1;
-  SequenceI s2;
-
-  String s1str;
-  String s2str;
-
-  int maxi;
-  int maxj;
-
-  int[] aseq1;
-  int[] aseq2;
-
-  String astr1 = "";
-  String astr2 = "";
-
-  public int seq1start;
-  public int seq1end;
-  public int seq2start;
-  public int seq2end;
-
-  int count;
-
-  public int maxscore;
-  float pid;
-  int prev = 0;
-
-  public static java.util.Hashtable dnaHash = new java.util.Hashtable();
-
-  static  {
-    dnaHash.put("C", new Integer(0));
-    dnaHash.put("T", new Integer(1));
-    dnaHash.put("A", new Integer(2));
-    dnaHash.put("G", new Integer(3));
-    dnaHash.put("-", new Integer(4));
-  }
-
-  static String dna[] = {"C","T","A","G","-"};
-  static String pep[] = {"A","R","N","D","C","Q","E","G","H","I","L","K","M","F","P","S","T","W","Y","V","B","Z","X","-"};
-
-  int gapOpen = 120;
-  int gapExtend = 20;
-
-  int lookup[][] = ResidueProperties.getBLOSUM62();
-  String intToStr[] = pep;
-  int defInt = 23;
-
-  String output = "";
-
-  String type;
-  Runtime rt;
-  public AlignSeq() {}
-
-  public AlignSeq(SequenceI s1, SequenceI s2,String type) {
-    rt  = Runtime.getRuntime();
-    SeqInit(s1,s2,type);
-  }
-
-  public int getMaxScore() {
-    return maxscore;
-  }
-
-  public int getSeq2Start() {
-    return seq2start;
-  }
-
-  public int getSeq2End() {
-    return seq2end;
-  }
-
-  public int getSeq1Start() {
-    return seq1start;
-  }
-
-  public int getSeq1End() {
-    return seq1end;
-  }
-
-  public String getOutput() {
-    return output;
-  }
-
-  public String getAStr1() {
-    return astr1;
-  }
-  public String getAStr2() {
-    return astr2;
-  }
-  public int [] getASeq1() {
-    return aseq1;
-  }
-  public int [] getASeq2() {
-    return aseq2;
-  }
-  public SequenceI getS1() {
-    return s1;
-  }
-  public SequenceI getS2() {
-    return s2;
-  }
-
-  public void SeqInit(SequenceI s1, SequenceI s2,String type) {
-    s1str = extractGaps(".",s1.getSequence());
-    s2str = extractGaps(".",s2.getSequence());
-    s1str = extractGaps("-",s1str);
-    s2str = extractGaps("-",s2str);
-    s1str = extractGaps(" ",s1str);
-    s2str = extractGaps(" ",s2str);
-
-    this.s1 = s1;
-    this.s2 = s2;
-
-    this.type = type;
-
-    if (type.equals("pep")) {
-      lookup = ResidueProperties.getBLOSUM62();
-      intToStr = pep;
-      defInt = 23;
-    } else if (type.equals("dna")) {
-      lookup = ResidueProperties.getDNA();
-      intToStr = dna;
-      defInt = 4;
-    } else {
-      output = output + ("Wrong type = dna or pep only");
-      System.exit(0);
+/**
+ *
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignSeq
+{
+    /** DOCUMENT ME!! */
+    public static java.util.Hashtable dnaHash = new java.util.Hashtable();
+
+    static
+    {
+        dnaHash.put("C", new Integer(0));
+        dnaHash.put("T", new Integer(1));
+        dnaHash.put("A", new Integer(2));
+        dnaHash.put("G", new Integer(3));
+        dnaHash.put("-", new Integer(4));
     }
 
