-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.analysis;\r
-\r
-import jalview.datamodel.SequenceI;\r
-\r
-import jalview.schemes.*;\r
-\r
-import jalview.util.*;\r
-\r
-import java.awt.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-/**\r
- *\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class AlignSeq\r
-{\r
- /** DOCUMENT ME!! */\r
- public static java.util.Hashtable dnaHash = new java.util.Hashtable();\r
-\r
- static\r
- {\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 =\r
- {\r
- "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",\r
- "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-"\r
- };\r
- int[][] score;\r
- int[][] E;\r
- int[][] F;\r
- int[][] traceback;\r
- int[] seq1;\r
- int[] seq2;\r
- SequenceI s1;\r
- SequenceI s2;\r
- public String s1str;\r
- public String s2str;\r
- int maxi;\r
- int maxj;\r
- int[] aseq1;\r
- int[] aseq2;\r
- public String astr1="";\r
- public String astr2="";\r
-\r
- /** DOCUMENT ME!! */\r
- public int seq1start;\r
-\r
- /** DOCUMENT ME!! */\r
- public int seq1end;\r
-\r
- /** DOCUMENT ME!! */\r
- public int seq2start;\r
-\r
- /** DOCUMENT ME!! */\r
- public int seq2end;\r
- int count;\r
-\r
- /** DOCUMENT ME!! */\r
- public int maxscore;\r
- float pid;\r
- int prev = 0;\r
- int gapOpen = 120;\r
- int gapExtend = 20;\r
- int[][] lookup = ResidueProperties.getBLOSUM62();\r
- String[] intToStr = pep;\r
- int defInt = 23;\r
- StringBuffer output = new StringBuffer();\r
- String type;\r
-\r
- /**\r
- * Creates a new AlignSeq object.\r
- *\r
- * @param s1 DOCUMENT ME!\r
- * @param s2 DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- */\r
- public AlignSeq(SequenceI s1, SequenceI s2, String type)\r
- {\r
- SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(), type);\r
- }\r
-\r
- /**\r
- * Creates a new AlignSeq object.\r
- *\r
- * @param s1 DOCUMENT ME!\r
- * @param s2 DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- */\r
- public AlignSeq(SequenceI s1,\r
- String string1,\r
- SequenceI s2,\r
- String string2,\r
- String type)\r
- {\r
- SeqInit(s1, string1, s2, string2, type);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getMaxScore()\r
- {\r
- return maxscore;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getSeq2Start()\r
- {\r
- return seq2start;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getSeq2End()\r
- {\r
- return seq2end;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getSeq1Start()\r
- {\r
- return seq1start;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getSeq1End()\r
- {\r
- return seq1end;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String getOutput()\r
- {\r
- return output.toString();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String getAStr1()\r
- {\r
- return astr1;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String getAStr2()\r
- {\r
- return astr2;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int[] getASeq1()\r
- {\r
- return aseq1;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int[] getASeq2()\r
- {\r
- return aseq2;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceI getS1()\r
- {\r
- return s1;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceI getS2()\r
- {\r
- return s2;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s1 DOCUMENT ME!\r
- * @param s2 DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- */\r
- public void SeqInit(SequenceI s1,\r
- String string1,\r
- SequenceI s2,\r
- String string2,\r
- String type)\r
- {\r
-\r
- s1str = extractGaps(jalview.util.Comparison.GapChars, string1);\r
- s2str = extractGaps(jalview.util.Comparison.GapChars, string2);\r
-\r
- if(s1str.length()==0 || s2str.length()==0)\r
- {\r
- System.out.println("ALL GAPS: " +\r
- (s1str.length()==0?s1.getName():" ")\r
- +(s2str.length()==0?s2.getName():""));\r
- return;\r
- }\r
-\r
- this.s1 = s1;\r
- this.s2 = s2;\r
-\r
- this.type = type;\r
-\r
- if (type.equals("pep"))\r
- {\r
- lookup = ResidueProperties.getBLOSUM62();\r
- intToStr = pep;\r
- defInt = 23;\r
- }\r
- else if (type.equals("dna"))\r
- {\r
- lookup = ResidueProperties.getDNA();\r
- intToStr = dna;\r
- defInt = 4;\r
- }\r
- else\r
- {\r
- output.append("Wrong type = dna or pep only");\r
- System.exit(0);\r
- }\r
-\r
- //System.out.println("lookuip " + rt.freeMemory() + " "+ rt.totalMemory());\r
- seq1 = new int[s1str.length()];\r
-\r
- //System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory());\r
- seq2 = new int[s2str.length()];\r
-\r
- //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory());\r
- score = new int[s1str.length()][s2str.length()];\r
-\r
- //System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory());\r
- E = new int[s1str.length()][s2str.length()];\r
-\r
- //System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory());\r
- F = new int[s1str.length()][s2str.length()];\r
- traceback = new int[s1str.length()][s2str.length()];\r
-\r
- //System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory());\r
- seq1 = stringToInt(s1str, type);\r
-\r
- //System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory());\r
- seq2 = stringToInt(s2str, type);\r
-\r
- //System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory());\r
- // long tstart = System.currentTimeMillis();\r
- // calcScoreMatrix();\r
- //long tend = System.currentTimeMillis();\r
- //System.out.println("Time take to calculate score matrix = " + (tend-tstart) + " ms");\r
- // printScoreMatrix(score);\r
- //System.out.println();\r
- //printScoreMatrix(traceback);\r
- //System.out.println();\r
- // printScoreMatrix(E);\r
- //System.out.println();\r
- ///printScoreMatrix(F);\r
- //System.out.println();\r
- // tstart = System.currentTimeMillis();\r
- //traceAlignment();\r
- //tend = System.currentTimeMillis();\r
- //System.out.println("Time take to traceback alignment = " + (tend-tstart) + " ms");\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void traceAlignment()\r
- {\r
- // Find the maximum score along the rhs or bottom row\r
- int max = -9999;\r
-\r
- for (int i = 0; i < seq1.length; i++)\r
- {\r
- if (score[i][seq2.length - 1] > max)\r
- {\r
- max = score[i][seq2.length - 1];\r
- maxi = i;\r
- maxj = seq2.length - 1;\r
- }\r
- }\r
-\r
- for (int j = 0; j < seq2.length; j++)\r
- {\r
- if (score[seq1.length - 1][j] > max)\r
- {\r
- max = score[seq1.length - 1][j];\r
- maxi = seq1.length - 1;\r
- maxj = j;\r
- }\r
- }\r
-\r
- // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]);\r
- int i = maxi;\r
- int j = maxj;\r
- int trace;\r
- maxscore = score[i][j] / 10;\r
-\r
- seq1end = maxi + 1;\r
- seq2end = maxj + 1;\r
-\r
- aseq1 = new int[seq1.length + seq2.length];\r
- aseq2 = new int[seq1.length + seq2.length];\r
-\r
- count = (seq1.length + seq2.length) - 1;\r
-\r
- while ((i > 0) && (j > 0))\r
- {\r
- if ((aseq1[count] != defInt) && (i >= 0))\r
- {\r
- aseq1[count] = seq1[i];\r
- astr1 = intToStr[seq1[i]] + astr1;\r
- }\r
-\r
- if ((aseq2[count] != defInt) && (j > 0))\r
- {\r
- aseq2[count] = seq2[j];\r
- astr2 = intToStr[seq2[j]] + astr2;\r
- }\r
-\r
- trace = findTrace(i, j);\r
-\r
- if (trace == 0)\r
- {\r
- i--;\r
- j--;\r
- }\r
- else if (trace == 1)\r
- {\r
- j--;\r
- aseq1[count] = defInt;\r
- astr1 = "-" + astr1.substring(1);\r
- }\r
- else if (trace == -1)\r
- {\r
- i--;\r
- aseq2[count] = defInt;\r
- astr2 = "-" + astr2.substring(1);\r
- }\r
-\r
- count--;\r
- }\r
-\r
- seq1start = i + 1;\r
- seq2start = j + 1;\r
-\r
- if (aseq1[count] != defInt)\r
- {\r
- aseq1[count] = seq1[i];\r
- astr1 = intToStr[seq1[i]] + astr1;\r
- }\r
-\r
- if (aseq2[count] != defInt)\r
- {\r
- aseq2[count] = seq2[j];\r
- astr2 = intToStr[seq2[j]] + astr2;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void printAlignment(java.io.PrintStream os)\r
- {\r
- // Find the biggest id length for formatting purposes\r
- int maxid = s1.getName().length();\r
-\r
- if (s2.getName().length() > maxid)\r
- {\r
- maxid = s2.getName().length();\r
- }\r
-\r
- int len = 72 - maxid - 1;\r
- int nochunks = ((aseq1.length - count) / len) + 1;\r
- pid = 0;\r
-\r
- output.append("Score = " + score[maxi][maxj] + "\n");\r
- output.append("Length of alignment = " + (aseq1.length - count) + "\n");\r
- output.append("Sequence ");\r
- output.append(new Format("%" + maxid + "s").form(s1.getName()));\r
- output.append(" : " + s1.getStart() + " - " + s1.getEnd() + " (Sequence length = " +\r
- s1str.length() + ")\n");\r
- output .append("Sequence ");\r
- output.append(new Format("%" + maxid + "s").form(s2.getName()));\r
- output.append(" : " + s2.getStart() + " - " + s2.getEnd() + " (Sequence length = " +\r
- s2str.length() + ")\n\n");\r
-\r
- for (int j = 0; j < nochunks; j++)\r
- {\r
- // Print the first aligned sequence\r
- output.append(new Format("%" + (maxid) + "s").form(s1.getName()) + " ");\r
-\r
- for (int i = 0; i < len; i++)\r
- {\r
- if ((count + i + (j * len)) < aseq1.length)\r
- {\r
- output.append(new Format("%s").form(intToStr[aseq1[count + i +\r
- (j * len)]]));\r
- }\r
- }\r
-\r
- output.append("\n");\r
- output.append(new Format("%" + (maxid) + "s").form(" ") + " ");\r
-\r
- // Print out the matching chars\r
- for (int i = 0; i < len; i++)\r
- {\r
- if ((count + i + (j * len)) < aseq1.length)\r
- {\r
- if (intToStr[aseq1[count + i + (j * len)]].equals(\r
- intToStr[aseq2[count + i + (j * len)]]) &&\r
- !intToStr[aseq1[count + i + (j * len)]].equals("-"))\r
- {\r
- pid++;\r
- output.append("|");\r
- }\r
- else if (type.equals("pep"))\r
- {\r
- if (ResidueProperties.getPAM250(\r
- intToStr[aseq1[count + i + (j * len)]],\r
- intToStr[aseq2[count + i + (j * len)]]) > 0)\r
- {\r
- output.append(".");\r
- }\r
- else\r
- {\r
- output.append(" ");\r
- }\r
- }\r
- else\r
- {\r
- output.append(" ");\r
- }\r
- }\r
- }\r
-\r
- // Now print the second aligned sequence\r
- output = output.append("\n");\r
- output = output.append(new Format("%" + (maxid) + "s").form(s2.getName()) + " ");\r
-\r
- for (int i = 0; i < len; i++)\r
- {\r
- if ((count + i + (j * len)) < aseq1.length)\r
- {\r
- output .append(new Format("%s").form(intToStr[aseq2[count + i +\r
- (j * len)]]));\r
- }\r
- }\r
-\r
- output = output .append("\n\n");\r
- }\r
-\r
- pid = pid / (float) (aseq1.length - count) * 100;\r
- output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));\r
-\r
- try{\r
- os.print(output.toString());\r
- }catch(Exception ex){}\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param mat DOCUMENT ME!\r
