X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSeqCigar.java;h=09b2e89eceb926fd363218b55e732e0ef380e9aa;hb=1152ad2009cfc7bf521b6bcb556f6031bbe5b86a;hp=77e9111b8851ca4a38d66a3cf5d4b5e0ea8c2e69;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 77e9111..09b2e89 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,8 +23,10 @@ package jalview.datamodel;
 import java.util.Enumeration;
 import java.util.Hashtable;
 
-import jalview.analysis.*;
-import jalview.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils;
+import jalview.util.MessageManager;
+import jalview.util.ShiftList;
 
 public class SeqCigar extends CigarSimple
 {
@@ -538,157 +540,6 @@ public class SeqCigar extends CigarSimple
   }
 
   /**
-   * non rigorous testing
-   */
-  /**
-   * 
-   * @param seq
-   *          Sequence
-   * @param ex_cs_gapped
-   *          String
-   * @return String
-   */
-  public static String testCigar_string(Sequence seq, String ex_cs_gapped)
-  {
-    SeqCigar c_sgapped = new SeqCigar(seq);
-    String cs_gapped = c_sgapped.getCigarstring();
-    if (!cs_gapped.equals(ex_cs_gapped))
-    {
-      System.err.println("Failed getCigarstring: incorect string '"
-              + cs_gapped + "' != " + ex_cs_gapped);
-    }
-    return cs_gapped;
-  }
-
-  public static boolean testSeqRecovery(SeqCigar gen_sgapped,
-          SequenceI s_gapped)
-  {
-    // this is non-rigorous - start and end recovery is not tested.
-    SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
-    if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
-    {
-      System.err.println("Couldn't reconstruct sequence.\n"
-              + gen_sgapped_s.getSequenceAsString() + "\n"
-              + s_gapped.getSequenceAsString());
-      return false;
-    }
-    return true;
-  }
-
-  public static void main(String argv[]) throws Exception
-  {
-    String o_seq;
-    Sequence s = new Sequence("MySeq",
-            o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt", 39, 80);
-    String orig_gapped;
-    Sequence s_gapped = new Sequence(
-            "MySeq",
-            orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt",
-            39, 80);
-    String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
-    s_gapped.setDatasetSequence(s);
-    String sub_gapped_s;
-    Sequence s_subsequence_gapped = new Sequence(
-            "MySeq",
-            sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh",
-            43, 77);
-
-    s_subsequence_gapped.setDatasetSequence(s);
-    SeqCigar c_null = new SeqCigar(s);
-    String cs_null = c_null.getCigarstring();
-    if (!cs_null.equals("42M"))
-    {
-      System.err
-              .println("Failed to recover ungapped sequence cigar operations:"
-                      + ((cs_null == "") ? "empty string" : cs_null));
-    }
-    testCigar_string(s_gapped, ex_cs_gapped);
-    SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
-    if (!gen_sgapped.getCigarstring().equals(ex_cs_gapped))
-    {
-      System.err.println("Failed parseCigar(" + ex_cs_gapped
-              + ")->getCigarString()->'" + gen_sgapped.getCigarstring()
-              + "'");
-    }
-    testSeqRecovery(gen_sgapped, s_gapped);
-    // Test dataset resolution
-    SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
-    if (!testSeqRecovery(sub_gapped, s_subsequence_gapped))
-    {
-      System.err
-              .println("Failed recovery for subsequence of dataset sequence");
-    }
-    // width functions
-    if (sub_gapped.getWidth() != sub_gapped_s.length())
-    {
-      System.err.println("Failed getWidth()");
-    }
-
-    sub_gapped.getFullWidth();
-    if (sub_gapped.hasDeletedRegions())
-    {
-      System.err.println("hasDeletedRegions is incorrect.");
-    }
-    // Test start-end region SeqCigar
-    SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
-    if (sub_se_gp.getWidth() != 41)
-    {
-      System.err
-              .println("SeqCigar(seq, start, end) not properly clipped alignsequence.");
-    }
-    System.out.println("Original sequence align:\n" + sub_gapped_s
-            + "\nReconstructed window from 8 to 48\n" + "XXXXXXXX"
-            + sub_se_gp.getSequenceString('-') + "..." + "\nCigar String:"
-            + sub_se_gp.getCigarstring() + "\n");
-    SequenceI ssgp = sub_se_gp.getSeq('-');
-    System.out.println("\t " + ssgp.getSequenceAsString());
-    for (int r = 0; r < 10; r++)
-    {
-      sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
-      int sl = sub_se_gp.getWidth();
-      int st = sl - 1 - r;
-      for (int rs = 0; rs < 10; rs++)
-      {
-        int e = st + rs;
-        sub_se_gp.deleteRange(st, e);
-        String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
-        System.out.println(st + "," + e + "\t:" + ssgapedseq);
-        st -= 3;
-      }
-    }
-    {
-      SeqCigar[] set = new SeqCigar[]
-      { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
-          new SeqCigar(s_gapped) };
-      Alignment al = new Alignment(set);
-      for (int i = 0; i < al.getHeight(); i++)
-      {
-        System.out.println("" + al.getSequenceAt(i).getName() + "\t"
-                + al.getSequenceAt(i).getStart() + "\t"
-                + al.getSequenceAt(i).getEnd() + "\t"
-                + al.getSequenceAt(i).getSequenceAsString());
-      }
-    }
-    {
-      System.out.println("Gapped.");
-      SeqCigar[] set = new SeqCigar[]
-      { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
-          new SeqCigar(s_gapped) };
-      set[0].deleteRange(20, 25);
-      Alignment al = new Alignment(set);
-      for (int i = 0; i < al.getHeight(); i++)
-      {
-        System.out.println("" + al.getSequenceAt(i).getName() + "\t"
-                + al.getSequenceAt(i).getStart() + "\t"
-                + al.getSequenceAt(i).getEnd() + "\t"
-                + al.getSequenceAt(i).getSequenceAsString());
-      }
-    }
-    // if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
-    // System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
-  }
-
-  /**
    * references to entities that this sequence cigar is associated with.
    */
   private Hashtable selGroups = null;