+    static String[] dna = { "C", "T", "A", "G", "-" };
+    static String[] pep =
+    {
+        "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
+        "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-"
+    };
+    int[][] score;
+    int[][] E;
+    int[][] F;
+    int[][] traceback;
+    int[] seq1;
+    int[] seq2;
+    SequenceI s1;
+    SequenceI s2;
+    String s1str;
+    String s2str;
+    int maxi;
+    int maxj;
+    int[] aseq1;
+    int[] aseq2;
+    String astr1 = "";
+    String astr2 = "";
+
+    /** DOCUMENT ME!! */
+    public int seq1start;
+
+    /** DOCUMENT ME!! */
+    public int seq1end;
+
+    /** DOCUMENT ME!! */
+    public int seq2start;
+
+    /** DOCUMENT ME!! */
+    public int seq2end;
+    int count;
+
+    /** DOCUMENT ME!! */
+    public int maxscore;
+    float pid;
+    int prev = 0;
+    int gapOpen = 120;
+    int gapExtend = 20;
+    int[][] lookup = ResidueProperties.getBLOSUM62();
+    String[] intToStr = pep;
+    int defInt = 23;
+    StringBuffer output = new StringBuffer();
+    String type;
+    Runtime rt;
+
+
+    /**
+     * Creates a new AlignSeq object.
+     *
+     * @param s1 DOCUMENT ME!
+     * @param s2 DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     */
+    public AlignSeq(SequenceI s1, SequenceI s2, String type)
+    {
+        rt = Runtime.getRuntime();
+        SeqInit(s1, s2, type);
+    }
 
-    //System.out.println("lookuip " + rt.freeMemory() + " "+  rt.totalMemory());
-    seq1 = new int[s1str.length()];
-    //System.out.println("seq1 " + rt.freeMemory() +" "  + rt.totalMemory());
-    seq2 = new int[s2str.length()];
-    //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
-    score = new int[s1str.length()][s2str.length()];
-    //System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());
-    E = new int[s1str.length()][s2str.length()];
-    //System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory());
-    F = new int[s1str.length()][s2str.length()];
-    traceback = new int[s1str.length()][s2str.length()];
-    //System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory());
-    seq1 = stringToInt(s1str,type);
-    //System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory());
-    seq2 = stringToInt(s2str,type);
-    //System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory());
-
-    //   long tstart = System.currentTimeMillis();
-    //    calcScoreMatrix();
-    //long tend = System.currentTimeMillis();
-
-    //System.out.println("Time take to calculate score matrix = " + (tend-tstart) + " ms");
-
-
-    //   printScoreMatrix(score);
-    //System.out.println();
-
-    //printScoreMatrix(traceback);
-    //System.out.println();
-
-    //  printScoreMatrix(E);
-    //System.out.println();
-
-    ///printScoreMatrix(F);
-    //System.out.println();
-    // tstart = System.currentTimeMillis();
-    //traceAlignment();
-    //tend = System.currentTimeMillis();
-    //System.out.println("Time take to traceback alignment = " + (tend-tstart) + " ms");
-  }
-
-  public void traceAlignment() {
-
-    // Find the maximum score along the rhs or bottom row
-    int max = -9999;
-    for (int i = 0; i < seq1.length; i++) {
-      if (score[i][seq2.length - 1] > max ) {
-        max = score[i][seq2.length - 1];
-        maxi = i;
-        maxj = seq2.length-1;
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getMaxScore()
+    {
+        return maxscore;
     }
-    for (int j = 0; j < seq2.length; j++) {
-      if (score[seq1.length - 1][j] > max ) {
-        max = score[seq1.length - 1][j];
-        maxi = seq1.length-1;
-        maxj = j;
-      }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getSeq2Start()
+    {
+        return seq2start;
     }
 
-    //  System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
-
-    int i = maxi;
-    int j = maxj;
-    int trace;
-    maxscore = score[i][j] / 10;
-
-    seq1end = maxi+1;
-    seq2end = maxj+1;
-
-    aseq1 = new int[seq1.length + seq2.length];
-    aseq2 = new int[seq1.length + seq2.length];
-
-    count = seq1.length + seq2.length - 1;
-
-    while (i>0 && j >0) {
-
-      if (aseq1[count] != defInt && i >=0) {
-        aseq1[count] = seq1[i];
-        astr1 = intToStr[seq1[i]] + astr1;
-      }
-
-      if (aseq2[count] != defInt && j > 0) {
-        aseq2[count] = seq2[j];
-        astr2 = intToStr[seq2[j]] + astr2;
-      }
-      trace = findTrace(i,j);
-      if (trace == 0) {
-        i--;
-        j--;
-
-      } else  if (trace == 1) {
-        j--;
-        aseq1[count] = defInt;
-        astr1 = "-" + astr1.substring(1);
-      } else  if (trace == -1) {
-        i--;
-        aseq2[count] = defInt;
-        astr2 = "-" + astr2.substring(1);
-      }
-      count--;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getSeq2End()
+    {
+        return seq2end;
     }
 