- */\r
- public void printScoreMatrix(int[][] mat)\r
- {\r
- int n = seq1.length;\r
- int m = seq2.length;\r
-\r
- for (int i = 0; i < n; i++)\r
- {\r
- // Print the top sequence\r
- if (i == 0)\r
- {\r
- Format.print(System.out, "%8s", s2str.substring(0, 1));\r
-\r
- for (int jj = 1; jj < m; jj++)\r
- {\r
- Format.print(System.out, "%5s", s2str.substring(jj, jj + 1));\r
- }\r
-\r
- System.out.println();\r
- }\r
-\r
- for (int j = 0; j < m; j++)\r
- {\r
- if (j == 0)\r
- {\r
- Format.print(System.out, "%3s", s1str.substring(i, i + 1));\r
- }\r
-\r
- Format.print(System.out, "%3d ", mat[i][j] / 10);\r
- }\r
-\r
- System.out.println();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- * @param j DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int findTrace(int i, int j)\r
- {\r
- int t = 0;\r
- int max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10);\r
-\r
- if (F[i][j] > max)\r
- {\r
- max = F[i][j];\r
- t = -1;\r
- }\r
- else if (F[i][j] == max)\r
- {\r
- if (prev == -1)\r
- {\r
- max = F[i][j];\r
- t = -1;\r
- }\r
- }\r
-\r
- if (E[i][j] >= max)\r
- {\r
- max = E[i][j];\r
- t = 1;\r
- }\r
- else if (E[i][j] == max)\r
- {\r
- if (prev == 1)\r
- {\r
- max = E[i][j];\r
- t = 1;\r
- }\r
- }\r
-\r
- prev = t;\r
-\r
- return t;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void calcScoreMatrix()\r
- {\r
- int n = seq1.length;\r
- int m = seq2.length;\r
-\r
- // top left hand element\r
- score[0][0] = lookup[seq1[0]][seq2[0]] * 10;\r
- E[0][0] = -gapExtend;\r
- F[0][0] = 0;\r
-\r
- // Calculate the top row first\r
- for (int j = 1; j < m; j++)\r
- {\r
- // What should these values be? 0 maybe\r
- E[0][j] = max(score[0][j - 1] - gapOpen, E[0][j - 1] - gapExtend);\r
- F[0][j] = -gapExtend;\r
-\r
- score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen,\r
- -gapExtend);\r
-\r
- traceback[0][j] = 1;\r
- }\r
-\r
- // Now do the left hand column\r
- for (int i = 1; i < n; i++)\r
- {\r
- E[i][0] = -gapOpen;\r
- F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend);\r
-\r
- score[i][0] = max(lookup[seq1[i]][seq2[0]] * 10, E[i][0], F[i][0]);\r
- traceback[i][0] = -1;\r
- }\r
-\r
- // Now do all the other rows\r
- for (int i = 1; i < n; i++)\r
- {\r
- for (int j = 1; j < m; j++)\r
- {\r
- E[i][j] = max(score[i][j - 1] - gapOpen, E[i][j - 1] -\r
- gapExtend);\r
- F[i][j] = max(score[i - 1][j] - gapOpen, F[i - 1][j] -\r
- gapExtend);\r
-\r
- score[i][j] = max(score[i - 1][j - 1] +\r
- (lookup[seq1[i]][seq2[j]] * 10), E[i][j], F[i][j]);\r
- traceback[i][j] = findTrace(i, j);\r
- }\r
- }\r
- }\r
-\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param gapChar DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static String extractGaps(String gapChar, String seq)\r
- {\r
- StringTokenizer str = new StringTokenizer(seq, gapChar);\r
- StringBuffer newString = new StringBuffer();\r
-\r
- while (str.hasMoreTokens())\r
- {\r
- newString.append( str.nextToken() );\r
- }\r
-\r
- return newString.toString();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i1 DOCUMENT ME!\r
- * @param i2 DOCUMENT ME!\r
- * @param i3 DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int max(int i1, int i2, int i3)\r
- {\r
- int max = i1;\r
-\r
- if (i2 > i1)\r
- {\r
- max = i2;\r
- }\r
-\r
- if (i3 > max)\r
- {\r
- max = i3;\r
- }\r
-\r
- return max;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i1 DOCUMENT ME!\r
- * @param i2 DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int max(int i1, int i2)\r
- {\r
- int max = i1;\r
-\r
- if (i2 > i1)\r
- {\r
- max = i2;\r
- }\r
-\r
- return max;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int[] stringToInt(String s, String type)\r
- {\r
- int[] seq1 = new int[s.length()];\r
-\r
- for (int i = 0; i < s.length(); i++)\r
- {\r
- // String ss = s.substring(i, i + 1).toUpperCase();\r
- char c = s.charAt(i);\r
- if ('a' <= c && c <= 'z')\r
- {\r
- // TO UPPERCASE !!!\r
- c -= ('a' - 'A');\r
- }\r
-\r
-\r
- try\r
- {\r
- if (type.equals("pep"))\r
- {\r
- seq1[i] = ResidueProperties.aaIndex[c];\r
- }\r
- else if (type.equals("dna"))\r
- {\r
- seq1[i] = ResidueProperties.nucleotideIndex[c];\r
- }\r
-\r
- if (seq1[i] > 23)\r
- {\r
- seq1[i] = 23;\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- if (type.equals("dna"))\r
- {\r
- seq1[i] = 4;\r
- }\r
- else\r
- {\r
- seq1[i] = 23;\r
- }\r
- }\r
- }\r
-\r
- return seq1;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- * @param mat DOCUMENT ME!\r
- * @param n DOCUMENT ME!\r
- * @param m DOCUMENT ME!\r
- * @param psize DOCUMENT ME!\r
- */\r
- public static void displayMatrix(Graphics g, int[][] mat, int n, int m,\r
- int psize)\r
- {\r
- int max = -1000;\r
- int min = 1000;\r
-\r
- for (int i = 0; i < n; i++)\r
- {\r
- for (int j = 0; j < m; j++)\r
- {\r
- if (mat[i][j] >= max)\r
- {\r
- max = mat[i][j];\r
- }\r
-\r
- if (mat[i][j] <= min)\r
- {\r
- min = mat[i][j];\r
- }\r
- }\r
- }\r
-\r
- System.out.println(max + " " + min);\r
-\r
- for (int i = 0; i < n; i++)\r
- {\r
- for (int j = 0; j < m; j++)\r
- {\r
- int x = psize * i;\r
- int y = psize * j;\r
-\r
- // System.out.println(mat[i][j]);\r
- float score = (float) (mat[i][j] - min) / (float) (max - min);\r
- g.setColor(new Color(score, 0, 0));\r
- g.fillRect(x, y, psize, psize);\r
-\r
- // System.out.println(x + " " + y + " " + score);\r
- }\r
- }\r
- }\r
-}\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program 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 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 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.datamodel.SequenceI;
+
+import jalview.schemes.*;
+
+import jalview.util.*;
+
+import java.awt.*;
+
+import java.util.*;
+
+
+/**
+ *
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignSeq
+{
+ 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)
+ {
+ 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)
+ {
+ output.append("ALL GAPS: " +
+ (s1str.length()==0?s1.getName():" ")
+ +(s2str.length()==0?s2.getName():""));
+ return;
+ }
+
+ //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");
+ }
+
+ private void setDefaultParams(String type) {
+ setType(type);
+
+ if (type.equals(AlignSeq.PEP))
+ {
+ lookup = ResidueProperties.getDefaultPeptideMatrix();
+ }
+ else if (type.equals(AlignSeq.DNA))
+ {
+ lookup = ResidueProperties.getDefaultDnaMatrix();
+ }
+ }
+
+ private void setType(String type2) {
+ this.type = type2;
+ if (type.equals(AlignSeq.PEP))
+ {
+ intToStr = pep;
+ defInt = 23;
+ }
+ else if (type.equals(AlignSeq.DNA))
+ {
+ intToStr = dna;
+ defInt = 4;
+ }
+ else
+ {
+ output.append("Wrong type = dna or pep only");
+ throw new Error("Unknown Type "+type2+" - dna or pep are the only allowed values.");
+ }
+ }
+
+ /**
+ * 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;
+ }
+ }
+
+ // 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--;
+ }
+
+ seq1start = i + 1;
+ seq2start = j + 1;
+
+ if (aseq1[count] != defInt)
+ {
+ aseq1[count] = seq1[i];
+ astr1 = intToStr[seq1[i]] + astr1;
+ }
+
+ if (aseq2[count] != defInt)
+ {
+ aseq2[count] = seq2[j];
+ astr2 = intToStr[seq2[j]] + astr2;
+ }
+ }
+
+ /**
+ * 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(" : " + s1.getStart() + " - " + s1.getEnd() + " (Sequence length = " +
+ s1str.length() + ")\n");
+ output .append("Sequence ");
+ output.append(new Format("%" + maxid + "s").form(s2.getName()));
+ output.append(" : " + s2.getStart() + " - " + s2.getEnd() + " (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));
+
+ try{
+ os.print(output.toString());
+ }catch(Exception ex){}
+ }
+
+ /**
+ * 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();
+ }
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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;
+ }
+
+ // 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;
+ }
+
+ // 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);
+ }
+ }
+ }
+
+
+
+ /**
+ * 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() );
+ }
+
+ 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;
+ }
+
+ /**
+ * 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();
+ char c = s.charAt(i);
+ if ('a' <= c && c <= 'z')
+ {
+ // TO UPPERCASE !!!
+ c -= ('a' - 'A');
+ }
+
+
+ try
+ {
+ if (type.equals("pep"))
+ {
+ seq1[i] = ResidueProperties.aaIndex[c];
+ }
+ else if (type.equals("dna"))
+ {
+ seq1[i] = ResidueProperties.nucleotideIndex[c];
+ }
+
+ 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);
+ }
+ }
+ }
+}
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.schemes;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-\r
-public class ResidueProperties\r
-{\r
- //Stores residue codes/names and colours and other things\r
- public static final int [] aaIndex; // aaHash version 2.1.1 and below\r
- public static final int [] nucleotideIndex;\r
- public static final Hashtable aa3Hash = new Hashtable();\r
- public static final Hashtable aa2Triplet = new Hashtable();\r
- public static final Hashtable nucleotideName = new Hashtable();\r
-\r
-\r
- static\r
- {\r
- aaIndex = new int[132];\r
- for(int i=0; i<132; i++)\r
- aaIndex[i] = -1;\r
-\r
- aaIndex['A'] = 0;\r
- aaIndex['R'] = 1;\r
- aaIndex['N'] = 2;\r
- aaIndex['D'] = 3;\r
- aaIndex['C'] = 4;\r
- aaIndex['Q'] = 5;\r
- aaIndex['E'] = 6;\r
- aaIndex['G'] = 7;\r
- aaIndex['H'] = 8;\r
- aaIndex['I'] = 9;\r
- aaIndex['L'] = 10;\r
- aaIndex['K'] = 11;\r
- aaIndex['M'] = 12;\r
- aaIndex['F'] = 13;\r
- aaIndex['P'] = 14;\r
- aaIndex['S'] = 15;\r
- aaIndex['T'] = 16;\r
- aaIndex['W'] = 17;\r
- aaIndex['Y'] = 18;\r
- aaIndex['V'] = 19;\r
- aaIndex['B'] = 20;\r
- aaIndex['Z'] = 21;\r
- aaIndex['X'] = 22;\r
- aaIndex['U'] = 22;\r
- aaIndex['a'] = 0;\r
- aaIndex['r'] = 1;\r
- aaIndex['n'] = 2;\r
- aaIndex['d'] = 3;\r
- aaIndex['c'] = 4;\r
- aaIndex['q'] = 5;\r
- aaIndex['e'] = 6;\r
- aaIndex['g'] = 7;\r
- aaIndex['h'] = 8;\r
- aaIndex['i'] = 9;\r
- aaIndex['l'] = 10;\r
- aaIndex['k'] = 11;\r
- aaIndex['m'] = 12;\r
- aaIndex['f'] = 13;\r
- aaIndex['p'] = 14;\r
- aaIndex['s'] = 15;\r
- aaIndex['t'] = 16;\r
- aaIndex['w'] = 17;\r
- aaIndex['y'] = 18;\r
- aaIndex['v'] = 19;\r
- aaIndex['b'] = 20;\r
- aaIndex['z'] = 21;\r
- aaIndex['x'] = 22;\r
- aaIndex['u'] = 22;\r
- aaIndex['-'] = 23;\r
- aaIndex['*'] = 23;\r
- aaIndex['.'] = 23;\r
- aaIndex[' '] = 23;\r
- }\r
-\r
- static\r
- {\r
- nucleotideIndex = new int[132];\r
- for (int i = 0; i < 132; i++)\r
