X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=3eae385a0473f4e266d627a85539abfd55f6fb0e;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=fcb117cedf9319850066e3056e952a9ac797cc67;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index fcb117c..3eae385 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,22 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview 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 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
-
 import java.util.*;
 
 import java.awt.*;
@@ -143,7 +143,7 @@ public class AlignSeq
   public AlignSeq(SequenceI s1, String string1, SequenceI s2,
           String string2, String type)
   {
-    SeqInit(s1, string1, s2, string2, type);
+    SeqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type);
   }
 
   /**
@@ -267,16 +267,11 @@ public class AlignSeq
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param s1
-   *          DOCUMENT ME!
-   * @param string1
-   *          - string to align for sequence1
-   * @param s2
-   *          sequence 2
-   * @param string2
-   *          - string to align for sequence2
+   * Construct score matrix for sequences with standard DNA or PEPTIDE matrix
+   * @param s1 - sequence 1
+   * @param string1 - string to use for s1
+   * @param s2 - sequence 2
+   * @param string2 - string to use for s2
    * @param type
    *          DNA or PEPTIDE
    */
@@ -289,6 +284,14 @@ public class AlignSeq
     SeqInit(string1, string2);
   }
 
+  /**
+   * Construct score matrix for sequences with custom substitution matrix
+   * @param s1 - sequence 1
+   * @param string1 - string to use for s1
+   * @param s2 - sequence 2
+   * @param string2 - string to use for s2
+   * @param scoreMatrix - substitution matrix to use for alignment
+   */
   public void SeqInit(SequenceI s1, String string1, SequenceI s2,
           String string2, ScoreMatrix scoreMatrix)
   {
@@ -302,7 +305,7 @@ public class AlignSeq
    * construct score matrix for string1 and string2 (after removing any existing
    * gaps
    * 
-   * @param string1
+   * @param string1 
    * @param string2
    */
   private void SeqInit(String string1, String string2)
@@ -382,13 +385,13 @@ public class AlignSeq
     {
       intToStr = pep;
       charToInt = ResidueProperties.aaIndex;
-      defInt = 23;
+      defInt = ResidueProperties.maxProteinIndex;
     }
     else if (type.equals(AlignSeq.DNA))
     {
       intToStr = dna;
       charToInt = ResidueProperties.nucleotideIndex;
-      defInt = 4;
+      defInt = ResidueProperties.maxNucleotideIndex;
     }
     else
     {
@@ -501,22 +504,23 @@ public class AlignSeq
     // TODO: Use original sequence characters rather than re-translated
     // characters in output
     // Find the biggest id length for formatting purposes
-    String s1id=s1.getName(),s2id=s2.getName();
+    String s1id = s1.getName(), s2id = s2.getName();
     int maxid = s1.getName().length();
     if (s2.getName().length() > maxid)
     {
       maxid = s2.getName().length();
     }
-    if (maxid>30) {
+    if (maxid > 30)
+    {
       maxid = 30;
       // JAL-527 - truncate the sequence ids
-      if (s1.getName().length()>maxid)
+      if (s1.getName().length() > maxid)
       {
-        s1id = s1.getName().substring(0,30);
+        s1id = s1.getName().substring(0, 30);
       }
-      if (s2.getName().length()>maxid)
+      if (s2.getName().length() > maxid)
       {
-        s2id = s2.getName().substring(0,30);
+        s2id = s2.getName().substring(0, 30);
       }
     }
     int len = 72 - maxid - 1;
@@ -537,8 +541,7 @@ public class AlignSeq
     for (int j = 0; j < nochunks; j++)
     {
       // Print the first aligned sequence
-      output.append(new Format("%" + (maxid) + "s").form(s1id)
-              + " ");
+      output.append(new Format("%" + (maxid) + "s").form(s1id) + " ");
 