-    seq1start = i+1;
-    seq2start = j+1;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getSeq1Start()
+    {
+        return seq1start;
+    }
 
-    if (aseq1[count] != defInt) {
-      aseq1[count] = seq1[i];
-      astr1 = intToStr[seq1[i]] + astr1;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getSeq1End()
+    {
+        return seq1end;
     }
 
-    if (aseq2[count] != defInt) {
-      aseq2[count] = seq2[j];
-      astr2 = intToStr[seq2[j]] + astr2;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getOutput()
+    {
+        return output.toString();
     }
-  }
 
-  public void printAlignment() {
-    // Find the biggest id length for formatting purposes
-    int maxid = s1.getName().length();
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getAStr1()
+    {
+        return astr1;
+    }
 
-    if (s2.getName().length() > maxid) {
-      maxid = s2.getName().length();
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getAStr2()
+    {
+        return astr2;
     }
 
-    int len = 72 - maxid - 1;
-    int nochunks = ((aseq1.length - count) / len) + 1;
-    pid = 0;
-    int overlap = 0;
-
-    output = output + ("Score = " + score[maxi][maxj] + "\n");
-    output = output + ("Length of alignment = " + (aseq1.length-count) + "\n");
-    output = output + ("Sequence ");
-    output = output + (new Format("%" + maxid + "s").form(s1.getName()));
-    output = output + (" :  " + seq1start + " - " + seq1end + " (Sequence length = " + s1str.length() + ")\n");
-    output = output + ("Sequence ");
-    output = output + (new Format("%" + maxid + "s").form(s2.getName()));
-    output = output + (" :  " + seq2start + " - " + seq2end + " (Sequence length = " + s2str.length() + ")\n\n");
-
-    for (int j = 0; j < nochunks; j++) {
-      // Print the first aligned sequence
-      output = output + (new Format("%" + (maxid) + "s").form(s1.getName()) + " ");
-      for (int i = 0; i < len ; i++) {
-
-        if ((count + i + j*len) < aseq1.length) {
-          output = output + (new Format("%s").form(intToStr[aseq1[count + i + j*len]]));
-        }
-      }
-
-      output = output + ("\n");
-      output = output + (new Format("%" + (maxid) + "s").form(" ") + " ");
-      // Print out the matching chars
-      for (int i = 0; i < len ; i++) {
-
-        if ((count + i + j*len) < aseq1.length) {
-          if ( intToStr[aseq1[count+i+j*len]].equals(intToStr[aseq2[count+i+j*len]]) && !intToStr[aseq1[count+i+j*len]].equals("-")) {
-            pid++;
-            output = output + ("|");
-          } else if (type.equals("pep")) {
-            if (ResidueProperties.getPAM250(intToStr[aseq1[count+i+j*len]],intToStr[aseq2[count+i+j*len]]) > 0) {
-              output  = output + (".");
-            } else {
-              output = output + (" ");
-            }
-          } else {
-            output = output + (" ");
-          }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int[] getASeq1()
+    {
+        return aseq1;
+    }
 
-        }
-      }
-      // Now print the second aligned sequence
-      output = output + ("\n");
-      output = output + (new Format("%" + (maxid) + "s").form(s2.getName()) + " " );
-      for (int i = 0; i < len ; i++) {
-        if ((count + i + j*len) < aseq1.length) {
-          output = output + (new Format("%s").form(intToStr[aseq2[count + i + j*len]]));
-        }
-      }
-      output = output + ("\n\n");
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int[] getASeq2()
+    {
+        return aseq2;
     }
-    pid = pid/(float)(aseq1.length-count)*100;
-    output = output + (new Format("Percentage ID = %2.2f\n\n").form(pid));
 