- nucleotideIndex[i] = -1;\r
-\r
- nucleotideIndex['A'] = 0;\r
- nucleotideIndex['a'] = 0;\r
- nucleotideIndex['C'] = 1;\r
- nucleotideIndex['c'] = 1;\r
- nucleotideIndex['G'] = 2;\r
- nucleotideIndex['g'] = 2;\r
- nucleotideIndex['T'] = 3;\r
- nucleotideIndex['t'] = 3;\r
- nucleotideIndex['U'] = 4;\r
- nucleotideIndex['u'] = 4;\r
- nucleotideIndex['I'] = 5;\r
- nucleotideIndex['i'] = 5;\r
- nucleotideIndex['X'] = 6;\r
- nucleotideIndex['x'] = 6;\r
- nucleotideIndex['R'] = 7;\r
- nucleotideIndex['r'] = 7;\r
- nucleotideIndex['Y'] = 8;\r
- nucleotideIndex['y'] = 8;\r
- nucleotideIndex['N'] = 9;\r
- nucleotideIndex['n'] = 9;\r
-\r
-\r
- nucleotideName.put("A", "Adenine");\r
- nucleotideName.put("a", "Adenine");\r
- nucleotideName.put("G", "Guanine");\r
- nucleotideName.put("g", "Guanine");\r
- nucleotideName.put("C", "Cytosine");\r
- nucleotideName.put("c", "Cytosine");\r
- nucleotideName.put("T", "Thymine");\r
- nucleotideName.put("t", "Thymine");\r
- nucleotideName.put("U", "Uracil");\r
- nucleotideName.put("u", "Uracil");\r
- nucleotideName.put("I", "Inosine");\r
- nucleotideName.put("i", "Inosine");\r
- nucleotideName.put("X", "Xanthine");\r
- nucleotideName.put("x", "Xanthine");\r
- nucleotideName.put("R", "Unknown Purine");\r
- nucleotideName.put("r", "Unknown Purine");\r
- nucleotideName.put("Y", "Unknown Pyrimidine");\r
- nucleotideName.put("y", "Unknown Pyrimidine");\r
- nucleotideName.put("N", "Unknown");\r
- nucleotideName.put("n", "Unknown");\r
- }\r
-\r
-\r
- static\r
- {\r
- aa3Hash.put("ALA", new Integer(0));\r
- aa3Hash.put("ARG", new Integer(1));\r
- aa3Hash.put("ASN", new Integer(2));\r
- aa3Hash.put("ASP", new Integer(3)); //D\r
- aa3Hash.put("CYS", new Integer(4));\r
- aa3Hash.put("GLN", new Integer(5)); //Q\r
- aa3Hash.put("GLU", new Integer(6)); // E\r
- aa3Hash.put("GLY", new Integer(7));\r
- aa3Hash.put("HIS", new Integer(8));\r
- aa3Hash.put("ILE", new Integer(9));\r
- aa3Hash.put("LEU", new Integer(10));\r
- aa3Hash.put("LYS", new Integer(11));\r
- aa3Hash.put("MET", new Integer(12));\r
- aa3Hash.put("PHE", new Integer(13));\r
- aa3Hash.put("PRO", new Integer(14));\r
- aa3Hash.put("SER", new Integer(15));\r
- aa3Hash.put("THR", new Integer(16));\r
- aa3Hash.put("TRP", new Integer(17));\r
- aa3Hash.put("TYR", new Integer(18));\r
- aa3Hash.put("VAL", new Integer(19));\r
- // IUB Nomenclature for ambiguous peptides\r
- aa3Hash.put("ASX", new Integer(20)); // "B";\r
- aa3Hash.put("GLX", new Integer(21)); // X\r
- aa3Hash.put("XAA", new Integer(22));// X unknown\r
- aa3Hash.put("-", new Integer(23));\r
- aa3Hash.put("*", new Integer(23));\r
- aa3Hash.put(".", new Integer(23));\r
- aa3Hash.put(" ", new Integer(23));\r
- aa3Hash.put("Gap", new Integer(23));\r
- }\r
-\r
- static\r
- {\r
- aa2Triplet.put("A", "ALA");\r
- aa2Triplet.put("a", "ALA");\r
- aa2Triplet.put("R", "ARG");\r
- aa2Triplet.put("r", "ARG");\r
- aa2Triplet.put("N", "ASN");\r
- aa2Triplet.put("n", "ASN");\r
- aa2Triplet.put("D", "ASP");\r
- aa2Triplet.put("d", "ASP");\r
- aa2Triplet.put("C", "CYS");\r
- aa2Triplet.put("c", "CYS");\r
- aa2Triplet.put("Q", "GLN");\r
- aa2Triplet.put("q", "GLN");\r
- aa2Triplet.put("E", "GLU");\r
- aa2Triplet.put("e", "GLU");\r
- aa2Triplet.put("G", "GLY");\r
- aa2Triplet.put("g", "GLY");\r
- aa2Triplet.put("H", "HIS");\r
- aa2Triplet.put("h", "HIS");\r
- aa2Triplet.put("I", "ILE");\r
- aa2Triplet.put("i", "ILE");\r
- aa2Triplet.put("L", "LEU");\r
- aa2Triplet.put("l", "LEU");\r
- aa2Triplet.put("K", "LYS");\r
- aa2Triplet.put("k", "LYS");\r
- aa2Triplet.put("M", "MET");\r
- aa2Triplet.put("m", "MET");\r
- aa2Triplet.put("F", "PHE");\r
- aa2Triplet.put("f", "PHE");\r
- aa2Triplet.put("P", "PRO");\r
- aa2Triplet.put("p", "PRO");\r
- aa2Triplet.put("S", "SER");\r
- aa2Triplet.put("s", "SER");\r
- aa2Triplet.put("T", "THR");\r
- aa2Triplet.put("t", "THR");\r
- aa2Triplet.put("W", "TRP");\r
- aa2Triplet.put("w", "TRP");\r
- aa2Triplet.put("Y", "TYR");\r
- aa2Triplet.put("y", "TYR");\r
- aa2Triplet.put("V", "VAL");\r
- aa2Triplet.put("v", "VAL");\r
- }\r
-\r
- public static final String[] aa =\r
- {\r
- "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",\r
- "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " "\r
- };\r
- public static final Color midBlue = new Color(100, 100, 255);\r
- public static final Vector scaleColours = new Vector();\r
-\r
- static\r
- {\r
- scaleColours.addElement(new Color(114, 0, 147));\r
- scaleColours.addElement(new Color(156, 0, 98));\r
- scaleColours.addElement(new Color(190, 0, 0));\r
- scaleColours.addElement(Color.red);\r
- scaleColours.addElement(new Color(255, 125, 0));\r
- scaleColours.addElement(Color.orange);\r
- scaleColours.addElement(new Color(255, 194, 85));\r
- scaleColours.addElement(Color.yellow);\r
- scaleColours.addElement(new Color(255, 255, 181));\r
- scaleColours.addElement(Color.white);\r
- }\r
-\r
- public static final Color[] taylor =\r
- {\r
- new Color(204, 255, 0), // A Greenish-yellowy-yellow\r
- new Color(0, 0, 255), // R Blueish-bluey-blue\r
- new Color(204, 0, 255), // N Blueish-reddy-blue\r
- new Color(255, 0, 0), // D Reddish-reddy-red\r
- new Color(255, 255, 0), // C Yellowish-yellowy-yellow\r
- new Color(255, 0, 204), // Q Reddish-bluey-red\r
- new Color(255, 0, 102), // E Blueish-reddy-red\r
- new Color(255, 153, 0), // G Yellowy-reddy-yellow\r
- new Color(0, 102, 255), // H Greenish-bluey-blue\r
- new Color(102, 255, 0), // I Greenish-yellowy-green\r
- new Color(51, 255, 0), // L Yellowish-greeny-green\r
- new Color(102, 0, 255), // K Reddish-bluey-blue\r
- new Color(0, 255, 0), // M Greenish-greeny-green\r
- new Color(0, 255, 102), // F Blueish-greeny-green\r
- new Color(255, 204, 0), // P Reddish-yellowy-yellow\r
- new Color(255, 51, 0), // S Yellowish-reddy-red\r
- new Color(255, 102, 0), // T Reddish-yellowy-red\r
- new Color(0, 204, 255), // W Blueish-greeny-green\r
- new Color(0, 255, 204), // Y Greenish-bluey-green\r
- new Color(153, 255, 0), // V Yellowish-greeny-yellow\r
- Color.white, // B\r
- Color.white, // Z\r
- Color.white, // X\r
- Color.white, // -\r
- Color.white, // *\r
- Color.white // .\r
- };\r
- public static final Color[] nucleotide =\r
- {\r
- new Color(100, 247, 63), // A\r
- new Color(255, 179, 64), // C\r
- new Color(235, 65, 60), // G\r
- new Color(60, 136, 238), // T\r
- new Color(60, 136, 238) // U\r
- };\r
- public static final Color[] color =\r
- {\r
- Color.pink, // A\r
- midBlue, // R\r
- Color.green, // N\r
- Color.red, // D\r
- Color.yellow, // C\r
- Color.green, // Q\r
- Color.red, // E\r
- Color.magenta, // G\r
- Color.red, // H\r
- Color.pink, // I\r
- Color.pink, // L\r
- midBlue, // K\r
- Color.pink, // M\r
- Color.orange, // F\r
- Color.magenta, // P\r
- Color.green, // S\r
- Color.green, // T\r
- Color.orange, // W\r
- Color.orange, // Y\r
- Color.pink, // V\r
- Color.white, // B\r
- Color.white, // Z\r
- Color.white, // X\r
- Color.white, // -\r
- Color.white, // *\r
- Color.white, // .\r
- Color.white // ' '\r
- };\r
-\r
- // Dunno where I got these numbers from\r
- public static final double[] hyd2 =\r
- {\r
- 0.62, //A\r
- 0.29, //R\r
- -0.90, //N\r
- -0.74, //D\r
- 1.19, //C\r
- 0.48, //Q\r
- -0.40, //E\r
- 1.38, //G\r
- -1.50, //H\r
- 1.06, //I\r
- 0.64, //L\r
- -0.78, //K\r
- 0.12, //M\r
- -0.85, //F\r
- -2.53, //P\r
- -0.18, //S\r
- -0.05, //T\r
- 1.08, //W\r
- 0.81, //Y\r
- 0.0, //V\r
- 0.26, //B\r
- 0.0, //Z\r
- 0.0 //X\r
- };\r
- public static final double[] helix =\r
- {\r
- 1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16,\r
- 1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0\r
- };\r
- public static final double helixmin = 0.57;\r
- public static final double helixmax = 1.51;\r
- public static final double[] strand =\r
- {\r
- 0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74,\r
- 1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0\r
- };\r
- public static final double strandmin = 0.37;\r
- public static final double strandmax = 1.7;\r
- public static final double[] turn =\r
- {\r
- 0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01,\r
- 0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0\r
- };\r
- public static final double turnmin = 0.47;\r
- public static final double turnmax = 1.56;\r
- public static final double[] buried =\r
- {\r
- 1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2,\r
- 0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00\r
- };\r
- public static final double buriedmin = 0.05;\r
- public static final double buriedmax = 4.6;\r
-\r
- // This is hydropathy index\r
- // Kyte, J., and Doolittle, R.F., J. Mol. Biol.\r
- // 1157, 105-132, 1982\r
- public static final double[] hyd =\r
- {\r
- 1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9,\r
- 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0\r
- };\r
- public static final double hydmax = 4.5;\r
- public static final double hydmin = -3.9;\r
-\r
- //public static final double hydmax = 1.38;\r
- //public static final double hydmin = -2.53;\r
- static final int[][] BLOSUM62 =\r
- {\r
- {\r
- 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,\r
- -2, 0, -2, -1, 0, -4\r
- },\r
- {\r
- -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2,\r
- -3, -1, 0, -1, -4\r
- },\r
- {\r
- -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3,\r
- 3, 0, -1, -4\r
- },\r
- {\r
- -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4,\r
- -3, -3, 4, 1, -1, -4\r
- },\r
- {\r
- 0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2,\r
- -2, -1, -3, -3, -2, -4\r
- },\r
- {\r
- -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1,\r
- -2, 0, 3, -1, -4\r
- },\r
- {\r
- -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2,\r
- -2, 1, 4, -1, -4\r
- },\r
- {\r
- 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2,\r
- -3, -3, -1, -2, -1, -4\r
- },\r
- {\r
- -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2,\r
- -3, 0, 0, -1, -4\r
- },\r
- {\r
- -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3,\r
- -1, 3, -3, -3, -1, -4\r
- },\r
- {\r
- -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2,\r
- -1, 1, -4, -3, -1, -4\r
- },\r
- {\r
- -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2,\r
- -2, 0, 1, -1, -4\r
- },\r
- {\r
- -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1,\r
- -1, 1, -3, -1, -1, -4\r
- },\r
- {\r
- -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3,\r
- -1, -3, -3, -1, -4\r
