From 067a6494124d4f1d0fe8b6d758b593145393b7dd Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 30 Jun 2008 09:48:06 +0000 Subject: [PATCH] included includeGaps flag in clustalW colour calculation - behaviour for includeGaps=false is not verified to match ClustalX as yet. --- src/jalview/schemes/ClustalxColourScheme.java | 623 +++++++++++++------------ src/jalview/schemes/Consensus.java | 170 +++---- 2 files changed, 411 insertions(+), 382 deletions(-) diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java index 8dd8994..bc2f9ea 100755 --- a/src/jalview/schemes/ClustalxColourScheme.java +++ b/src/jalview/schemes/ClustalxColourScheme.java @@ -1,303 +1,320 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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.*; - -import jalview.datamodel.*; - -public class ClustalxColourScheme - extends ResidueColourScheme -{ - public static Hashtable colhash = new Hashtable(); - Hashtable[] cons; - int[][] cons2; - ConsensusColour[] colours; - ConsensusColour[] ResidueColour; - int size; - Consensus[] conses = new Consensus[32]; - Vector colourTable = new Vector(); - - { - colhash.put("RED", new Color( (float) 0.9, (float) 0.2, (float) 0.1)); - colhash.put("BLUE", new Color( (float) 0.5, (float) 0.7, (float) 0.9)); - colhash.put("GREEN", new Color( (float) 0.1, (float) 0.8, (float) 0.1)); - colhash.put("ORANGE", new Color( (float) 0.9, (float) 0.6, (float) 0.3)); - colhash.put("CYAN", new Color( (float) 0.1, (float) 0.7, (float) 0.7)); - colhash.put("PINK", new Color( (float) 0.9, (float) 0.5, (float) 0.5)); - colhash.put("MAGENTA", new Color( (float) 0.8, (float) 0.3, (float) 0.8)); - colhash.put("YELLOW", new Color( (float) 0.8, (float) 0.8, (float) 0.0)); - } - - public ClustalxColourScheme(Vector seqs, int maxWidth) - { - resetClustalX(seqs, maxWidth); - } - - public void resetClustalX(Vector seqs, int maxWidth) - { - cons2 = new int[maxWidth][24]; - - int start = 0; - - // Initialize the array - for (int j = 0; j < 24; j++) - { - for (int i = 0; i < maxWidth; i++) - { - cons2[i][j] = 0; - } - } - - int res; - int i; - int j = 0; - char[] seq; - - while (j < seqs.size()) - { - seq = ( (SequenceI) seqs.elementAt(j)).getSequence(); - - int end_j = seq.length - 1; - - for (i = start; i <= end_j; i++) - { - if ( (seq.length - 1) < i) - { - res = 23; - } - else - { - res = ResidueProperties.aaIndex[seq[i]]; - } - - cons2[i][res]++; - } - - j++; - } - - this.size = seqs.size(); - makeColours(); - } - - public void makeColours() - { - conses[0] = new Consensus("WLVIMAFCYHP", 60); - conses[1] = new Consensus("WLVIMAFCYHP", 80); - conses[2] = new Consensus("ED", 50); - conses[3] = new Consensus("KR", 60); - conses[4] = new Consensus("G", 50); - conses[5] = new Consensus("N", 50); - conses[6] = new Consensus("QE", 50); - conses[7] = new Consensus("P", 50); - conses[8] = new Consensus("TS", 50); - - conses[26] = new Consensus("A", 85); - conses[27] = new Consensus("C", 85); - conses[10] = new Consensus("E", 85); - conses[11] = new Consensus("F", 85); - conses[12] = new Consensus("G", 85); - conses[13] = new Consensus("H", 85); - conses[14] = new Consensus("I", 85); - conses[15] = new Consensus("L", 85); - conses[16] = new Consensus("M", 85); - conses[17] = new Consensus("N", 85); - conses[18] = new Consensus("P", 85); - conses[19] = new Consensus("Q", 85); - conses[20] = new Consensus("R", 85); - conses[21] = new Consensus("S", 85); - conses[22] = new