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceI getS1()
+    {
+        return s1;
+    }
 
-  public void printScoreMatrix(int[][] mat) {
-    int n = seq1.length;
-    int m = seq2.length;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceI getS2()
+    {
+        return s2;
+    }
 
-    for (int i = 0; i < n;i++) {
-      // Print the top sequence
-      if (i == 0) {
-        Format.print(System.out,"%8s",s2str.substring(0,1));
-        for (int jj = 1;jj < m; jj++) {
-          Format.print(System.out,"%5s",s2str.substring(jj,jj+1));
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s1 DOCUMENT ME!
+     * @param s2 DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     */
+    public void SeqInit(SequenceI s1, SequenceI s2, String type)
+    {
+        s1str = extractGaps(jalview.util.Comparison.GapChars, s1.getSequence());
+        s2str = extractGaps(jalview.util.Comparison.GapChars, s2.getSequence());
+
+        this.s1 = s1;
+        this.s2 = s2;
+
+        this.type = type;
+
+        if (type.equals("pep"))
+        {
+            lookup = ResidueProperties.getBLOSUM62();
+            intToStr = pep;
+            defInt = 23;
         }
-        System.out.println();
-      }
-
-      for (int j = 0;j < m; j++) {
-        if (j == 0) {
-          Format.print(System.out,"%3s",s1str.substring(i,i+1));
+        else if (type.equals("dna"))
+        {
+            lookup = ResidueProperties.getDNA();
+            intToStr = dna;
+            defInt = 4;
         }
-        Format.print(System.out,"%3d ",mat[i][j]/10);
-      }
-      System.out.println();
-    }
-  }
-
-  public int findTrace(int i,int j) {
-    int t = 0;
-    int max = score[i-1][j-1] + lookup[seq1[i]][seq2[j]] * 10;
-
-    if (F[i][j] > max) {
-      max = F[i][j];
-      t = -1;
-    } else if (F[i][j] == max) {
-      if (prev == -1) {
-        max = F[i][j];
-        t = -1;
-      }
-    }
-    if (E[i][j] >= max) {
-      max = E[i][j];
-      t = 1;
-    } else if (E[i][j] == max) {
-      if (prev == 1) {
-        max = E[i][j];
-        t = 1;
-      }
+        else
+        {
+            output.append("Wrong type = dna or pep only");
+            System.exit(0);
+        }
+
+        //System.out.println("lookuip " + rt.freeMemory() + " "+  rt.totalMemory());
+        seq1 = new int[s1str.length()];
+
+        //System.out.println("seq1 " + rt.freeMemory() +" "  + rt.totalMemory());
+        seq2 = new int[s2str.length()];
+
+        //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());
+        score = new int[s1str.length()][s2str.length()];
+
+        //System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());
+        E = new int[s1str.length()][s2str.length()];
+
+        //System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory());
+        F = new int[s1str.length()][s2str.length()];
+        traceback = new int[s1str.length()][s2str.length()];
+
+        //System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory());
+        seq1 = stringToInt(s1str, type);
+
+        //System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory());
+        seq2 = stringToInt(s2str, type);
+
+        //System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory());
+        //   long tstart = System.currentTimeMillis();
+        //    calcScoreMatrix();
+        //long tend = System.currentTimeMillis();
+        //System.out.println("Time take to calculate score matrix = " + (tend-tstart) + " ms");
+        //   printScoreMatrix(score);
+        //System.out.println();
+        //printScoreMatrix(traceback);
+        //System.out.println();
+        //  printScoreMatrix(E);
+        //System.out.println();
+        ///printScoreMatrix(F);
+        //System.out.println();
+        // tstart = System.currentTimeMillis();
+        //traceAlignment();
+        //tend = System.currentTimeMillis();
+        //System.out.println("Time take to traceback alignment = " + (tend-tstart) + " ms");
     }
-    prev = t;
-    return t;
-  }
 