- },\r
- {\r
- -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1,\r
- -4, -3, -2, -2, -1, -2, -4\r
- },\r
- {\r
- 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2,\r
- -2, 0, 0, 0, -4\r
- },\r
- {\r
- 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2,\r
- -2, 0, -1, -1, 0, -4\r
- },\r
- {\r
- -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2,\r
- 11, 2, -3, -4, -3, -2, -4\r
- },\r
- {\r
- -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2,\r
- 7, -1, -3, -2, -1, -4\r
- },\r
- {\r
- 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3,\r
- -1, 4, -3, -2, -1, -4\r
- },\r
- {\r
- -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3,\r
- -3, 4, 1, -1, -4\r
- },\r
- {\r
- -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2,\r
- -2, 1, 4, -1, -4\r
- },\r
- {\r
- 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2,\r
- -1, -1, -1, -1, -1, -4\r
- },\r
- {\r
- -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,\r
- -4, -4, -4, -4, -4, -4, 1\r
- },\r
- };\r
- static final int[][] PAM250 =\r
- {\r
- {\r
- 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0,\r
- 0, 0, 0, -8\r
- },\r
- {\r
- -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,\r
- -2, -1, 0, -1, -8\r
- },\r
- {\r
- 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2,\r
- 2, 1, 0, -8\r
- },\r
- {\r
- 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2,\r
- 3, 3, -1, -8\r
- },\r
- {\r
- -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2,\r
- -8, 0, -2, -4, -5, -3, -8\r
- },\r
- {\r
- 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4,\r
- -2, 1, 3, -1, -8\r
- },\r
- {\r
- 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2,\r
- 3, 3, -1, -8\r
- },\r
- {\r
- 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5,\r
- -1, 0, 0, -1, -8\r
- },\r
- {\r
- -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0,\r
- -2, 1, 2, -1, -8\r
- },\r
- {\r
- -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5,\r
- -1, 4, -2, -2, -1, -8\r
- },\r
- {\r
- -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2,\r
- -1, 2, -3, -3, -1, -8\r
- },\r
- {\r
- -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2,\r
- 1, 0, -1, -8\r
- },\r
- {\r
- -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2,\r
- 2, -2, -2, -1, -8\r
- },\r
- {\r
- -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7,\r
- -1, -4, -5, -2, -8\r
- },\r
- {\r
- 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5,\r
- -1, -1, 0, -1, -8\r
- },\r
- {\r
- 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1,\r
- 0, 0, 0, -8\r
- },\r
- {\r
- 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0,\r
- 0, -1, 0, -8\r
- },\r
- {\r
- -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17,\r
- 0, -6, -5, -6, -4, -8\r
- },\r
- {\r
- -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0,\r
- 10, -2, -3, -4, -2, -8\r
- },\r
- {\r
- 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6,\r
- -2, 4, -2, -2, -1, -8\r
- },\r
- {\r
- 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2,\r
- 3, 2, -1, -8\r
- },\r
- {\r
- 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2,\r
- 2, 3, -1, -8\r
- },\r
- {\r
- 0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4,\r
- -2, -1, -1, -1, -1, -8\r
- },\r
- {\r
- -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,\r
- -8, -8, -8, -8, -8, -8, 1\r
- },\r
- };\r
- public static final Hashtable ssHash = new Hashtable(); // stores the number value of the aa\r
-\r
- static\r
- {\r
- ssHash.put("H", Color.magenta);\r
- ssHash.put("E", Color.yellow);\r
- ssHash.put("-", Color.white);\r
- ssHash.put(".", Color.white);\r
- ssHash.put("S", Color.cyan);\r
- ssHash.put("T", Color.blue);\r
- ssHash.put("G", Color.pink);\r
- ssHash.put("I", Color.pink);\r
- ssHash.put("B", Color.yellow);\r
- }\r
-\r
- static final int[][] DNA =\r
- {\r
- {\r
- 5, -4, -4, -4, 1}, // C\r
- {\r
- -4, 5, -4, -4, 1}, // T\r
- {\r
- -4, -4, 5, -4, 1}, // A\r
- {\r
- -4, -4, -4, 5, 1}, // G\r
- {\r
- 1, 1, 1, 1, 1}, // -\r
- };\r
- public static final Color[] pidColours =\r
- {\r
- midBlue, new Color(153, 153, 255),\r
- // Color.lightGray,\r
- new Color(204, 204, 255),\r
- };\r
- public static final float[] pidThresholds =\r
- {\r
- 80, 60, 40, };\r
- public static Hashtable codonHash = new Hashtable();\r
- public static Vector Lys = new Vector();\r
- public static Vector Asn = new Vector();\r
- public static Vector Gln = new Vector();\r
- public static Vector His = new Vector();\r
- public static Vector Glu = new Vector();\r
- public static Vector Asp = new Vector();\r
- public static Vector Tyr = new Vector();\r
- public static Vector Thr = new Vector();\r
- public static Vector Pro = new Vector();\r
- public static Vector Ala = new Vector();\r
- public static Vector Ser = new Vector();\r
- public static Vector Arg = new Vector();\r
- public static Vector Gly = new Vector();\r
- public static Vector Trp = new Vector();\r
- public static Vector Cys = new Vector();\r
- public static Vector Ile = new Vector();\r
- public static Vector Met = new Vector();\r
- public static Vector Leu = new Vector();\r
- public static Vector Val = new Vector();\r
- public static Vector Phe = new Vector();\r
- public static Vector STOP = new Vector();\r
-\r
- static\r
- {\r
- codonHash.put("K", Lys);\r
- codonHash.put("N", Asn);\r
- codonHash.put("Q", Gln);\r
- codonHash.put("H", His);\r
- codonHash.put("E", Glu);\r
- codonHash.put("D", Asp);\r
- codonHash.put("Y", Tyr);\r
- codonHash.put("T", Thr);\r
- codonHash.put("P", Pro);\r
- codonHash.put("A", Ala);\r
- codonHash.put("S", Ser);\r
- codonHash.put("R", Arg);\r
- codonHash.put("G", Gly);\r
- codonHash.put("W", Trp);\r
- codonHash.put("C", Cys);\r
- codonHash.put("I", Ile);\r
- codonHash.put("M", Met);\r
- codonHash.put("L", Leu);\r
- codonHash.put("V", Val);\r
- codonHash.put("F", Phe);\r
- codonHash.put("STOP", STOP);\r
- }\r
-\r
- public static Hashtable codonHash2 = new Hashtable();\r
-\r
- static\r
- {\r
- codonHash2.put("AAA", "K");\r
- codonHash2.put("AAG", "K");\r
- codonHash2.put("AAC", "N");\r
- codonHash2.put("AAT", "N");\r
-\r
- codonHash2.put("CAA", "E");\r
- codonHash2.put("CAG", "E");\r
- codonHash2.put("CAC", "H");\r
- codonHash2.put("CAT", "H");\r
-\r
- codonHash2.put("GAA", "Q");\r
- codonHash2.put("GAG", "Q");\r
- codonHash2.put("GAC", "D");\r
- codonHash2.put("GAT", "D");\r
-\r
- codonHash2.put("TAC", "Y");\r
- codonHash2.put("TAT", "Y");\r
-\r
- codonHash2.put("ACA", "T");\r
- codonHash2.put("AAG", "T");\r
- codonHash2.put("ACC", "T");\r
- codonHash2.put("ACT", "T");\r
-\r
- codonHash2.put("CCA", "P");\r
- codonHash2.put("CCG", "P");\r
- codonHash2.put("CCC", "P");\r
- codonHash2.put("CCT", "P");\r
-\r
- codonHash2.put("GCA", "A");\r
- codonHash2.put("GCG", "A");\r
- codonHash2.put("GCC", "A");\r
- codonHash2.put("GCT", "A");\r
-\r
- codonHash2.put("TCA", "S");\r
- codonHash2.put("TCG", "S");\r
- codonHash2.put("TCC", "S");\r
- codonHash2.put("TCT", "S");\r
- codonHash2.put("AGC", "S");\r
- codonHash2.put("AGT", "S");\r
-\r
- codonHash2.put("AGA", "R");\r
- codonHash2.put("AGG", "R");\r
- codonHash2.put("CGA", "R");\r
- codonHash2.put("CGG", "R");\r
- codonHash2.put("CGC", "R");\r
- codonHash2.put("CGT", "R");\r
-\r
- codonHash2.put("GGA", "G");\r
- codonHash2.put("GGG", "G");\r
- codonHash2.put("GGC", "G");\r
- codonHash2.put("GGT", "G");\r
-\r
- codonHash2.put("TGA", "*");\r
- codonHash2.put("TAA", "*");\r
- codonHash2.put("TAG", "*");\r
-\r
- codonHash2.put("TGG", "W");\r
-\r
- codonHash2.put("TGC", "C");\r
- codonHash2.put("TGT", "C");\r
-\r
- codonHash2.put("ATA", "I");\r
- codonHash2.put("ATC", "I");\r
- codonHash2.put("ATT", "I");\r
-\r
- codonHash2.put("ATG", "M");\r
-\r
- codonHash2.put("CTA", "L");\r
- codonHash2.put("CTG", "L");\r
- codonHash2.put("CTC", "L");\r
- codonHash2.put("CTT", "L");\r
- codonHash2.put("TTA", "L");\r
- codonHash2.put("TTG", "L");\r
-\r
- codonHash2.put("GTA", "V");\r
- codonHash2.put("GTG", "V");\r
- codonHash2.put("GTC", "V");\r
- codonHash2.put("GTT", "V");\r
-\r
- codonHash2.put("TTC", "F");\r
- codonHash2.put("TTT", "F");\r
- }\r
-\r
- static\r
- {\r
- Lys.addElement("AAA");\r
- Lys.addElement("AAG");\r
- Asn.addElement("AAC");\r
- Asn.addElement("AAT");\r
-\r
- Gln.addElement("CAA");\r
- Gln.addElement("CAG");\r
- His.addElement("CAC");\r
- His.addElement("CAT");\r
-\r
- Glu.addElement("GAA");\r
- Glu.addElement("GAG");\r
- Asp.addElement("GAC");\r
- Asp.addElement("GAT");\r
-\r
- Tyr.addElement("TAC");\r
- Tyr.addElement("TAT");\r
-\r
- Thr.addElement("ACA");\r
- Thr.addElement("ACG");\r
- Thr.addElement("ACC");\r
- Thr.addElement("ACT");\r
-\r
- Pro.addElement("CCA");\r
- Pro.addElement("CCG");\r
- Pro.addElement("CCC");\r
- Pro.addElement("CCT");\r
-\r
- Ala.addElement("GCA");\r
- Ala.addElement("GCG");\r
- Ala.addElement("GCC");\r
- Ala.addElement("GCT");\r
-\r
- Ser.addElement("TCA");\r
- Ser.addElement("TCG");\r
- Ser.addElement("TCC");\r
- Ser.addElement("TCT");\r
- Ser.addElement("AGC");\r
- Ser.addElement("AGT");\r
-\r
- Arg.addElement("AGA");\r
- Arg.addElement("AGG");\r
- Arg.addElement("CGA");\r
- Arg.addElement("CGG");\r
- Arg.addElement("CGC");\r
- Arg.addElement("CGT");\r
-\r
- Gly.addElement("GGA");\r
- Gly.addElement("GGG");\r
- Gly.addElement("GGC");\r
- Gly.addElement("GGT");\r
-\r
- STOP.addElement("TGA");\r
- STOP.addElement("TAA");\r
- STOP.addElement("TAG");\r
-\r
- Trp.addElement("TGG");\r
-\r
- Cys.addElement("TGC");\r
- Cys.addElement("TGT");\r
-\r
- Ile.addElement("ATA");\r
- Ile.addElement("ATC");\r
- Ile.addElement("ATT");\r
-\r
- Met.addElement("ATG");\r
-\r
- Leu.addElement("CTA");\r
- Leu.addElement("CTG");\r
- Leu.addElement("CTC");\r
- Leu.addElement("CTT");\r
- Leu.addElement("TTA");\r
- Leu.addElement("TTG");\r
-\r
- Val.addElement("GTA");\r
- Val.addElement("GTG");\r
- Val.addElement("GTC");\r
- Val.addElement("GTT");\r
-\r
- Phe.addElement("TTC");\r
- Phe.addElement("TTT");\r
- }\r
-\r
-\r
- //Stores residue codes/names and colours and other things\r
- public static Hashtable propHash = new Hashtable();\r
- public static Hashtable hydrophobic = new Hashtable();\r
- public static Hashtable polar = new Hashtable();\r
- public static Hashtable small = new Hashtable();\r
- public static Hashtable positive = new Hashtable();\r
- public static Hashtable negative = new Hashtable();\r
- public static Hashtable charged = new Hashtable();\r
