- public static final String PEP = "pep";
- public static final String DNA = "dna";
- /** 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;
- public String s1str;
- public String s2str;
- int maxi;
- int maxj;
- int[] aseq1;
- int[] aseq2;
- public String astr1="";
- public 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;
-
- /**
- * 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)
- {
- SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(), type);
- }
-
- /**
- * Creates a new AlignSeq object.
- *
- * @param s1 DOCUMENT ME!
- * @param s2 DOCUMENT ME!
- * @param type DOCUMENT ME!
- */
- public AlignSeq(SequenceI s1,
- String string1,
- SequenceI s2,
- String string2,
- String type)
+ public static final String PEP = "pep";
+ public static final String DNA = "dna";
+
+ static String[] dna =
+ {
+ "A", "C", "G", "T", "-"};
+ //"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;
+ public String s1str;
+ public String s2str;
+ int maxi;
+ int maxj;
+ int[] aseq1;
+ int[] aseq2;
+ public String astr1 = "";
+ public 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;
+
+ /**
+ * 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)
+ {
+ SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(), type);
+ }
+
+ /**
+ * Creates a new AlignSeq object.
+ *
+ * @param s1 DOCUMENT ME!
+ * @param s2 DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ */
+ public AlignSeq(SequenceI s1,
+ String string1,
+ SequenceI s2,
+ String string2,
+ String type)
+ {
+ SeqInit(s1, string1, s2, string2, type);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getMaxScore()
+ {
+ return maxscore;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getSeq2Start()
+ {
+ return seq2start;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getSeq2End()
+ {
+ return seq2end;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getSeq1Start()
+ {
+ return seq1start;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getSeq1End()
+ {
+ return seq1end;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getOutput()
+ {
+ return output.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getAStr1()
+ {
+ return astr1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getAStr2()
+ {
+ return astr2;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getASeq1()
+ {
+ return aseq1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int[] getASeq2()
+ {
+ return aseq2;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceI getS1()
+ {
+ return s1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceI getS2()
+ {
+ return s2;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s1 DOCUMENT ME!
+ * @param string1 - string to align for sequence1
+ * @param s2 sequence 2
+ * @param string2 - string to align for sequence2
+ * @param type DNA or PEPTIDE
+ */
+ public void SeqInit(SequenceI s1,
+ String string1,
+ SequenceI s2,
+ String string2,
+ String type)
+ {
+ this.s1 = s1;
+ this.s2 = s2;
+ setDefaultParams(type);
+ SeqInit(string1, string2);
+ }
+
+ public void SeqInit(SequenceI s1,
+ String string1,
+ SequenceI s2,
+ String string2,
+ ScoreMatrix scoreMatrix)
+ {
+ this.s1 = s1;
+ this.s2 = s2;
+ setType(scoreMatrix.isDNA() ? AlignSeq.DNA : AlignSeq.PEP);
+ lookup = scoreMatrix.getMatrix();
+ }
+
+ /**
+ * construct score matrix for string1 and string2 (after removing any existing gaps
+ * @param string1
+ * @param string2
+ */
+ private void SeqInit(String string1, String string2)
+ {
+ s1str = extractGaps(jalview.util.Comparison.GapChars, string1);
+ s2str = extractGaps(jalview.util.Comparison.GapChars, string2);
+
+ if (s1str.length() == 0 || s2str.length() == 0)