- SequenceI s1;\r
- SequenceI s2;\r
-\r
- String s1str;\r
- String s2str;\r
-\r
- int maxi;\r
- int maxj;\r
-\r
- int[] aseq1;\r
- int[] aseq2;\r
-\r
- String astr1 = "";\r
- String astr2 = "";\r
-\r
- public int seq1start;\r
- public int seq1end;\r
- public int seq2start;\r
- public int seq2end;\r
-\r
- int count;\r
-\r
- public int maxscore;\r
- float pid;\r
- int prev = 0;\r
-\r
- public static java.util.Hashtable dnaHash = new java.util.Hashtable();\r
-\r
- static {\r
- dnaHash.put("C", new Integer(0));\r
- dnaHash.put("T", new Integer(1));\r
- dnaHash.put("A", new Integer(2));\r
- dnaHash.put("G", new Integer(3));\r
- dnaHash.put("-", new Integer(4));\r
- }\r
-\r
- static String dna[] = {"C","T","A","G","-"};\r
- 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","-"};\r
-\r
- int gapOpen = 120;\r
- int gapExtend = 20;\r
-\r
- int lookup[][] = ResidueProperties.getBLOSUM62();\r
- String intToStr[] = pep;\r
- int defInt = 23;\r
-\r
- String output = "";\r
-\r
- String type;\r
- Runtime rt;\r
- public AlignSeq() {}\r
-\r
- public AlignSeq(SequenceI s1, SequenceI s2,String type) {\r
- rt = Runtime.getRuntime();\r
- SeqInit(s1,s2,type);\r
- }\r
-\r
- public int getMaxScore() {\r
- return maxscore;\r
- }\r
-\r
- public int getSeq2Start() {\r
- return seq2start;\r
- }\r
-\r
- public int getSeq2End() {\r
- return seq2end;\r
- }\r
-\r
- public int getSeq1Start() {\r
- return seq1start;\r
- }\r
-\r
- public int getSeq1End() {\r
- return seq1end;\r
- }\r
-\r
- public String getOutput() {\r
- return output;\r
- }\r
-\r
- public String getAStr1() {\r
- return astr1;\r
- }\r
- public String getAStr2() {\r
- return astr2;\r
- }\r
- public int [] getASeq1() {\r
- return aseq1;\r
- }\r
- public int [] getASeq2() {\r
- return aseq2;\r
- }\r
- public SequenceI getS1() {\r
- return s1;\r
- }\r
- public SequenceI getS2() {\r
- return s2;\r
- }\r
-\r
- public void SeqInit(SequenceI s1, SequenceI s2,String type) {\r
- s1str = extractGaps(".",s1.getSequence());\r
- s2str = extractGaps(".",s2.getSequence());\r
- s1str = extractGaps("-",s1str);\r
- s2str = extractGaps("-",s2str);\r
- s1str = extractGaps(" ",s1str);\r
- s2str = extractGaps(" ",s2str);\r
-\r
- this.s1 = s1;\r
- this.s2 = s2;\r
-\r
- this.type = type;\r
-\r
- if (type.equals("pep")) {\r
- lookup = ResidueProperties.getBLOSUM62();\r
- intToStr = pep;\r
- defInt = 23;\r
- } else if (type.equals("dna")) {\r
- lookup = ResidueProperties.getDNA();\r
- intToStr = dna;\r
- defInt = 4;\r
- } else {\r
- output = output + ("Wrong type = dna or pep only");\r
- System.exit(0);\r