- public static Hashtable aromatic = new Hashtable();\r
- public static Hashtable aliphatic = new Hashtable();\r
- public static Hashtable tiny = new Hashtable();\r
- public static Hashtable proline = new Hashtable();\r
-\r
- static\r
- {\r
- hydrophobic.put("I", new Integer(1));\r
- hydrophobic.put("L", new Integer(1));\r
- hydrophobic.put("V", new Integer(1));\r
- hydrophobic.put("C", new Integer(1));\r
- hydrophobic.put("A", new Integer(1));\r
- hydrophobic.put("G", new Integer(1));\r
- hydrophobic.put("M", new Integer(1));\r
- hydrophobic.put("F", new Integer(1));\r
- hydrophobic.put("Y", new Integer(1));\r
- hydrophobic.put("W", new Integer(1));\r
- hydrophobic.put("H", new Integer(1));\r
- hydrophobic.put("K", new Integer(1));\r
- hydrophobic.put("X", new Integer(1));\r
- hydrophobic.put("-", new Integer(1));\r
- hydrophobic.put("*", new Integer(1));\r
- hydrophobic.put("R", new Integer(0));\r
- hydrophobic.put("E", new Integer(0));\r
- hydrophobic.put("Q", new Integer(0));\r
- hydrophobic.put("D", new Integer(0));\r
- hydrophobic.put("N", new Integer(0));\r
- hydrophobic.put("S", new Integer(0));\r
- hydrophobic.put("T", new Integer(0));\r
- hydrophobic.put("P", new Integer(0));\r
- }\r
-\r
- static\r
- {\r
- polar.put("Y", new Integer(1));\r
- polar.put("W", new Integer(1));\r
- polar.put("H", new Integer(1));\r
- polar.put("K", new Integer(1));\r
- polar.put("R", new Integer(1));\r
- polar.put("E", new Integer(1));\r
- polar.put("Q", new Integer(1));\r
- polar.put("D", new Integer(1));\r
- polar.put("N", new Integer(1));\r
- polar.put("S", new Integer(1));\r
- polar.put("T", new Integer(1));\r
- polar.put("X", new Integer(1));\r
- polar.put("-", new Integer(1));\r
- polar.put("*", new Integer(1));\r
- polar.put("I", new Integer(0));\r
- polar.put("L", new Integer(0));\r
- polar.put("V", new Integer(0));\r
- polar.put("C", new Integer(0));\r
- polar.put("A", new Integer(0));\r
- polar.put("G", new Integer(0));\r
- polar.put("M", new Integer(0));\r
- polar.put("F", new Integer(0));\r
- polar.put("P", new Integer(0));\r
- }\r
-\r
- static\r
- {\r
- small.put("I", new Integer(0));\r
- small.put("L", new Integer(0));\r
- small.put("V", new Integer(1));\r
- small.put("C", new Integer(1));\r
- small.put("A", new Integer(1));\r
- small.put("G", new Integer(1));\r
- small.put("M", new Integer(0));\r
- small.put("F", new Integer(0));\r
- small.put("Y", new Integer(0));\r
- small.put("W", new Integer(0));\r
- small.put("H", new Integer(0));\r
- small.put("K", new Integer(0));\r
- small.put("R", new Integer(0));\r
- small.put("E", new Integer(0));\r
- small.put("Q", new Integer(0));\r
- small.put("D", new Integer(1));\r
- small.put("N", new Integer(1));\r
- small.put("S", new Integer(1));\r
- small.put("T", new Integer(1));\r
- small.put("P", new Integer(1));\r
- small.put("-", new Integer(1));\r
- small.put("*", new Integer(1));\r
- }\r
-\r
- static\r
- {\r
- positive.put("I", new Integer(0));\r
- positive.put("L", new Integer(0));\r
- positive.put("V", new Integer(0));\r
- positive.put("C", new Integer(0));\r
- positive.put("A", new Integer(0));\r
- positive.put("G", new Integer(0));\r
- positive.put("M", new Integer(0));\r
- positive.put("F", new Integer(0));\r
- positive.put("Y", new Integer(0));\r
- positive.put("W", new Integer(0));\r
- positive.put("H", new Integer(1));\r
- positive.put("K", new Integer(1));\r
- positive.put("R", new Integer(1));\r
- positive.put("E", new Integer(0));\r
- positive.put("Q", new Integer(0));\r
- positive.put("D", new Integer(0));\r
- positive.put("N", new Integer(0));\r
- positive.put("S", new Integer(0));\r
- positive.put("T", new Integer(0));\r
- positive.put("P", new Integer(0));\r
- positive.put("-", new Integer(1));\r
- positive.put("*", new Integer(1));\r
- }\r
-\r
- static\r
- {\r
- negative.put("I", new Integer(0));\r
- negative.put("L", new Integer(0));\r
- negative.put("V", new Integer(0));\r
- negative.put("C", new Integer(0));\r
- negative.put("A", new Integer(0));\r
- negative.put("G", new Integer(0));\r
- negative.put("M", new Integer(0));\r
- negative.put("F", new Integer(0));\r
- negative.put("Y", new Integer(0));\r
- negative.put("W", new Integer(0));\r
- negative.put("H", new Integer(0));\r
- negative.put("K", new Integer(0));\r
- negative.put("R", new Integer(0));\r
- negative.put("E", new Integer(1));\r
- negative.put("Q", new Integer(0));\r
- negative.put("D", new Integer(1));\r
- negative.put("N", new Integer(0));\r
- negative.put("S", new Integer(0));\r
- negative.put("T", new Integer(0));\r
- negative.put("P", new Integer(0));\r
- negative.put("-", new Integer(1));\r
- negative.put("*", new Integer(1));\r
- }\r
-\r
- static\r
- {\r
- charged.put("I", new Integer(0));\r
- charged.put("L", new Integer(0));\r
- charged.put("V", new Integer(0));\r
- charged.put("C", new Integer(0));\r
- charged.put("A", new Integer(0));\r
- charged.put("G", new Integer(0));\r
- charged.put("M", new Integer(0));\r
- charged.put("F", new Integer(0));\r
- charged.put("Y", new Integer(0));\r
- charged.put("W", new Integer(0));\r
- charged.put("H", new Integer(1));\r
- charged.put("K", new Integer(1));\r
- charged.put("R", new Integer(1));\r
- charged.put("E", new Integer(1));\r
- charged.put("Q", new Integer(0));\r
- charged.put("D", new Integer(1));\r
- charged.put("N", new Integer(1));\r
- charged.put("S", new Integer(0));\r
- charged.put("T", new Integer(0));\r
- charged.put("P", new Integer(0));\r
- charged.put("-", new Integer(1));\r
- charged.put("*", new Integer(1));\r
- }\r
-\r
- static\r
- {\r
- aromatic.put("I", new Integer(0));\r
- aromatic.put("L", new Integer(0));\r
- aromatic.put("V", new Integer(0));\r
- aromatic.put("C", new Integer(0));\r
- aromatic.put("A", new Integer(0));\r
- aromatic.put("G", new Integer(0));\r
- aromatic.put("M", new Integer(0));\r
- aromatic.put("F", new Integer(1));\r
- aromatic.put("Y", new Integer(1));\r
- aromatic.put("W", new Integer(1));\r
- aromatic.put("H", new Integer(1));\r
- aromatic.put("K", new Integer(0));\r
- aromatic.put("R", new Integer(0));\r
- aromatic.put("E", new Integer(0));\r
- aromatic.put("Q", new Integer(0));\r
- aromatic.put("D", new Integer(0));\r
- aromatic.put("N", new Integer(0));\r
- aromatic.put("S", new Integer(0));\r
- aromatic.put("T", new Integer(0));\r
- aromatic.put("P", new Integer(0));\r
- aromatic.put("-", new Integer(1));\r
- aromatic.put("*", new Integer(1));\r
- }\r
-\r
- static\r
- {\r
- aliphatic.put("I", new Integer(1));\r
- aliphatic.put("L", new Integer(1));\r
- aliphatic.put("V", new Integer(1));\r
- aliphatic.put("C", new Integer(0));\r
- aliphatic.put("A", new Integer(0));\r
- aliphatic.put("G", new Integer(0));\r
- aliphatic.put("M", new Integer(0));\r
- aliphatic.put("F", new Integer(0));\r
- aliphatic.put("Y", new Integer(0));\r
- aliphatic.put("W", new Integer(0));\r
- aliphatic.put("H", new Integer(0));\r
- aliphatic.put("K", new Integer(0));\r
- aliphatic.put("R", new Integer(0));\r
- aliphatic.put("E", new Integer(0));\r
- aliphatic.put("Q", new Integer(0));\r
- aliphatic.put("D", new Integer(0));\r
- aliphatic.put("N", new Integer(0));\r
- aliphatic.put("S", new Integer(0));\r
- aliphatic.put("T", new Integer(0));\r
- aliphatic.put("P", new Integer(0));\r
- aliphatic.put("-", new Integer(1));\r
- aliphatic.put("*", new Integer(1));\r
- }\r
-\r
- static\r
- {\r
- tiny.put("I", new Integer(0));\r
- tiny.put("L", new Integer(0));\r
- tiny.put("V", new Integer(0));\r
- tiny.put("C", new Integer(0));\r
- tiny.put("A", new Integer(1));\r
- tiny.put("G", new Integer(1));\r
- tiny.put("M", new Integer(0));\r
- tiny.put("F", new Integer(0));\r
- tiny.put("Y", new Integer(0));\r
- tiny.put("W", new Integer(0));\r
- tiny.put("H", new Integer(0));\r
- tiny.put("K", new Integer(0));\r
- tiny.put("R", new Integer(0));\r
- tiny.put("E", new Integer(0));\r
- tiny.put("Q", new Integer(0));\r
- tiny.put("D", new Integer(0));\r
- tiny.put("N", new Integer(0));\r
- tiny.put("S", new Integer(1));\r
- tiny.put("T", new Integer(0));\r
- tiny.put("P", new Integer(0));\r
- tiny.put("-", new Integer(1));\r
- tiny.put("*", new Integer(1));\r
- }\r
-\r
- static\r
- {\r
- proline.put("I", new Integer(0));\r
- proline.put("L", new Integer(0));\r
- proline.put("V", new Integer(0));\r
- proline.put("C", new Integer(0));\r
- proline.put("A", new Integer(0));\r
- proline.put("G", new Integer(0));\r
- proline.put("M", new Integer(0));\r
- proline.put("F", new Integer(0));\r
- proline.put("Y", new Integer(0));\r
- proline.put("W", new Integer(0));\r
- proline.put("H", new Integer(0));\r
- proline.put("K", new Integer(0));\r
- proline.put("R", new Integer(0));\r
- proline.put("E", new Integer(0));\r
- proline.put("Q", new Integer(0));\r
- proline.put("D", new Integer(0));\r
- proline.put("N", new Integer(0));\r
- proline.put("S", new Integer(0));\r
- proline.put("T", new Integer(0));\r
- proline.put("P", new Integer(1));\r
- proline.put("-", new Integer(1));\r
- proline.put("*", new Integer(1));\r
- }\r
-\r
- static\r
- {\r
- propHash.put("hydrophobic", hydrophobic);\r
- propHash.put("small", small);\r
- propHash.put("positive", positive);\r
- propHash.put("negative", negative);\r
- propHash.put("charged", charged);\r
- propHash.put("aromatic", aromatic);\r
- propHash.put("aliphatic", aliphatic);\r
- propHash.put("tiny", tiny);\r
- propHash.put("proline", proline);\r
- propHash.put("polar", polar);\r
- }\r
-\r
- private ResidueProperties()\r
- {\r
- }\r
-\r
- public static double getHydmax()\r
- {\r
- return hydmax;\r
- }\r
-\r
- public static double getHydmin()\r
- {\r
- return hydmin;\r
- }\r
-\r
- public static double[] getHyd()\r
- {\r
- return hyd;\r
- }\r
-\r
- public static Hashtable getAA3Hash()\r
- {\r
- return aa3Hash;\r
- }\r
-\r
- public static int[][] getDNA()\r
- {\r
- return ResidueProperties.DNA;\r
- }\r
-\r
- public static int[][] getBLOSUM62()\r
- {\r
- return ResidueProperties.BLOSUM62;\r
- }\r
-\r
- public static int getPAM250(String A1, String A2)\r
- {\r
- int a = aaIndex[A1.charAt(0)];\r
- int b = aaIndex[A2.charAt(0)];\r
-\r
- int pog = ResidueProperties.PAM250[a][b];\r
-\r
- return pog;\r
- }\r
-\r
- public static int getBLOSUM62(char c1, char c2)\r
- {\r
- int pog = 0;\r
-\r
- try\r
- {\r
- int a = aaIndex[c1];\r
- int b = aaIndex[c2];\r
-\r
- pog = ResidueProperties.BLOSUM62[a][b];\r
- }\r
- catch (Exception e)\r
- {\r
- //System.out.println("Unknown residue in " + A1 + " " + A2);\r
