X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtil.java;h=a2e1c71b167baba40e6b3706d291f2e9093e983a;hb=1627d5f04287be852b799ba51bf2b6ded9acecda;hp=21928663596b1b5aaab19f49afaeb811c8d07cb0;hpb=6f62124bf8277dd898f43f75e81bbde027fb2ebc;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtil.java b/src/jalview/analysis/AlignmentUtil.java
index 2192866..a2e1c71 100755
--- a/src/jalview/analysis/AlignmentUtil.java
+++ b/src/jalview/analysis/AlignmentUtil.java
@@ -1,198 +1,205 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 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.*;
-import jalview.util.*;
-import java.util.*;
 
-public class AlignmentUtil {
+import jalview.util.*;
 
-  private AlignmentUtil() {
-  }
+import java.util.*;
 
-  public static int[][] percentIdentity2(AlignmentI align) {
-    return percentIdentity2(align,0,align.getWidth()-1);
-  }
 
-  public static int[][] percentIdentity2(AlignmentI align, int start, int end) {
-    int [][] cons2 = new int[align.getWidth()][24];
-    // Initialize the array
-    for (int j=0;j<24;j++) {
-      for (int i=0; i < align.getWidth();i++) {
-        cons2[i][j] = 0;
-      }
+public class AlignmentUtil {
+    private AlignmentUtil() {
     }
 
-    return cons2;
-  }
-  public static int getPixelHeight(int i, int j,int charHeight) {
-    int h=0;
-    while (i < j) {
-      h += charHeight;
-      i++;
+    public static int[][] percentIdentity2(AlignmentI align) {
+        return percentIdentity2(align, 0, align.getWidth() - 1);
     }
-    return h;
-  }
-
-
-    public static Vector substitution_rates (AlignmentI align, int start, int end) {
-
-	Vector rates = new Vector();
-
-	int len = (end-start+1);
-
-	// Turn seqs into char arrays
-
-	int[][] seqint = new int[align.getHeight()][len];
-
-
-	for (int j = 0; j < align.getHeight(); j++) {
-
-	    SequenceI seq = align.getSequenceAt(j);
-
-	    for (int i = 0 ; i < len; i++) {
-		char c = seq.getCharAt(start + i - 1);
-
-		if (c == 'A') {
-		    seqint[j][i] = 0;
-		} else if (c == 'C') {
-		    seqint[j][i] = 1;
-		} else if (c == 'T') {
-		    seqint[j][i] = 2;
-		} else if (c == 'G') {
-		    seqint[j][i] = 3;
-		} else {
-		    seqint[j][i] = -1;
-		}
-
-	    }
-
-	}
-
-
-	//	print_matrix(seqint,2,len);	for (int j = 0; j < align.getHeight(); j++) {
-
-	    for (int j = 0; j < align.getHeight(); j++) {
-
-		for (int k = 0; k < align.getHeight(); k++) {
-
-		int counts[][] = new int[4][4];
-		int tot  = 0;
-		int tots[] = new int[4];
-		int fulltot = 0;
-		int fulltots[] = new int[4];
-
-		for (int i = 0 ; i < len; i++) {
-
-		    if (k != j) {
 
-			//			System.out.println("Seq " + j + " " + k + " " + i + " " + seqint[j][i] + " " + seqint[k][i]);
-			if (seqint[j][i] >= 0 &&
-			    seqint[k][i] >= 0) {
-			    counts[seqint[k][i]][seqint[j][i]]++;
+    public static int[][] percentIdentity2(AlignmentI align, int start, int end) {
+        int[][] cons2 = new int[align.getWidth()][24];
 
-			    //  print_matrix(counts,4,4);
-			    tots[seqint[j][i]]++;
-			    tot++;
-			}
-			if (seqint[j][i] != -1) {
-			    fulltots[seqint[j][i]]++;
-			    fulltot++;
-			}
-		    }
-		}
+        // Initialize the array
+        for (int j = 0; j < 24; j++) {
+            for (int i = 0; i < align.getWidth(); i++) {
+                cons2[i][j] = 0;
+            }
+        }
 
-		if (k != j) {
-
-		    System.out.println();
-
-		    System.out.println("Sequence " + align.getSequenceAt(j).getName() + " "  + align.getSequenceAt(k).getName());
-
-		    System.out.println();
-		    print_matrix(counts,4,4);
-		    System.out.println();
-
-
-
-		    double[][] out = new double[4][4];// = constant_multiply_matrix(counts,1.0/tot,4,4);
-
-		    for (int i = 0; i < 4; i++) {
-			for (int jj = 0; jj < 4; jj++) {
-			    out[i][jj] = (double)counts[i][jj]/tots[jj];
-			}
-		    }
-
-		    print_matrix(out,4,4);
-		    System.out.println();
-
-
-		    System.out.print("RATES\t");
-		    System.out.print(align.getSequenceAt(j).getName() + "\t"  + align.getSequenceAt(k).getName() + "\t");
-
-		    for (int i = 0; i < 4; i++) {
-			for (int jj = 0; jj < 4; jj++) {
-			    Format.print(System.out,"%4.3f\t",out[i][jj]);
-			}
-		    }
-		    System.out.println();
-
- 		    for (int i = 0; i < 4; i++) {
-			Format.print(System.out,"%4.3f\t",(double)fulltots[i]*1.0/fulltot);
-		    }
-
-		    System.out.println();
-		    System.out.print("\nGC ");
-
-		    Format.print(System.out,"%4.3f\t",(double)(100*fulltots[1]+fulltots[3])/fulltot);
-
-		    System.out.print((fulltots[1]+fulltots[3]) + "\t" + fulltot);
+        return cons2;
+    }
 
+    public static int getPixelHeight(int i, int j, int charHeight) {
+        int h = 0;
 
