+++ /dev/null
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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.*;\r
-\r
-import jalview.util.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-public class AlignmentUtil {\r
- private AlignmentUtil() {\r
- }\r
-\r
- public static int[][] percentIdentity2(AlignmentI align) {\r
- return percentIdentity2(align, 0, align.getWidth() - 1);\r
- }\r
-\r
- public static int[][] percentIdentity2(AlignmentI align, int start, int end) {\r
- int[][] cons2 = new int[align.getWidth()][24];\r
-\r
- // Initialize the array\r
- for (int j = 0; j < 24; j++) {\r
- for (int i = 0; i < align.getWidth(); i++) {\r
- cons2[i][j] = 0;\r
- }\r
- }\r
-\r
- return cons2;\r
- }\r
-\r
- public static int getPixelHeight(int i, int j, int charHeight) {\r
- int h = 0;\r
-\r
- while (i < j) {\r
- h += charHeight;\r
- i++;\r
- }\r
-\r
- return h;\r
- }\r
-\r
- public static Vector substitution_rates(AlignmentI align, int start, int end) {\r
- Vector rates = new Vector();\r
-\r
- int len = (end - start + 1);\r
-\r
- // Turn seqs into char arrays\r
- int[][] seqint = new int[align.getHeight()][len];\r
-\r
- for (int j = 0; j < align.getHeight(); j++) {\r
- SequenceI seq = align.getSequenceAt(j);\r
-\r
- for (int i = 0; i < len; i++) {\r
- char c = seq.getCharAt((start + i) - 1);\r
-\r
- if (c == 'A') {\r
- seqint[j][i] = 0;\r
- } else if (c == 'C') {\r
- seqint[j][i] = 1;\r
- } else if (c == 'T') {\r
- seqint[j][i] = 2;\r
- } else if (c == 'G') {\r
- seqint[j][i] = 3;\r
- } else {\r
- seqint[j][i] = -1;\r
- }\r
- }\r
- }\r
-\r
- // print_matrix(seqint,2,len); for (int j = 0; j < align.getHeight(); j++) {\r
- for (int j = 0; j < align.getHeight(); j++) {\r
- for (int k = 0; k < align.getHeight(); k++) {\r
- int[][] counts = new int[4][4];\r
- int tot = 0;\r
- int[] tots = new int[4];\r
- int fulltot = 0;\r
- int[] fulltots = new int[4];\r
-\r
- for (int i = 0; i < len; i++) {\r
- if (k != j) {\r
- // System.out.println("Seq " + j + " " + k + " " + i + " " + seqint[j][i] + " " + seqint[k][i]);\r
- if ((seqint[j][i] >= 0) && (seqint[k][i] >= 0)) {\r
- counts[seqint[k][i]][seqint[j][i]]++;\r
-\r
- // print_matrix(counts,4,4);\r
- tots[seqint[j][i]]++;\r
- tot++;\r
- }\r
-\r
- if (seqint[j][i] != -1) {\r
- fulltots[seqint[j][i]]++;\r
- fulltot++;\r
- }\r
- }\r
- }\r
-\r
- if (k != j) {\r
- System.out.println();\r
-\r
- System.out.println("Sequence " +\r
- align.getSequenceAt(j).getName() + " " +\r
- align.getSequenceAt(k).getName());\r
-\r
- System.out.println();\r
- print_matrix(counts, 4, 4);\r
- System.out.println();\r
-\r
- double[][] out = new double[4][4]; // = constant_multiply_matrix(counts,1.0/tot,4,4);\r
-\r
- for (int i = 0; i < 4; i++) {\r
- for (int jj = 0; jj < 4; jj++) {\r
- out[i][jj] = (double) counts[i][jj] / tots[jj];\r
- }\r
- }\r
-\r
- print_matrix(out, 4, 4);\r
- System.out.println();\r
-\r
- System.out.print("RATES\t");\r
- System.out.print(align.getSequenceAt(j).getName() + "\t" +\r
- align.getSequenceAt(k).getName() + "\t");\r
-\r
- for (int i = 0; i < 4; i++) {\r
- for (int jj = 0; jj < 4; jj++) {\r
- Format.print(System.out, "%4.3f\t", out[i][jj]);\r
- }\r
- }\r
-\r
- System.out.println();\r
-\r
- for (int i = 0; i < 4; i++) {\r
- Format.print(System.out, "%4.3f\t",\r
- ((double) fulltots[i] * 1.0) / fulltot);\r
- }\r
-\r
- System.out.println();\r
- System.out.print("\nGC ");\r
-\r
- Format.print(System.out, "%4.3f\t",\r
- (double) ((100 * fulltots[1]) + fulltots[3]) / fulltot);\r
-\r
- System.out.print((fulltots[1] + fulltots[3]) + "\t" +\r
- fulltot);\r
-\r
- System.out.println();\r
-\r
- rates.addElement(out);\r
- }\r
- }\r
- }\r
-\r
- return rates;\r
- }\r
-\r
- public static double[][] constant_multiply_matrix(int[][] matrix, double c,\r
- int n, int m) {\r
- double[][] out = new double[n][m];\r
-\r
- for (int i = 0; i < n; i++) {\r
- for (int j = 0; j < m; j++) {\r
- out[i][j] = matrix[i][j] * c;\r
- }\r
- }\r
-\r
- return out;\r
- }\r
-\r