- }\r
-\r
- return pog;\r
- }\r
-\r
- public static Vector getCodons(String res)\r
- {\r
- if (codonHash.containsKey(res))\r
- {\r
- return (Vector) codonHash.get(res);\r
- }\r
-\r
- return null;\r
- }\r
-\r
- public static String codonTranslate(String codon)\r
- {\r
- Enumeration e = codonHash.keys();\r
-\r
- while (e.hasMoreElements())\r
- {\r
- String key = (String) e.nextElement();\r
- Vector tmp = (Vector) codonHash.get(key);\r
-\r
- if (tmp.contains(codon.toUpperCase()))\r
- {\r
- return key;\r
- }\r
- }\r
-\r
- return null;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.util.*;
+
+import java.awt.*;
+
+public class ResidueProperties
+{
+ public static Hashtable scoreMatrices=new Hashtable();
+ //Stores residue codes/names and colours and other things
+ public static final int [] aaIndex; // aaHash version 2.1.1 and below
+ public static final int [] nucleotideIndex;
+ public static final Hashtable aa3Hash = new Hashtable();
+ public static final Hashtable aa2Triplet = new Hashtable();
+ public static final Hashtable nucleotideName = new Hashtable();
+
+
+ static
+ {
+ aaIndex = new int[132];
+ for(int i=0; i<132; i++)
+ aaIndex[i] = -1;
+
+ aaIndex['A'] = 0;
+ aaIndex['R'] = 1;
+ aaIndex['N'] = 2;
+ aaIndex['D'] = 3;
+ aaIndex['C'] = 4;
+ aaIndex['Q'] = 5;
+ aaIndex['E'] = 6;
+ aaIndex['G'] = 7;
+ aaIndex['H'] = 8;
+ aaIndex['I'] = 9;
+ aaIndex['L'] = 10;
+ aaIndex['K'] = 11;
+ aaIndex['M'] = 12;
+ aaIndex['F'] = 13;
+ aaIndex['P'] = 14;
+ aaIndex['S'] = 15;
+ aaIndex['T'] = 16;
+ aaIndex['W'] = 17;
+ aaIndex['Y'] = 18;
+ aaIndex['V'] = 19;
+ aaIndex['B'] = 20;
+ aaIndex['Z'] = 21;
+ aaIndex['X'] = 22;
+ aaIndex['U'] = 22;
+ aaIndex['a'] = 0;
+ aaIndex['r'] = 1;
+ aaIndex['n'] = 2;
+ aaIndex['d'] = 3;
+ aaIndex['c'] = 4;
+ aaIndex['q'] = 5;
+ aaIndex['e'] = 6;
+ aaIndex['g'] = 7;
+ aaIndex['h'] = 8;
+ aaIndex['i'] = 9;
+ aaIndex['l'] = 10;
+ aaIndex['k'] = 11;
+ aaIndex['m'] = 12;
+ aaIndex['f'] = 13;
+ aaIndex['p'] = 14;
+ aaIndex['s'] = 15;
+ aaIndex['t'] = 16;
+ aaIndex['w'] = 17;
+ aaIndex['y'] = 18;
+ aaIndex['v'] = 19;
+ aaIndex['b'] = 20;
+ aaIndex['z'] = 21;
+ aaIndex['x'] = 22;
+ aaIndex['u'] = 22;
+ aaIndex['-'] = 23;
+ aaIndex['*'] = 23;
+ aaIndex['.'] = 23;
+ aaIndex[' '] = 23;
+ }
+
+ static
+ {
+ nucleotideIndex = new int[132];
+ for (int i = 0; i < 132; i++)
+ nucleotideIndex[i] = -1;
+
+ nucleotideIndex['A'] = 0;
+ nucleotideIndex['a'] = 0;
+ nucleotideIndex['C'] = 1;
+ nucleotideIndex['c'] = 1;
+ nucleotideIndex['G'] = 2;
+ nucleotideIndex['g'] = 2;
+ nucleotideIndex['T'] = 3;
+ nucleotideIndex['t'] = 3;
+ nucleotideIndex['U'] = 4;
+ nucleotideIndex['u'] = 4;
+ nucleotideIndex['I'] = 5;
+ nucleotideIndex['i'] = 5;
+ nucleotideIndex['X'] = 6;
+ nucleotideIndex['x'] = 6;
+ nucleotideIndex['R'] = 7;
+ nucleotideIndex['r'] = 7;
+ nucleotideIndex['Y'] = 8;
+ nucleotideIndex['y'] = 8;
+ nucleotideIndex['N'] = 9;
+ nucleotideIndex['n'] = 9;
+
+
+ nucleotideName.put("A", "Adenine");
+ nucleotideName.put("a", "Adenine");
+ nucleotideName.put("G", "Guanine");
+ nucleotideName.put("g", "Guanine");
+ nucleotideName.put("C", "Cytosine");
+ nucleotideName.put("c", "Cytosine");
+ nucleotideName.put("T", "Thymine");
+ nucleotideName.put("t", "Thymine");
+ nucleotideName.put("U", "Uracil");
+ nucleotideName.put("u", "Uracil");
+ nucleotideName.put("I", "Inosine");
+ nucleotideName.put("i", "Inosine");
+ nucleotideName.put("X", "Xanthine");
+ nucleotideName.put("x", "Xanthine");
+ nucleotideName.put("R", "Unknown Purine");
+ nucleotideName.put("r", "Unknown Purine");
+ nucleotideName.put("Y", "Unknown Pyrimidine");
+ nucleotideName.put("y", "Unknown Pyrimidine");
+ nucleotideName.put("N", "Unknown");
+ nucleotideName.put("n", "Unknown");
+ }
+
+
+ static
+ {
+ aa3Hash.put("ALA", new Integer(0));
+ aa3Hash.put("ARG", new Integer(1));
+ aa3Hash.put("ASN", new Integer(2));
+ aa3Hash.put("ASP", new Integer(3)); //D
+ aa3Hash.put("CYS", new Integer(4));
+ aa3Hash.put("GLN", new Integer(5)); //Q
+ aa3Hash.put("GLU", new Integer(6)); // E
+ aa3Hash.put("GLY", new Integer(7));
+ aa3Hash.put("HIS", new Integer(8));
+ aa3Hash.put("ILE", new Integer(9));
+ aa3Hash.put("LEU", new Integer(10));
+ aa3Hash.put("LYS", new Integer(11));
+ aa3Hash.put("MET", new Integer(12));
+ aa3Hash.put("PHE", new Integer(13));
+ aa3Hash.put("PRO", new Integer(14));
+ aa3Hash.put("SER", new Integer(15));
+ aa3Hash.put("THR", new Integer(16));
+ aa3Hash.put("TRP", new Integer(17));
+ aa3Hash.put("TYR", new Integer(18));
+ aa3Hash.put("VAL", new Integer(19));
+ // IUB Nomenclature for ambiguous peptides
+ aa3Hash.put("ASX", new Integer(20)); // "B";
+ aa3Hash.put("GLX", new Integer(21)); // X
+ aa3Hash.put("XAA", new Integer(22));// X unknown
+ aa3Hash.put("-", new Integer(23));
+ aa3Hash.put("*", new Integer(23));
+ aa3Hash.put(".", new Integer(23));
+ aa3Hash.put(" ", new Integer(23));
+ aa3Hash.put("Gap", new Integer(23));
+ }
+
+ static
+ {
+ aa2Triplet.put("A", "ALA");
+ aa2Triplet.put("a", "ALA");
+ aa2Triplet.put("R", "ARG");
+ aa2Triplet.put("r", "ARG");
+ aa2Triplet.put("N", "ASN");
+ aa2Triplet.put("n", "ASN");
+ aa2Triplet.put("D", "ASP");
+ aa2Triplet.put("d", "ASP");
+ aa2Triplet.put("C", "CYS");
+ aa2Triplet.put("c", "CYS");
+ aa2Triplet.put("Q", "GLN");
+ aa2Triplet.put("q", "GLN");
+ aa2Triplet.put("E", "GLU");
+ aa2Triplet.put("e", "GLU");
+ aa2Triplet.put("G", "GLY");
+ aa2Triplet.put("g", "GLY");
+ aa2Triplet.put("H", "HIS");
+ aa2Triplet.put("h", "HIS");
+ aa2Triplet.put("I", "ILE");
+ aa2Triplet.put("i", "ILE");
+ aa2Triplet.put("L", "LEU");
+ aa2Triplet.put("l", "LEU");
+ aa2Triplet.put("K", "LYS");
+ aa2Triplet.put("k", "LYS");
+ aa2Triplet.put("M", "MET");
+ aa2Triplet.put("m", "MET");
+ aa2Triplet.put("F", "PHE");
+ aa2Triplet.put("f", "PHE");
+ aa2Triplet.put("P", "PRO");
+ aa2Triplet.put("p", "PRO");
+ aa2Triplet.put("S", "SER");
+ aa2Triplet.put("s", "SER");
+ aa2Triplet.put("T", "THR");
+ aa2Triplet.put("t", "THR");
+ aa2Triplet.put("W", "TRP");
+ aa2Triplet.put("w", "TRP");
+ aa2Triplet.put("Y", "TYR");
+ aa2Triplet.put("y", "TYR");
+ aa2Triplet.put("V", "VAL");
+ aa2Triplet.put("v", "VAL");
+ }
+
+ public static final String[] aa =
+ {
+ "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
+ "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " "
+ };
+ public static final Color midBlue = new Color(100, 100, 255);
+ public static final Vector scaleColours = new Vector();
+
+ static
+ {
+ scaleColours.addElement(new Color(114, 0, 147));
+ scaleColours.addElement(new Color(156, 0, 98));
+ scaleColours.addElement(new Color(190, 0, 0));
+ scaleColours.addElement(Color.red);
+ scaleColours.addElement(new Color(255, 125, 0));
+ scaleColours.addElement(Color.orange);
+ scaleColours.addElement(new Color(255, 194, 85));
+ scaleColours.addElement(Color.yellow);
+ scaleColours.addElement(new Color(255, 255, 181));
+ scaleColours.addElement(Color.white);
+ }
+
+ public static final Color[] taylor =
+ {
+ new Color(204, 255, 0), // A Greenish-yellowy-yellow
+ new Color(0, 0, 255), // R Blueish-bluey-blue
+ new Color(204, 0, 255), // N Blueish-reddy-blue
+ new Color(255, 0, 0), // D Reddish-reddy-red
+ new Color(255, 255, 0), // C Yellowish-yellowy-yellow
+ new Color(255, 0, 204), // Q Reddish-bluey-red
+ new Color(255, 0, 102), // E Blueish-reddy-red
+ new Color(255, 153, 0), // G Yellowy-reddy-yellow
+ new Color(0, 102, 255), // H Greenish-bluey-blue
+ new Color(102, 255, 0), // I Greenish-yellowy-green
+ new Color(51, 255, 0), // L Yellowish-greeny-green
+ new Color(102, 0, 255), // K Reddish-bluey-blue
+ new Color(0, 255, 0), // M Greenish-greeny-green
+ new Color(0, 255, 102), // F Blueish-greeny-green
+ new Color(255, 204, 0), // P Reddish-yellowy-yellow
+ new Color(255, 51, 0), // S Yellowish-reddy-red
+ new Color(255, 102, 0), // T Reddish-yellowy-red
+ new Color(0, 204, 255), // W Blueish-greeny-green
+ new Color(0, 255, 204), // Y Greenish-bluey-green
+ new Color(153, 255, 0), // V Yellowish-greeny-yellow
+ Color.white, // B
+ Color.white, // Z
+ Color.white, // X
+ Color.white, // -
+ Color.white, // *
+ Color.white // .
+ };
+ public static final Color[] nucleotide =
+ {
+ new Color(100, 247, 63), // A
+ new Color(255, 179, 64), // C
+ new Color(235, 65, 60), // G
+ new Color(60, 136, 238), // T
+ new Color(60, 136, 238) // U
+ };
+ public static final Color[] color =
+ {
+ Color.pink, // A
+ midBlue, // R
+ Color.green, // N
+ Color.red, // D
+ Color.yellow, // C
+ Color.green, // Q
+ Color.red, // E
+ Color.magenta, // G
+ Color.red, // H
+ Color.pink, // I
+ Color.pink, // L
+ midBlue, // K
+ Color.pink, // M
+ Color.orange, // F
+ Color.magenta, // P
+ Color.green, // S
+ Color.green, // T
+ Color.orange, // W
+ Color.orange, // Y
+ Color.pink, // V
+ Color.white, // B
+ Color.white, // Z
+ Color.white, // X
+ Color.white, // -
+ Color.white, // *
+ Color.white, // .
+ Color.white // ' '
+ };
+
+ // Dunno where I got these numbers from
+ public static final double[] hyd2 =
+ {
+ 0.62, //A
+ 0.29, //R
+ -0.90, //N
+ -0.74, //D
+ 1.19, //C
+ 0.48, //Q
+ -0.40, //E
+ 1.38, //G
+ -1.50, //H
+ 1.06, //I
+ 0.64, //L
+ -0.78, //K
+ 0.12, //M
+ -0.85, //F
+ -2.53, //P
+ -0.18, //S
+ -0.05, //T
+ 1.08, //W
+ 0.81, //Y
+ 0.0, //V
+ 0.26, //B
+ 0.0, //Z
+ 0.0 //X
+ };
+ public static final double[] helix =
+ {
+ 1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16,
+ 1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0
+ };
+ public static final double helixmin = 0.57;
+ public static final double helixmax = 1.51;
+ public static final double[] strand =
+ {
+ 0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74,
+ 1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0
+ };
+ public static final double strandmin = 0.37;
+ public static final double strandmax = 1.7;
+ public static final double[] turn =
+ {
+ 0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01,
+ 0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0
+ };
+ public static final double turnmin = 0.47;
+ public static final double turnmax = 1.56;
+ public static final double[] buried =
+ {
+ 1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2,
+ 0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00
+ };
+ public static final double buriedmin = 0.05;
+ public static final double buriedmax = 4.6;
+
+ // This is hydropathy index
+ // Kyte, J., and Doolittle, R.F., J. Mol. Biol.