-  public void calcScoreMatrix() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void traceAlignment()
+    {
+        // Find the maximum score along the rhs or bottom row
+        int max = -9999;
+
+        for (int i = 0; i < seq1.length; i++)
+        {
+            if (score[i][seq2.length - 1] > max)
+            {
+                max = score[i][seq2.length - 1];
+                maxi = i;
+                maxj = seq2.length - 1;
+            }
+        }
 
+        for (int j = 0; j < seq2.length; j++)
+        {
+            if (score[seq1.length - 1][j] > max)
+            {
+                max = score[seq1.length - 1][j];
+                maxi = seq1.length - 1;
+                maxj = j;
+            }
+        }
 
-    int n = seq1.length;
-    int m = seq2.length;
+        //  System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);
+        int i = maxi;
+        int j = maxj;
+        int trace;
+        maxscore = score[i][j] / 10;
 
+        seq1end = maxi + 1;
+        seq2end = maxj + 1;
 
-    // top left hand element
-    score[0][0] =  lookup[seq1[0]][seq2[0]] * 10;
-    E[0][0] = -gapExtend;
-    F[0][0] = 0;
+        aseq1 = new int[seq1.length + seq2.length];
+        aseq2 = new int[seq1.length + seq2.length];
 
-    // Calculate the top row first
-    for (int j=1; j < m; j++) {
-      // What should these values be? 0 maybe
-      E[0][j] = max(score[0][j-1] - gapOpen,E[0][j-1] - gapExtend);
-      F[0][j] = -gapExtend;
+        count = (seq1.length + seq2.length) - 1;
 
-      score[0][j] = max( lookup[seq1[0]][seq2[j]] * 10 ,-gapOpen,-gapExtend);
+        while ((i > 0) && (j > 0))
+        {
+            if ((aseq1[count] != defInt) && (i >= 0))
+            {
+                aseq1[count] = seq1[i];
+                astr1 = intToStr[seq1[i]] + astr1;
+            }
 
-      traceback[0][j] = 1;
-    }
+            if ((aseq2[count] != defInt) && (j > 0))
+            {
+                aseq2[count] = seq2[j];
+                astr2 = intToStr[seq2[j]] + astr2;
+            }
 
-    // Now do the left hand column
-    for (int i=1; i < n; i++) {
-      E[i][0] =  -gapOpen;
-      F[i][0] =  max(score[i-1][0]-gapOpen,F[i-1][0]-gapExtend);
+            trace = findTrace(i, j);
 
-      score[i][0] = max( lookup[seq1[i]][seq2[0]] * 10 ,E[i][0],F[i][0]);
-      traceback[i][0] = -1;
-    }
+            if (trace == 0)
+            {
+                i--;
+                j--;
+            }
+            else if (trace == 1)
+            {
+                j--;
+                aseq1[count] = defInt;
+                astr1 = "-" + astr1.substring(1);
+            }
+            else if (trace == -1)
+            {
+                i--;
+                aseq2[count] = defInt;
+                astr2 = "-" + astr2.substring(1);
+            }
 
-    // Now do all the other rows
-    for (int i = 1; i < n; i++) {
-      for (int j = 1; j < m; j++) {
+            count--;
+        }
 
-        E[i][j] = max(score[i][j-1] - gapOpen,  E[i][j-1] - gapExtend);
-        F[i][j] = max(score[i-1][j] - gapOpen,  F[i-1][j] - gapExtend);
+        seq1start = i + 1;
+        seq2start = j + 1;
 
-        score[i][j] = max(score[i-1][j-1] + lookup[seq1[i]][seq2[j]]*10,
-                          E[i][j],
-                          F[i][j]);
-        traceback[i][j] = findTrace(i,j);
-      }
-    }
+        if (aseq1[count] != defInt)
+        {
+            aseq1[count] = seq1[i];
+            astr1 = intToStr[seq1[i]] + astr1;
+        }
 