- public static void print_matrix(int[][] matrix, int n, int m) {\r
- for (int i = 0; i < n; i++) {\r
- for (int j = 0; j < m; j++) {\r
- System.out.print(matrix[i][j] + "\t");\r
- }\r
-\r
- System.out.println();\r
- }\r
- }\r
-\r
- public static void print_matrix(double[][] matrix, int n, int m) {\r
- for (int i = 0; i < n; i++) {\r
- for (int j = 0; j < m; j++) {\r
- Format.print(System.out, "%4.3f\t", matrix[i][j]);\r
- }\r
-\r
- System.out.println();\r
- }\r
- }\r
-}\r
+++ /dev/null
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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.*;\r
-\r
-import jalview.io.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-public class CompareAlignments {\r
- Vector align;\r
- String refId;\r
- Vector ids;\r
-\r
- public CompareAlignments(Vector align) {\r
- this.align = align;\r
-\r
- ids = new Vector();\r
-\r
- Alignment al0 = (Alignment) align.elementAt(0);\r
-\r
- for (int i = 0; i < al0.getHeight(); i++) {\r
- SequenceI seq = al0.getSequenceAt(i);\r
-\r
- ids.addElement(seq.getName());\r
-\r
- if (i == 0) {\r
- setReferenceId(seq.getName());\r
- }\r
- }\r
- }\r
-\r
- public void compare() {\r
- Hashtable positions = new Hashtable();\r
-\r
- for (int k = 0; k < ids.size(); k++) {\r
- String id = (String) ids.elementAt(k);\r
-\r
- System.out.println("Ids " + id + " " + refId);\r
-\r
- if (!id.equals(refId)) {\r
- Hashtable fullhash = new Hashtable();\r
-\r
- for (int i = 0; i < align.size(); i++) {\r
- System.out.println("Alignment " + i);\r
-\r
- Alignment al = (Alignment) align.elementAt(i);\r
-\r
- SequenceI refseq = null;\r
-\r
- for (int j = 0; j < al.getHeight(); j++) {\r
- if (((SequenceI) al.getSequenceAt(j)).getName().equals(refId)) {\r
- refseq = (SequenceI) al.getSequenceAt(j);\r
- }\r
- }\r
-\r
- if (refseq != null) {\r
- System.out.println("Refseq " + refseq.getName());\r
-\r
- for (int jj = 0; jj < al.getHeight(); jj++) {\r
- SequenceI seq = (SequenceI) al.getSequenceAt(jj);\r
-\r
- if (seq.getName().equals(id)) {\r
- Hashtable hash = getAlignPositions(seq, refseq);\r
-\r
- Enumeration keys = hash.keys();\r
-\r
- while (keys.hasMoreElements()) {\r
- Integer key = (Integer) keys.nextElement();\r
-\r
- // System.out.println(key + " " + hash.get(key));\r
- if (fullhash.get(key) == null) {\r
- fullhash.put(key, new Vector());\r
- }\r
-\r
- Vector tmp = (Vector) fullhash.get(key);\r
-\r
- tmp.addElement(hash.get(key));\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- System.out.println("\nId " + id);\r
-\r
- Enumeration keys = fullhash.keys();\r
-\r
- int totdiff = 0;\r
-\r
- while (keys.hasMoreElements()) {\r
- Integer key = (Integer) keys.nextElement();\r
-\r
- Vector tmp = (Vector) fullhash.get(key);\r
-\r
- int diff0 = ((Integer) tmp.elementAt(0)).intValue();\r
- ;\r
-\r
- int diff = 0;\r
-\r
- for (int l = 1; l < tmp.size(); l++) {\r
- diff += Math.abs(diff0 -\r
- ((Integer) tmp.elementAt(l)).intValue());\r
- }\r
-\r
- if (diff > 0) {\r
- totdiff++;\r
- System.out.print(id + " Ref pos " + key + " : " +\r
- diff0 + " " + diff + " : ");\r
-\r
- for (int l = 1; l < tmp.size(); l++) {\r
- System.out.print(diff0 -\r
- ((Integer) tmp.elementAt(l)).intValue() + " ");\r
- }\r
-\r
- System.out.println();\r
- }\r
- }\r
-\r
- System.out.println("Total " + id + " " + totdiff);\r
- }\r
- }\r
- }\r
-\r
- public void setReferenceId(String id) {\r
- this.refId = id;\r
- }\r
-\r
- public Hashtable getAlignPositions(SequenceI seq1, SequenceI seq2) {\r
- Hashtable hash = new Hashtable();\r
-\r
- int i = 0;\r
-\r
- int pos1 = 0;\r
- int pos2 = 0;\r
-\r
- while (i < seq1.getLength()) {\r
- char c1 = seq1.getCharAt(i);\r
- char c2 = seq2.getCharAt(i);\r
-\r
- if (c1 != '-') {\r
- pos1++;\r
- }\r
-\r
- if (c2 != '-') {\r
- pos2++;\r
- }\r
-\r
- if (c1 != '-') {\r
- hash.put(new Integer(pos1), new Integer(pos2));\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return hash;\r
- }\r
-}\r
git://source.jalview.org / jalview.git / commitdiff