       for (int i = 0; i < len; i++)
       {
@@ -918,4 +921,181 @@ public class AlignSeq
       }
     }
   }
+
+  /**
+   * Compute a globally optimal needleman and wunsch alignment between two
+   * sequences
+   * 
+   * @param s1
+   * @param s2
+   * @param type
+   *          AlignSeq.DNA or AlignSeq.PEP
+   */
+  public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2,
+          String type)
+  {
+    AlignSeq as = new AlignSeq(s1, s2, type);
+
+    as.calcScoreMatrix();
+    as.traceAlignment();
+    return as;
+  }
+
+  /**
+   * 
+   * @return mapping from positions in S1 to corresponding positions in S2
+   */
+  public jalview.datamodel.Mapping getMappingFromS1(boolean allowmismatch)
+  {
+    ArrayList<Integer> as1 = new ArrayList<Integer>(), as2 = new ArrayList<Integer>();
+    int pdbpos = s2.getStart() + getSeq2Start() - 2;
+    int alignpos = s1.getStart() + getSeq1Start() - 2;
+    int lp2 = pdbpos - 3, lp1 = alignpos - 3;
+    boolean lastmatch = false;
+    // and now trace the alignment onto the atom set.
+    for (int i = 0; i < astr1.length(); i++)
+    {
+      char c1 = astr1.charAt(i), c2 = astr2.charAt(i);
+      if (c1 != '-')
+      {
+        alignpos++;
+      }
+
+      if (c2 != '-')
+      {
+        pdbpos++;
+      }
+
+      if (allowmismatch || c1 == c2)
+      {
+        lastmatch = true;
+        // extend mapping interval.
+        if (lp1 + 1 != alignpos || lp2+1 !=pdbpos)
+        {
+          as1.add(Integer.valueOf(alignpos));
+          as2.add(Integer.valueOf(pdbpos));
+        }
+        lp1 = alignpos;
+        lp2 = pdbpos;
+      }
+      else
+      {
+        lastmatch = false;
+      }
+    }
+    // construct range pairs
+    int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)], mapseq2 = new int[as2
+            .size() + (lastmatch ? 1 : 0)];
+    int i = 0;
+    for (Integer ip : as1)
+    {
+      mapseq1[i++] = ip;
+    }
+    ;
+    i = 0;
+    for (Integer ip : as2)
+    {
+      mapseq2[i++] = ip;
+    }
+    ;
+    if (lastmatch)
+    {
+      mapseq1[mapseq1.length - 1] = alignpos;
+      mapseq2[mapseq2.length - 1] = pdbpos;
+    }
+    MapList map = new MapList(mapseq1, mapseq2, 1, 1);
+
+    jalview.datamodel.Mapping mapping = new Mapping(map);
+    mapping.setTo(s2);
+    return mapping;
+  }
+
+  /**
+   * compute the PID vector used by the redundancy filter.
+   * 
+   * @param originalSequences
+   *          - sequences in alignment that are to filtered
+   * @param omitHidden
+   *          - null or strings to be analysed (typically, visible portion of
+   *          each sequence in alignment)
+   * @param start
+   *          - first column in window for calculation
+   * @param end
+   *          - last column in window for calculation
+   * @param ungapped
+   *          - if true then use ungapped sequence to compute PID
+   * @return vector containing maximum PID for i-th sequence and any sequences
+   *         longer than that seuqence
+   */
+  public static float[] computeRedundancyMatrix(
+          SequenceI[] originalSequences, String[] omitHidden, int start,
+          int end, boolean ungapped)
+  {
+    int height = originalSequences.length;
+    float[] redundancy = new float[height];
+    int[] lngth = new int[height];
+    for (int i = 0; i < height; i++)
+    {
+      redundancy[i] = 0f;
+      lngth[i] = -1;
+    }
+
+    // long start = System.currentTimeMillis();
+
+    float pid;
+    String seqi, seqj;
+    for (int i = 0; i < height; i++)
+    {
+
+      for (int j = 0; j < i; j++)
+      {
+        if (i == j)
+        {
+          continue;
+        }
+
+        if (omitHidden == null)
+        {
+          seqi = originalSequences[i].getSequenceAsString(start, end);
+          seqj = originalSequences[j].getSequenceAsString(start, end);
+        }
+        else
+        {
+          seqi = omitHidden[i];
+          seqj = omitHidden[j];
+        }
+        if (lngth[i] == -1)
+        {
+          String ug = AlignSeq.extractGaps(Comparison.GapChars, seqi);
+          lngth[i] = ug.length();
+          if (ungapped)
+          {
+            seqi = ug;
+          }
+        }
+        if (lngth[j] == -1)
+        {
+          String ug = AlignSeq.extractGaps(Comparison.GapChars, seqj);
+          lngth[j] = ug.length();
+          if (ungapped)
+          {
+            seqj = ug;
+          }
+        }
+        pid = Comparison.PID(seqi, seqj);
+
+        // use real sequence length rather than string length
+        if (lngth[j] < lngth[i])
+        {
+          redundancy[j] = Math.max(pid, redundancy[j]);
+        }
+        else
+        {
+          redundancy[i] = Math.max(pid, redundancy[i]);
+        }
+
+      }
+    }
+    return redundancy;
+  }
 }