-  }
-  public static String extractChars(String chars, String seq) {
-    String out = seq;
-    for (int i=0; i < chars.length(); i++) {
-      String gap = chars.substring(i,i+1);
-      out = extractGaps(gap,out);
-    }
-    return out;
-  }
-  public static String extractGaps(String gapChar, String seq) {
-    StringTokenizer str = new StringTokenizer(seq,gapChar);
-    String newString = "";
-
-    while (str.hasMoreTokens()) {
-      newString  = newString + str.nextToken();
+        if (aseq2[count] != defInt)
+        {
+            aseq2[count] = seq2[j];
+            astr2 = intToStr[seq2[j]] + astr2;
+        }
     }
-    return newString;
-  }
 
+    /**
+     * DOCUMENT ME!
+     */
+    public void printAlignment(java.io.PrintStream os)
+    {
+        // Find the biggest id length for formatting purposes
+        int maxid = s1.getName().length();
+
+        if (s2.getName().length() > maxid)
+        {
+            maxid = s2.getName().length();
+        }
+
+        int len = 72 - maxid - 1;
+        int nochunks = ((aseq1.length - count) / len) + 1;
+        pid = 0;
+
+        output.append("Score = " + score[maxi][maxj] + "\n");
+        output.append("Length of alignment = " + (aseq1.length - count) + "\n");
+        output.append("Sequence ");
+        output.append(new Format("%" + maxid + "s").form(s1.getName()));
+        output.append(" :  " + seq1start + " - " + seq1end + " (Sequence length = " +
+            s1str.length() + ")\n");
+        output .append("Sequence ");
+        output.append(new Format("%" + maxid + "s").form(s2.getName()));
+        output .append(" :  " + seq2start + " - " + seq2end + " (Sequence length = " +
+            s2str.length() + ")\n\n");
+
+        for (int j = 0; j < nochunks; j++)
+        {
+            // Print the first aligned sequence
+            output.append(new Format("%" + (maxid) + "s").form(s1.getName()) + " ");
+
+            for (int i = 0; i < len; i++)
+            {
+                if ((count + i + (j * len)) < aseq1.length)
+                {
+                    output.append(new Format("%s").form(intToStr[aseq1[count + i +
+                            (j * len)]]));
+                }
+            }
+
+            output.append("\n");
+            output.append(new Format("%" + (maxid) + "s").form(" ") + " ");
+
+            // Print out the matching chars
+            for (int i = 0; i < len; i++)
+            {
+                if ((count + i + (j * len)) < aseq1.length)
+                {
+                    if (intToStr[aseq1[count + i + (j * len)]].equals(
+                                intToStr[aseq2[count + i + (j * len)]]) &&
+                            !intToStr[aseq1[count + i + (j * len)]].equals("-"))
+                    {
+                        pid++;
+                        output.append("|");
+                    }
+                    else if (type.equals("pep"))
+                    {
+                        if (ResidueProperties.getPAM250(
+                                    intToStr[aseq1[count + i + (j * len)]],
+                                    intToStr[aseq2[count + i + (j * len)]]) > 0)
+                        {
+                            output.append(".");
+                        }
+                        else
+                        {
+                            output.append(" ");
+                        }
+                    }
+                    else
+                    {
+                        output.append(" ");
+                    }
+                }
+            }
+
+            // Now print the second aligned sequence
+            output = output.append("\n");
+            output = output.append(new Format("%" + (maxid) + "s").form(s2.getName()) + " ");
+
+            for (int i = 0; i < len; i++)
+            {
+                if ((count + i + (j * len)) < aseq1.length)
+                {
+                    output .append(new Format("%s").form(intToStr[aseq2[count + i +
+                            (j * len)]]));
+                }
+            }
+
+            output = output .append("\n\n");
+        }
+
+        pid = pid / (float) (aseq1.length - count) * 100;
+        output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));
 