+ // 1157, 105-132, 1982
+ public static final double[] hyd =
+ {
+ 1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9,
+ 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0
+ };
+ public static final double hydmax = 4.5;
+ public static final double hydmin = -3.9;
+
+ //public static final double hydmax = 1.38;
+ //public static final double hydmin = -2.53;
+ private static final int[][] BLOSUM62 =
+ {
+ {
+ 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,
+ -2, 0, -2, -1, 0, -4
+ },
+ {
+ -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2,
+ -3, -1, 0, -1, -4
+ },
+ {
+ -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3,
+ 3, 0, -1, -4
+ },
+ {
+ -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4,
+ -3, -3, 4, 1, -1, -4
+ },
+ {
+ 0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2,
+ -2, -1, -3, -3, -2, -4
+ },
+ {
+ -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1,
+ -2, 0, 3, -1, -4
+ },
+ {
+ -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2,
+ -2, 1, 4, -1, -4
+ },
+ {
+ 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2,
+ -3, -3, -1, -2, -1, -4
+ },
+ {
+ -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2,
+ -3, 0, 0, -1, -4
+ },
+ {
+ -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3,
+ -1, 3, -3, -3, -1, -4
+ },
+ {
+ -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2,
+ -1, 1, -4, -3, -1, -4
+ },
+ {
+ -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2,
+ -2, 0, 1, -1, -4
+ },
+ {
+ -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1,
+ -1, 1, -3, -1, -1, -4
+ },
+ {
+ -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3,
+ -1, -3, -3, -1, -4
+ },
+ {
+ -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1,
+ -4, -3, -2, -2, -1, -2, -4
+ },
+ {
+ 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2,
+ -2, 0, 0, 0, -4
+ },
+ {
+ 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2,
+ -2, 0, -1, -1, 0, -4
+ },
+ {
+ -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2,
+ 11, 2, -3, -4, -3, -2, -4
+ },
+ {
+ -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2,
+ 7, -1, -3, -2, -1, -4
+ },
+ {
+ 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3,
+ -1, 4, -3, -2, -1, -4
+ },
+ {
+ -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3,
+ -3, 4, 1, -1, -4
+ },
+ {
+ -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2,
+ -2, 1, 4, -1, -4
+ },
+ {
+ 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2,
+ -1, -1, -1, -1, -1, -4
+ },
+ {
+ -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,
+ -4, -4, -4, -4, -4, -4, 1
+ },
+ };
+ static final int[][] PAM250 =
+ {
+ {
+ 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0,
+ 0, 0, 0, -8
+ },
+ {
+ -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,
+ -2, -1, 0, -1, -8
+ },
+ {
+ 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2,
+ 2, 1, 0, -8
+ },
+ {
+ 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2,
+ 3, 3, -1, -8
+ },
+ {
+ -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2,
+ -8, 0, -2, -4, -5, -3, -8
+ },
+ {
+ 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4,
+ -2, 1, 3, -1, -8
+ },
+ {
+ 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2,
+ 3, 3, -1, -8
+ },
+ {
+ 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5,
+ -1, 0, 0, -1, -8
+ },
+ {
+ -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0,
+ -2, 1, 2, -1, -8
+ },
+ {
+ -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5,
+ -1, 4, -2, -2, -1, -8
+ },
+ {
+ -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2,
+ -1, 2, -3, -3, -1, -8
+ },
+ {
+ -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2,
+ 1, 0, -1, -8
+ },
+ {
+ -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2,
+ 2, -2, -2, -1, -8
+ },
+ {
+ -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7,
+ -1, -4, -5, -2, -8
+ },
+ {
+ 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5,
+ -1, -1, 0, -1, -8
+ },
+ {
+ 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1,
+ 0, 0, 0, -8
+ },
+ {
+ 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0,
+ 0, -1, 0, -8
+ },
+ {
+ -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17,
+ 0, -6, -5, -6, -4, -8
+ },
+ {
+ -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0,
+ 10, -2, -3, -4, -2, -8
+ },
+ {
+ 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6,
+ -2, 4, -2, -2, -1, -8
+ },
+ {
+ 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2,
+ 3, 2, -1, -8
+ },
+ {
+ 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2,
+ 2, 3, -1, -8
+ },
+ {
+ 0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4,
+ -2, -1, -1, -1, -1, -8
+ },
+ {
+ -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
+ -8, -8, -8, -8, -8, -8, 1
+ },
+ };
+ public static final Hashtable ssHash = new Hashtable(); // stores the number value of the aa
+
+ static
+ {
+ ssHash.put("H", Color.magenta);
+ ssHash.put("E", Color.yellow);
+ ssHash.put("-", Color.white);
+ ssHash.put(".", Color.white);
+ ssHash.put("S", Color.cyan);
+ ssHash.put("T", Color.blue);
+ ssHash.put("G", Color.pink);
+ ssHash.put("I", Color.pink);
+ ssHash.put("B", Color.yellow);
+ }
+
+ static final int[][] DNA =
+ {
+ {
+ 5, -4, -4, -4, 1}, // C
+ {
+ -4, 5, -4, -4, 1}, // T
+ {
+ -4, -4, 5, -4, 1}, // A
+ {
+ -4, -4, -4, 5, 1}, // G
+ {
+ 1, 1, 1, 1, 1}, // -
+ };
+ /**
+ * register matrices in list
+ */
+ static {
+ scoreMatrices.put("BLOSUM62", new ScoreMatrix("BLOSUM62",BLOSUM62, 0));
+ scoreMatrices.put("PAM250", new ScoreMatrix("PAM250",PAM250, 0));
+ scoreMatrices.put("DNA", new ScoreMatrix("DNA", DNA, 1));
+ }
+ public static final Color[] pidColours =
+ {
+ midBlue, new Color(153, 153, 255),
+ // Color.lightGray,
+ new Color(204, 204, 255),
+ };
+ public static final float[] pidThresholds =
+ {
+ 80, 60, 40, };
+ public static Hashtable codonHash = new Hashtable();
+ public static Vector Lys = new Vector();
+ public static Vector Asn = new Vector();
+ public static Vector Gln = new Vector();
+ public static Vector His = new Vector();
+ public static Vector Glu = new Vector();
+ public static Vector Asp = new Vector();
+ public static Vector Tyr = new Vector();
+ public static Vector Thr = new Vector();
+ public static Vector Pro = new Vector();
+ public static Vector Ala = new Vector();
+ public static Vector Ser = new Vector();
+ public static Vector Arg = new Vector();
+ public static Vector Gly = new Vector();
+ public static Vector Trp = new Vector();
+ public static Vector Cys = new Vector();
+ public static Vector Ile = new Vector();
+ public static Vector Met = new Vector();
+ public static Vector Leu = new Vector();
+ public static Vector Val = new Vector();
+ public static Vector Phe = new Vector();
+ public static Vector STOP = new Vector();
+
+ static
+ {
+ codonHash.put("K", Lys);
+ codonHash.put("N", Asn);
+ codonHash.put("Q", Gln);
+ codonHash.put("H", His);
+ codonHash.put("E", Glu);
+ codonHash.put("D", Asp);
+ codonHash.put("Y", Tyr);
+ codonHash.put("T", Thr);
+ codonHash.put("P", Pro);
+ codonHash.put("A", Ala);
+ codonHash.put("S", Ser);
+ codonHash.put("R", Arg);
+ codonHash.put("G", Gly);
+ codonHash.put("W", Trp);
+ codonHash.put("C", Cys);
+ codonHash.put("I", Ile);
+ codonHash.put("M", Met);
+ codonHash.put("L", Leu);
+ codonHash.put("V", Val);
+ codonHash.put("F", Phe);
+ codonHash.put("STOP", STOP);
+ }
+
+ public static Hashtable codonHash2 = new Hashtable();
+
+ static
+ {
+ codonHash2.put("AAA", "K");
+ codonHash2.put("AAG", "K");
+ codonHash2.put("AAC", "N");
+ codonHash2.put("AAT", "N");
+
+ codonHash2.put("CAA", "E");
+ codonHash2.put("CAG", "E");
+ codonHash2.put("CAC", "H");
+ codonHash2.put("CAT", "H");
+
+ codonHash2.put("GAA", "Q");
+ codonHash2.put("GAG", "Q");
+ codonHash2.put("GAC", "D");
+ codonHash2.put("GAT", "D");
+
+ codonHash2.put("TAC", "Y");
+ codonHash2.put("TAT", "Y");
+
+ codonHash2.put("ACA", "T");
+ codonHash2.put("AAG", "T");
+ codonHash2.put("ACC", "T");
+ codonHash2.put("ACT", "T");
+
+ codonHash2.put("CCA", "P");
+ codonHash2.put("CCG", "P");
+ codonHash2.put("CCC", "P");
+ codonHash2.put("CCT", "P");
+
+ codonHash2.put("GCA", "A");
+ codonHash2.put("GCG", "A");
+ codonHash2.put("GCC", "A");
+ codonHash2.put("GCT", "A");
+
+ codonHash2.put("TCA", "S");
+ codonHash2.put("TCG", "S");
+ codonHash2.put("TCC", "S");
+ codonHash2.put("TCT", "S");
+ codonHash2.put("AGC", "S");
+ codonHash2.put("AGT", "S");
+
+ codonHash2.put("AGA", "R");
+ codonHash2.put("AGG", "R");
+ codonHash2.put("CGA", "R");
+ codonHash2.put("CGG", "R");
+ codonHash2.put("CGC", "R");
+ codonHash2.put("CGT", "R");
+
+ codonHash2.put("GGA", "G");
+ codonHash2.put("GGG", "G");
+ codonHash2.put("GGC", "G");
+ codonHash2.put("GGT", "G");
+
+ codonHash2.put("TGA", "*");
+ codonHash2.put("TAA", "*");
+ codonHash2.put("TAG", "*");
+
+ codonHash2.put("TGG", "W");
+
+ codonHash2.put("TGC", "C");
+ codonHash2.put("TGT", "C");
+
+ codonHash2.put("ATA", "I");
+ codonHash2.put("ATC", "I");
+ codonHash2.put("ATT", "I");
+
+ codonHash2.put("ATG", "M");
+
+ codonHash2.put("CTA", "L");
+ codonHash2.put("CTG", "L");
+ codonHash2.put("CTC", "L");
+ codonHash2.put("CTT", "L");
+ codonHash2.put("TTA", "L");
+ codonHash2.put("TTG", "L");
+
+ codonHash2.put("GTA", "V");
+ codonHash2.put("GTG", "V");
+ codonHash2.put("GTC", "V");
+ codonHash2.put("GTT", "V");
+
+ codonHash2.put("TTC", "F");
+ codonHash2.put("TTT", "F");
+ }
+
+ static
+ {
+ Lys.addElement("AAA");
+ Lys.addElement("AAG");
+ Asn.addElement("AAC");
+ Asn.addElement("AAT");
+
+ Gln.addElement("CAA");
+ Gln.addElement("CAG");
+ His.addElement("CAC");
+ His.addElement("CAT");
+
+ Glu.addElement("GAA");
+ Glu.addElement("GAG");
+ Asp.addElement("GAC");
+ Asp.addElement("GAT");
+
+ Tyr.addElement("TAC");
+ Tyr.addElement("TAT");
+
+ Thr.addElement("ACA");
+ Thr.addElement("ACG");
+ Thr.addElement("ACC");
+ Thr.addElement("ACT");
+
+ Pro.addElement("CCA");
+ Pro.addElement("CCG");
+ Pro.addElement("CCC");
+ Pro.addElement("CCT");
+
+ Ala.addElement("GCA");
+ Ala.addElement("GCG");
+ Ala.addElement("GCC");
+ Ala.addElement("GCT");
+
+ Ser.addElement("TCA");
+ Ser.addElement("TCG");
+ Ser.addElement("TCC");
+ Ser.addElement("TCT");
+ Ser.addElement("AGC");
+ Ser.addElement("AGT");
+
+ Arg.addElement("AGA");
+ Arg.addElement("AGG");
+ Arg.addElement("CGA");
+ Arg.addElement("CGG");
+ Arg.addElement("CGC");
+ Arg.addElement("CGT");
+
+ Gly.addElement("GGA");
+ Gly.addElement("GGG");
+ Gly.addElement("GGC");
+ Gly.addElement("GGT");
+
+ STOP.addElement("TGA");
+ STOP.addElement("TAA");
+ STOP.addElement("TAG");
+
+ Trp.addElement("TGG");
+
+ Cys.addElement("TGC");
+ Cys.addElement("TGT");
+
+ Ile.addElement("ATA");
+ Ile.addElement("ATC");
+ Ile.addElement("ATT");
+
+ Met.addElement("ATG");
+
+ Leu.addElement("CTA");
+ Leu.addElement("CTG");
+ Leu.addElement("CTC");
+ Leu.addElement("CTT");
+ Leu.addElement("TTA");
+ Leu.addElement("TTG");
+
+ Val.addElement("GTA");
+ Val.addElement("GTG");
+ Val.addElement("GTC");
+ Val.addElement("GTT");
+
+ Phe.addElement("TTC");
+ Phe.addElement("TTT");
+ }
+
+
+ //Stores residue codes/names and colours and other things
+ public static Hashtable propHash = new Hashtable();