-		    System.out.println();
+        while (i < j) {
+            h += charHeight;
+            i++;
+        }
 
-		    rates.addElement(out);
-		}
+        return h;
+    }
 
-	    }
-	}
-	return rates;
+    public static Vector substitution_rates(AlignmentI align, int start, int end) {
+        Vector rates = new Vector();
+
+        int len = (end - start + 1);
+
+        // Turn seqs into char arrays
+        int[][] seqint = new int[align.getHeight()][len];
+
+        for (int j = 0; j < align.getHeight(); j++) {
+            SequenceI seq = align.getSequenceAt(j);
+
+            for (int i = 0; i < len; i++) {
+                char c = seq.getCharAt((start + i) - 1);
+
+                if (c == 'A') {
+                    seqint[j][i] = 0;
+                } else if (c == 'C') {
+                    seqint[j][i] = 1;
+                } else if (c == 'T') {
+                    seqint[j][i] = 2;
+                } else if (c == 'G') {
+                    seqint[j][i] = 3;
+                } else {
+                    seqint[j][i] = -1;
+                }
+            }
+        }
+
+        //	print_matrix(seqint,2,len);	for (int j = 0; j < align.getHeight(); j++) {
+        for (int j = 0; j < align.getHeight(); j++) {
+            for (int k = 0; k < align.getHeight(); k++) {
+                int[][] counts = new int[4][4];
+                int tot = 0;
+                int[] tots = new int[4];
+                int fulltot = 0;
+                int[] fulltots = new int[4];
+
+                for (int i = 0; i < len; i++) {
+                    if (k != j) {
+                        //			System.out.println("Seq " + j + " " + k + " " + i + " " + seqint[j][i] + " " + seqint[k][i]);
+                        if ((seqint[j][i] >= 0) && (seqint[k][i] >= 0)) {
+                            counts[seqint[k][i]][seqint[j][i]]++;
+
+                            //  print_matrix(counts,4,4);
+                            tots[seqint[j][i]]++;
+                            tot++;
+                        }
+
+                        if (seqint[j][i] != -1) {
+                            fulltots[seqint[j][i]]++;
+                            fulltot++;
+                        }
+                    }
+                }
+
+                if (k != j) {
+                    System.out.println();
+
+                    System.out.println("Sequence " +
+                        align.getSequenceAt(j).getName() + " " +
+                        align.getSequenceAt(k).getName());
+
+                    System.out.println();
+                    print_matrix(counts, 4, 4);
+                    System.out.println();
+
+                    double[][] out = new double[4][4]; // = constant_multiply_matrix(counts,1.0/tot,4,4);
+
+                    for (int i = 0; i < 4; i++) {
+                        for (int jj = 0; jj < 4; jj++) {
+                            out[i][jj] = (double) counts[i][jj] / tots[jj];
+                        }
+                    }
+
+                    print_matrix(out, 4, 4);
+                    System.out.println();
+
+                    System.out.print("RATES\t");
+                    System.out.print(align.getSequenceAt(j).getName() + "\t" +
+                        align.getSequenceAt(k).getName() + "\t");
+
+                    for (int i = 0; i < 4; i++) {
+                        for (int jj = 0; jj < 4; jj++) {
+                            Format.print(System.out, "%4.3f\t", out[i][jj]);
+                        }
+                    }
+
+                    System.out.println();
+
+                    for (int i = 0; i < 4; i++) {
+                        Format.print(System.out, "%4.3f\t",
+                            ((double) fulltots[i] * 1.0) / fulltot);
+                    }
+
+                    System.out.println();
+                    System.out.print("\nGC ");
+
+                    Format.print(System.out, "%4.3f\t",
+                        (double) ((100 * fulltots[1]) + fulltots[3]) / fulltot);
+
+                    System.out.print((fulltots[1] + fulltots[3]) + "\t" +
+                        fulltot);
+
+                    System.out.println();
+
+                    rates.addElement(out);
+                }
+            }
+        }
+
+        return rates;
     }
 
-    public static double[][]  constant_multiply_matrix(int[][] matrix, double c,int n, int m) {
-	double[][] out = new double[n][m];
+    public static double[][] constant_multiply_matrix(int[][] matrix, double c,
+        int n, int m) {
+        double[][] out = new double[n][m];
 
-	for (int i = 0; i < n; i++) {
-	    for (int j = 0; j < m; j++) {
+        for (int i = 0; i < n; i++) {
+            for (int j = 0; j < m; j++) {
+                out[i][j] = matrix[i][j] * c;
+            }
+        }
 
-		out[i][j] = matrix[i][j]*c;
-	    }
-	}
-	return out;
+        return out;
     }
 
-
     public static void print_matrix(int[][] matrix, int n, int m) {
+        for (int i = 0; i < n; i++) {
+            for (int j = 0; j < m; j++) {
+                System.out.print(matrix[i][j] + "\t");
+            }
 
-
-	for (int i = 0; i < n; i++) {
-	    for (int j = 0; j < m; j++) {
-
-		System.out.print(matrix[i][j] + "\t");
-	    }
-	    System.out.println();
-	}
+            System.out.println();
+        }
     }
-    public static void print_matrix(double[][] matrix, int n, int m) {
-
-
-	for (int i = 0; i < n; i++) {
-	    for (int j = 0; j < m; j++) {
 
-		Format.print(System.out,"%4.3f\t",matrix[i][j]);
+    public static void print_matrix(double[][] matrix, int n, int m) {
+        for (int i = 0; i < n; i++) {
+            for (int j = 0; j < m; j++) {
+                Format.print(System.out, "%4.3f\t", matrix[i][j]);
+            }
 
-	    }
-	    System.out.println();
-	}
+            System.out.println();
+        }
     }
-
-
 }