-  public int max(int i1, int i2, int i3) {
-    int max = i1;
-    if (i2 > i1)  {
-      max = i2;
+        try{
+          os.println(output.toString());
+        }catch(Exception ex){}
     }
-    if (i3 > max) {
-      max = i3;
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param mat DOCUMENT ME!
+     */
+    public void printScoreMatrix(int[][] mat)
+    {
+        int n = seq1.length;
+        int m = seq2.length;
+
+        for (int i = 0; i < n; i++)
+        {
+            // Print the top sequence
+            if (i == 0)
+            {
+                Format.print(System.out, "%8s", s2str.substring(0, 1));
+
+                for (int jj = 1; jj < m; jj++)
+                {
+                    Format.print(System.out, "%5s", s2str.substring(jj, jj + 1));
+                }
+
+                System.out.println();
+            }
+
+            for (int j = 0; j < m; j++)
+            {
+                if (j == 0)
+                {
+                    Format.print(System.out, "%3s", s1str.substring(i, i + 1));
+                }
+
+                Format.print(System.out, "%3d ", mat[i][j] / 10);
+            }
+
+            System.out.println();
+        }
     }
-    return max;
-  }
 
-  public int max(int i1, int i2) {
-    int max = i1;
-    if (i2 > i1)  {
-      max = i2;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int findTrace(int i, int j)
+    {
+        int t = 0;
+        int max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10);
+
+        if (F[i][j] > max)
+        {
+            max = F[i][j];
+            t = -1;
+        }
+        else if (F[i][j] == max)
+        {
+            if (prev == -1)
+            {
+                max = F[i][j];
+                t = -1;
+            }
+        }
+
+        if (E[i][j] >= max)
+        {
+            max = E[i][j];
+            t = 1;
+        }
+        else if (E[i][j] == max)
+        {
+            if (prev == 1)
+            {
+                max = E[i][j];
+                t = 1;
+            }
+        }
+
+        prev = t;
+
+        return t;
     }
-    return max;
-  }
-
-  public int[] stringToInt(String s,String type) {
-    int[] seq1 = new int[s.length()];
-
-    for (int i = 0;i < s.length(); i++) {
-      String ss = s.substring(i,i+1).toUpperCase();
-      try {
-        if (type.equals("pep")) {
-          seq1[i] = ((Integer)ResidueProperties.aaHash.get(ss)).intValue();
-        } else if (type.equals("dna")) {
-          seq1[i] = ((Integer)dnaHash.get(ss)).intValue();
+
+    /**
+     * DOCUMENT ME!
+     */
+    public void calcScoreMatrix()
+    {
+        int n = seq1.length;
+        int m = seq2.length;
+
+        // top left hand element
+        score[0][0] = lookup[seq1[0]][seq2[0]] * 10;
+        E[0][0] = -gapExtend;
+        F[0][0] = 0;
+
+        // Calculate the top row first
+        for (int j = 1; j < m; j++)
+        {
+            // What should these values be? 0 maybe
+            E[0][j] = max(score[0][j - 1] - gapOpen, E[0][j - 1] - gapExtend);
+            F[0][j] = -gapExtend;
+
+            score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen,
+                    -gapExtend);
+
+            traceback[0][j] = 1;
         }
-        if (seq1[i] > 23) {
-          seq1[i] = 23;
+
+        // Now do the left hand column
+        for (int i = 1; i < n; i++)
+        {
+            E[i][0] = -gapOpen;
+            F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend);
+
+            score[i][0] = max(lookup[seq1[i]][seq2[0]] * 10, E[i][0], F[i][0]);
+            traceback[i][0] = -1;
         }
-      } catch (Exception e) {
-        if (type.equals("dna")) {
-          seq1[i] = 4;
-        } else {
-          seq1[i] = 23;
+
+        // Now do all the other rows
+        for (int i = 1; i < n; i++)
+        {
+            for (int j = 1; j < m; j++)
+            {
+                E[i][j] = max(score[i][j - 1] - gapOpen, E[i][j - 1] -
+                        gapExtend);
+                F[i][j] = max(score[i - 1][j] - gapOpen, F[i - 1][j] -
+                        gapExtend);
+
+                score[i][j] = max(score[i - 1][j - 1] +
+                        (lookup[seq1[i]][seq2[j]] * 10), E[i][j], F[i][j]);
+                traceback[i][j] = findTrace(i, j);
+            }
         }
-      }
     }
-    return seq1;
-  }
 