+ public static Hashtable hydrophobic = new Hashtable();
+ public static Hashtable polar = new Hashtable();
+ public static Hashtable small = new Hashtable();
+ public static Hashtable positive = new Hashtable();
+ public static Hashtable negative = new Hashtable();
+ public static Hashtable charged = new Hashtable();
+ public static Hashtable aromatic = new Hashtable();
+ public static Hashtable aliphatic = new Hashtable();
+ public static Hashtable tiny = new Hashtable();
+ public static Hashtable proline = new Hashtable();
+
+ static
+ {
+ hydrophobic.put("I", new Integer(1));
+ hydrophobic.put("L", new Integer(1));
+ hydrophobic.put("V", new Integer(1));
+ hydrophobic.put("C", new Integer(1));
+ hydrophobic.put("A", new Integer(1));
+ hydrophobic.put("G", new Integer(1));
+ hydrophobic.put("M", new Integer(1));
+ hydrophobic.put("F", new Integer(1));
+ hydrophobic.put("Y", new Integer(1));
+ hydrophobic.put("W", new Integer(1));
+ hydrophobic.put("H", new Integer(1));
+ hydrophobic.put("K", new Integer(1));
+ hydrophobic.put("X", new Integer(1));
+ hydrophobic.put("-", new Integer(1));
+ hydrophobic.put("*", new Integer(1));
+ hydrophobic.put("R", new Integer(0));
+ hydrophobic.put("E", new Integer(0));
+ hydrophobic.put("Q", new Integer(0));
+ hydrophobic.put("D", new Integer(0));
+ hydrophobic.put("N", new Integer(0));
+ hydrophobic.put("S", new Integer(0));
+ hydrophobic.put("T", new Integer(0));
+ hydrophobic.put("P", new Integer(0));
+ }
+
+ static
+ {
+ polar.put("Y", new Integer(1));
+ polar.put("W", new Integer(1));
+ polar.put("H", new Integer(1));
+ polar.put("K", new Integer(1));
+ polar.put("R", new Integer(1));
+ polar.put("E", new Integer(1));
+ polar.put("Q", new Integer(1));
+ polar.put("D", new Integer(1));
+ polar.put("N", new Integer(1));
+ polar.put("S", new Integer(1));
+ polar.put("T", new Integer(1));
+ polar.put("X", new Integer(1));
+ polar.put("-", new Integer(1));
+ polar.put("*", new Integer(1));
+ polar.put("I", new Integer(0));
+ polar.put("L", new Integer(0));
+ polar.put("V", new Integer(0));
+ polar.put("C", new Integer(0));
+ polar.put("A", new Integer(0));
+ polar.put("G", new Integer(0));
+ polar.put("M", new Integer(0));
+ polar.put("F", new Integer(0));
+ polar.put("P", new Integer(0));
+ }
+
+ static
+ {
+ small.put("I", new Integer(0));
+ small.put("L", new Integer(0));
+ small.put("V", new Integer(1));
+ small.put("C", new Integer(1));
+ small.put("A", new Integer(1));
+ small.put("G", new Integer(1));
+ small.put("M", new Integer(0));
+ small.put("F", new Integer(0));
+ small.put("Y", new Integer(0));
+ small.put("W", new Integer(0));
+ small.put("H", new Integer(0));
+ small.put("K", new Integer(0));
+ small.put("R", new Integer(0));
+ small.put("E", new Integer(0));
+ small.put("Q", new Integer(0));
+ small.put("D", new Integer(1));
+ small.put("N", new Integer(1));
+ small.put("S", new Integer(1));
+ small.put("T", new Integer(1));
+ small.put("P", new Integer(1));
+ small.put("-", new Integer(1));
+ small.put("*", new Integer(1));
+ }
+
+ static
+ {
+ positive.put("I", new Integer(0));
+ positive.put("L", new Integer(0));
+ positive.put("V", new Integer(0));
+ positive.put("C", new Integer(0));
+ positive.put("A", new Integer(0));
+ positive.put("G", new Integer(0));
+ positive.put("M", new Integer(0));
+ positive.put("F", new Integer(0));
+ positive.put("Y", new Integer(0));
+ positive.put("W", new Integer(0));
+ positive.put("H", new Integer(1));
+ positive.put("K", new Integer(1));
+ positive.put("R", new Integer(1));
+ positive.put("E", new Integer(0));
+ positive.put("Q", new Integer(0));
+ positive.put("D", new Integer(0));
+ positive.put("N", new Integer(0));
+ positive.put("S", new Integer(0));
+ positive.put("T", new Integer(0));
+ positive.put("P", new Integer(0));
+ positive.put("-", new Integer(1));
+ positive.put("*", new Integer(1));
+ }
+
+ static
+ {
+ negative.put("I", new Integer(0));
+ negative.put("L", new Integer(0));
+ negative.put("V", new Integer(0));
+ negative.put("C", new Integer(0));
+ negative.put("A", new Integer(0));
+ negative.put("G", new Integer(0));
+ negative.put("M", new Integer(0));
+ negative.put("F", new Integer(0));
+ negative.put("Y", new Integer(0));
+ negative.put("W", new Integer(0));
+ negative.put("H", new Integer(0));
+ negative.put("K", new Integer(0));
+ negative.put("R", new Integer(0));
+ negative.put("E", new Integer(1));
+ negative.put("Q", new Integer(0));
+ negative.put("D", new Integer(1));
+ negative.put("N", new Integer(0));
+ negative.put("S", new Integer(0));
+ negative.put("T", new Integer(0));
+ negative.put("P", new Integer(0));
+ negative.put("-", new Integer(1));
+ negative.put("*", new Integer(1));
+ }
+
+ static
+ {
+ charged.put("I", new Integer(0));
+ charged.put("L", new Integer(0));
+ charged.put("V", new Integer(0));
+ charged.put("C", new Integer(0));
+ charged.put("A", new Integer(0));
+ charged.put("G", new Integer(0));
+ charged.put("M", new Integer(0));
+ charged.put("F", new Integer(0));
+ charged.put("Y", new Integer(0));
+ charged.put("W", new Integer(0));
+ charged.put("H", new Integer(1));
+ charged.put("K", new Integer(1));
+ charged.put("R", new Integer(1));
+ charged.put("E", new Integer(1));
+ charged.put("Q", new Integer(0));
+ charged.put("D", new Integer(1));
+ charged.put("N", new Integer(1));
+ charged.put("S", new Integer(0));
+ charged.put("T", new Integer(0));
+ charged.put("P", new Integer(0));
+ charged.put("-", new Integer(1));
+ charged.put("*", new Integer(1));
+ }
+
+ static
+ {
+ aromatic.put("I", new Integer(0));
+ aromatic.put("L", new Integer(0));
+ aromatic.put("V", new Integer(0));
+ aromatic.put("C", new Integer(0));
+ aromatic.put("A", new Integer(0));
+ aromatic.put("G", new Integer(0));
+ aromatic.put("M", new Integer(0));
+ aromatic.put("F", new Integer(1));
+ aromatic.put("Y", new Integer(1));
+ aromatic.put("W", new Integer(1));
+ aromatic.put("H", new Integer(1));
+ aromatic.put("K", new Integer(0));
+ aromatic.put("R", new Integer(0));
+ aromatic.put("E", new Integer(0));
+ aromatic.put("Q", new Integer(0));
+ aromatic.put("D", new Integer(0));
+ aromatic.put("N", new Integer(0));
+ aromatic.put("S", new Integer(0));
+ aromatic.put("T", new Integer(0));
+ aromatic.put("P", new Integer(0));
+ aromatic.put("-", new Integer(1));
+ aromatic.put("*", new Integer(1));
+ }
+
+ static
+ {
+ aliphatic.put("I", new Integer(1));
+ aliphatic.put("L", new Integer(1));
+ aliphatic.put("V", new Integer(1));
+ aliphatic.put("C", new Integer(0));
+ aliphatic.put("A", new Integer(0));
+ aliphatic.put("G", new Integer(0));
+ aliphatic.put("M", new Integer(0));
+ aliphatic.put("F", new Integer(0));
+ aliphatic.put("Y", new Integer(0));
+ aliphatic.put("W", new Integer(0));
+ aliphatic.put("H", new Integer(0));
+ aliphatic.put("K", new Integer(0));
+ aliphatic.put("R", new Integer(0));
+ aliphatic.put("E", new Integer(0));
+ aliphatic.put("Q", new Integer(0));
+ aliphatic.put("D", new Integer(0));
+ aliphatic.put("N", new Integer(0));
+ aliphatic.put("S", new Integer(0));
+ aliphatic.put("T", new Integer(0));
+ aliphatic.put("P", new Integer(0));
+ aliphatic.put("-", new Integer(1));
+ aliphatic.put("*", new Integer(1));
+ }
+
+ static
+ {
+ tiny.put("I", new Integer(0));
+ tiny.put("L", new Integer(0));
+ tiny.put("V", new Integer(0));
+ tiny.put("C", new Integer(0));
+ tiny.put("A", new Integer(1));
+ tiny.put("G", new Integer(1));
+ tiny.put("M", new Integer(0));
+ tiny.put("F", new Integer(0));
+ tiny.put("Y", new Integer(0));
+ tiny.put("W", new Integer(0));
+ tiny.put("H", new Integer(0));
+ tiny.put("K", new Integer(0));
+ tiny.put("R", new Integer(0));
+ tiny.put("E", new Integer(0));
+ tiny.put("Q", new Integer(0));
+ tiny.put("D", new Integer(0));
+ tiny.put("N", new Integer(0));
+ tiny.put("S", new Integer(1));
+ tiny.put("T", new Integer(0));
+ tiny.put("P", new Integer(0));
+ tiny.put("-", new Integer(1));
+ tiny.put("*", new Integer(1));
+ }
+
+ static
+ {
+ proline.put("I", new Integer(0));
+ proline.put("L", new Integer(0));
+ proline.put("V", new Integer(0));
+ proline.put("C", new Integer(0));
+ proline.put("A", new Integer(0));
+ proline.put("G", new Integer(0));
+ proline.put("M", new Integer(0));
+ proline.put("F", new Integer(0));
+ proline.put("Y", new Integer(0));
+ proline.put("W", new Integer(0));
+ proline.put("H", new Integer(0));
+ proline.put("K", new Integer(0));
+ proline.put("R", new Integer(0));
+ proline.put("E", new Integer(0));
+ proline.put("Q", new Integer(0));
+ proline.put("D", new Integer(0));
+ proline.put("N", new Integer(0));
+ proline.put("S", new Integer(0));
+ proline.put("T", new Integer(0));
+ proline.put("P", new Integer(1));
+ proline.put("-", new Integer(1));
+ proline.put("*", new Integer(1));
+ }
+
+ static
+ {
+ propHash.put("hydrophobic", hydrophobic);
+ propHash.put("small", small);
+ propHash.put("positive", positive);
+ propHash.put("negative", negative);
+ propHash.put("charged", charged);
+ propHash.put("aromatic", aromatic);
+ propHash.put("aliphatic", aliphatic);
+ propHash.put("tiny", tiny);
+ propHash.put("proline", proline);
+ propHash.put("polar", polar);
+ }
+
+ private ResidueProperties()
+ {
+ }
+
+ public static double getHydmax()
+ {
+ return hydmax;
+ }
+
+ public static double getHydmin()
+ {
+ return hydmin;
+ }
+
+ public static double[] getHyd()
+ {
+ return hyd;
+ }
+
+ public static Hashtable getAA3Hash()
+ {
+ return aa3Hash;
+ }
+
+ public static int[][] getDNA()
+ {
+ return ResidueProperties.DNA;
+ }
+
+ public static int[][] getBLOSUM62()
+ {
+ return ResidueProperties.BLOSUM62;
+ }
+
+ public static int getPAM250(String A1, String A2)
+ {
+ int a = aaIndex[A1.charAt(0)];
+ int b = aaIndex[A2.charAt(0)];
+
+ int pog = ResidueProperties.PAM250[a][b];
+
+ return pog;
+ }
+
+ public static int getBLOSUM62(char c1, char c2)
+ {
+ int pog = 0;
+
+ try
+ {
+ int a = aaIndex[c1];
+ int b = aaIndex[c2];
+
+ pog = ResidueProperties.BLOSUM62[a][b];
+ }
+ catch (Exception e)
+ {
+ //System.out.println("Unknown residue in " + A1 + " " + A2);
+ }
+
+ return pog;
+ }
+
+ public static Vector getCodons(String res)
+ {
+ if (codonHash.containsKey(res))
+ {
+ return (Vector) codonHash.get(res);
+ }
+
+ return null;
+ }
+
+ public static String codonTranslate(String codon)
+ {
+ Enumeration e = codonHash.keys();
+
+ while (e.hasMoreElements())
+ {
+ String key = (String) e.nextElement();
+ Vector tmp = (Vector) codonHash.get(key);
+
+ if (tmp.contains(codon.toUpperCase()))
+ {
+ return key;
+ }
+ }
+
+ return null;
+ }
+
+ public static int[][] getDefaultPeptideMatrix() {
+ return ResidueProperties.getBLOSUM62();
+ }
+ public static int[][] getDefaultDnaMatrix() {
+ return ResidueProperties.getDNA();
+ }
+
+ /**
+ * get a ScoreMatrix based on its string name
+ * @param pwtype
+ * @return matrix in scoreMatrices with key pwtype or null
+ */
+ public static ScoreMatrix getScoreMatrix(String pwtype) {
+ Object val=scoreMatrices.get(pwtype);
+ if (val!=null)
+ return (ScoreMatrix) val;
+ return null;
+ }
+}
git://source.jalview.org / jalview.git / commitdiff