-  public static void displayMatrix(Graphics g, int[][] mat, int n, int m,int psize) {
 
-    int max = -1000;
-    int min = 1000;
 
-    for (int i=0; i < n; i++) {
-      for (int j=0; j < m; j++) {
-        if (mat[i][j] >= max) {
-          max = mat[i][j];
+    /**
+     * DOCUMENT ME!
+     *
+     * @param gapChar DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String extractGaps(String gapChar, String seq)
+    {
+        StringTokenizer str = new StringTokenizer(seq, gapChar);
+        StringBuffer newString = new StringBuffer();
+
+        while (str.hasMoreTokens())
+        {
+            newString.append( str.nextToken() );
         }
-        if (mat[i][j] <= min) {
-          min = mat[i][j];
+
+        return newString.toString();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i1 DOCUMENT ME!
+     * @param i2 DOCUMENT ME!
+     * @param i3 DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int max(int i1, int i2, int i3)
+    {
+        int max = i1;
+
+        if (i2 > i1)
+        {
+            max = i2;
         }
-      }
+
+        if (i3 > max)
+        {
+            max = i3;
+        }
+
+        return max;
     }
-    System.out.println(max + " " + min);
-    for (int i=0; i < n; i++) {
-      for (int j=0; j < m; j++) {
-        int x = psize*i;
-        int y = psize*j;
-        //	System.out.println(mat[i][j]);
-        float score = (float)(mat[i][j] - min)/(float)(max-min);
-        g.setColor(new Color(score,0,0));
-        g.fillRect(x,y,psize,psize);
-        //	System.out.println(x + " " + y + " " + score);
-      }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i1 DOCUMENT ME!
+     * @param i2 DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int max(int i1, int i2)
+    {
+        int max = i1;
+
+        if (i2 > i1)
+        {
+            max = i2;
+        }
+
+        return max;
     }
-  }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int[] stringToInt(String s, String type)
+    {
+        int[] seq1 = new int[s.length()];
+
+        for (int i = 0; i < s.length(); i++)
+        {
+            String ss = s.substring(i, i + 1).toUpperCase();
+
+            try
+            {
+                if (type.equals("pep"))
+                {
+                    seq1[i] = ((Integer) ResidueProperties.aaHash.get(ss)).intValue();
+                }
+                else if (type.equals("dna"))
+                {
+                    seq1[i] = ((Integer) dnaHash.get(ss)).intValue();
+                }
+
+                if (seq1[i] > 23)
+                {
+                    seq1[i] = 23;
+                }
+            }
+            catch (Exception e)
+            {
+                if (type.equals("dna"))
+                {
+                    seq1[i] = 4;
+                }
+                else
+                {
+                    seq1[i] = 23;
+                }
+            }
+        }
+
+        return seq1;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param mat DOCUMENT ME!
+     * @param n DOCUMENT ME!
+     * @param m DOCUMENT ME!
+     * @param psize DOCUMENT ME!
+     */
+    public static void displayMatrix(Graphics g, int[][] mat, int n, int m,
+        int psize)
+    {
+        int max = -1000;
+        int min = 1000;
+
+        for (int i = 0; i < n; i++)
+        {
+            for (int j = 0; j < m; j++)
+            {
+                if (mat[i][j] >= max)
+                {
+                    max = mat[i][j];
+                }
+
+                if (mat[i][j] <= min)
+                {
+                    min = mat[i][j];
+                }
+            }
+        }
+
+        System.out.println(max + " " + min);
+
+        for (int i = 0; i < n; i++)
+        {
+            for (int j = 0; j < m; j++)
+            {
+                int x = psize * i;
+                int y = psize * j;
+
+                //	System.out.println(mat[i][j]);
+                float score = (float) (mat[i][j] - min) / (float) (max - min);
+                g.setColor(new Color(score, 0, 0));
+                g.fillRect(x, y, psize, psize);
+
+                //	System.out.println(x + " " + y + " " + score);
+            }
+        }
+    }
 }