Consensus("T", 85); - conses[23] = new Consensus("V", 85); - conses[24] = new Consensus("W", 85); - conses[25] = new Consensus("Y", 85); - conses[28] = new Consensus("K", 85); - conses[29] = new Consensus("D", 85); - - conses[30] = new Consensus("G", 0); - conses[31] = new Consensus("P", 0); - - // We now construct the colours - colours = new ConsensusColour[11]; - - Consensus[] tmp8 = new Consensus[1]; - tmp8[0] = conses[30]; //G - colours[7] = new ConsensusColour( (Color) colhash.get("ORANGE"), tmp8); - - Consensus[] tmp9 = new Consensus[1]; - tmp9[0] = conses[31]; //P - colours[8] = new ConsensusColour( (Color) colhash.get("YELLOW"), tmp9); - - Consensus[] tmp10 = new Consensus[1]; - tmp10[0] = conses[27]; //C - colours[9] = new ConsensusColour( (Color) colhash.get("PINK"), tmp8); - - Consensus[] tmp1 = new Consensus[14]; - tmp1[0] = conses[0]; //% - tmp1[1] = conses[1]; //# - tmp1[2] = conses[26]; //A - tmp1[3] = conses[27]; //C - tmp1[4] = conses[11]; //F - tmp1[5] = conses[13]; //H - tmp1[6] = conses[14]; //I - tmp1[7] = conses[15]; //L - tmp1[8] = conses[16]; //M - tmp1[9] = conses[23]; //V - tmp1[10] = conses[24]; //W - tmp1[11] = conses[25]; //Y - tmp1[12] = conses[18]; //P - tmp1[13] = conses[19]; //p - colours[0] = new ConsensusColour( (Color) colhash.get("BLUE"), tmp1); - - colours[10] = new ConsensusColour( (Color) colhash.get("CYAN"), tmp1); - - Consensus[] tmp2 = new Consensus[5]; - tmp2[0] = conses[8]; //t - tmp2[1] = conses[21]; //S - tmp2[2] = conses[22]; //T - tmp2[3] = conses[0]; //% - tmp2[4] = conses[1]; //# - colours[1] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp2); - - Consensus[] tmp3 = new Consensus[3]; - - tmp3[0] = conses[17]; //N - tmp3[1] = conses[29]; //D - tmp3[2] = conses[5]; //n - colours[2] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp3); - - Consensus[] tmp4 = new Consensus[6]; - tmp4[0] = conses[6]; // q = QE - tmp4[1] = conses[19]; //Q - tmp4[2] = conses[22]; //E - tmp4[3] = conses[3]; //+ - tmp4[4] = conses[28]; //K - tmp4[5] = conses[20]; //R - colours[3] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp4); - - Consensus[] tmp5 = new Consensus[4]; - tmp5[0] = conses[3]; //+ - tmp5[1] = conses[28]; //K - tmp5[2] = conses[20]; //R - tmp5[3] = conses[19]; //Q - colours[4] = new ConsensusColour( (Color) colhash.get("RED"), tmp5); - - Consensus[] tmp6 = new Consensus[5]; - tmp6[0] = conses[3]; //- - tmp6[1] = conses[29]; //D - tmp6[2] = conses[10]; //E - tmp6[3] = conses[6]; //q - tmp6[4] = conses[19]; //Q - colours[5] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp6); - - Consensus[] tmp7 = new Consensus[5]; - tmp7[0] = conses[3]; //- - tmp7[1] = conses[29]; //D - tmp7[2] = conses[10]; //E - tmp7[3] = conses[17]; //N - tmp7[4] = conses[2]; //DE - colours[6] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp7); - - // Now attach the ConsensusColours to the residue letters - ResidueColour = new ConsensusColour[20]; - ResidueColour[0] = colours[0]; // A - ResidueColour[1] = colours[4]; // R - ResidueColour[2] = colours[2]; // N - ResidueColour[3] = colours[6]; // D - ResidueColour[4] = colours[0]; // C - ResidueColour[5] = colours[3]; // Q - ResidueColour[6] = colours[5]; // E - ResidueColour[7] = colours[7]; // G - ResidueColour[8] = colours[10]; // H - ResidueColour[9] = colours[0]; // I - ResidueColour[10] = colours[0]; // L - ResidueColour[11] = colours[4]; // K - ResidueColour[12] = colours[0]; // M - ResidueColour[13] = colours[0]; // F - ResidueColour[14] = colours[8]; // P - ResidueColour[15] = colours[1]; // S - ResidueColour[16] = colours[1]; // T - ResidueColour[17] = colours[0]; // W - ResidueColour[18] = colours[10]; // Y - ResidueColour[19] = colours[0]; // V - } - - public Color findColour(char c) - { - return Color.pink; - } - - public Color findColour(char c, int j) - { - Color currentColour; - - if (cons2.length <= j || (threshold != 0 && !aboveThreshold(c, j))) - { - return Color.white; - } - - int i = ResidueProperties.aaIndex[c]; - - currentColour = Color.white; - - if (i > 19) - { - return currentColour; - } - - for (int k = 0; k < ResidueColour[i].conses.length; k++) - { - if (ResidueColour[i].conses[k].isConserved(cons2, j, size)) - { - currentColour = ResidueColour[i].c; - } - } - - if (i == 4) - { - if (conses[27].isConserved(cons2, j, size)) - { - currentColour = (Color) colhash.get("PINK"); - } - } - - if (conservationColouring) - { - currentColour = applyConservation(currentColour, j); - } - - return currentColour; - } -} - -class ConsensusColour -{ - Consensus[] conses; - Color c; - - public ConsensusColour(Color c, Consensus[] conses) - { - this.conses = conses; - - // this.list = list; - this.c = c; - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 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.*; + +import jalview.datamodel.*; + +public class ClustalxColourScheme + extends ResidueColourScheme // implements IParameterizable +{ + public static Hashtable colhash = new Hashtable(); + Hashtable[] cons; + int[][] cons2; + ConsensusColour[] colours; + ConsensusColour[] ResidueColour; + int size; + Consensus[] conses = new Consensus[32]; + Vector colourTable = new Vector(); + private boolean includeGaps=true; + + { + colhash.put("RED", new Color( (float) 0.9, (float) 0.2, (float) 0.1)); + colhash.put("BLUE", new Color( (float) 0.5, (float) 0.7, (float) 0.9)); + colhash.put("GREEN", new Color( (float) 0.1, (float) 0.8, (float) 0.1)); + colhash.put("ORANGE", new Color( (float) 0.9, (float) 0.6, (float) 0.3)); + colhash.put("CYAN", new Color( (float) 0.1, (float) 0.7, (float) 0.7)); + colhash.put("PINK", new Color( (float) 0.9, (float) 0.5, (float) 0.5)); + colhash.put("MAGENTA", new Color( (float) 0.8, (float) 0.3, (float) 0.8)); + colhash.put("YELLOW", new Color( (float) 0.8, (float) 0.8, (float) 0.0)); + } + + public ClustalxColourScheme(Vector seqs, int maxWidth) + { + resetClustalX(seqs, maxWidth); + } + + public void resetClustalX(Vector seqs, int maxWidth) + { + cons2 = new int[maxWidth][24]; + includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to get the current setting of the includeGaps param. + int start = 0; + + // Initialize the array + for (int j = 0; j < 24; j++) + { + for (int i = 0; i < maxWidth; i++) + { + cons2[i][j] = 0; + } + } + + int res; + int i; + int j = 0; + char[] seq; + + while (j < seqs.size()) + { + seq = ( (SequenceI) seqs.elementAt(j)).getSequence(); + + int end_j = seq.length - 1; + + for (i = start; i <= end_j; i++) + { + if ( (seq.length - 1) < i) + { + res = 23; + } + else + { + res = ResidueProperties.aaIndex[seq[i]]; + } + + cons2[i][res]++; + } + + j++; + } + + this.size = seqs.size(); + makeColours(); + } + + public void makeColours() + { + conses[0] = new Consensus("WLVIMAFCYHP", 60); + conses[1] = new Consensus("WLVIMAFCYHP", 80); + conses[2] = new Consensus("ED", 50); + conses[3] = new Consensus("KR", 60); + conses[4] = new Consensus("G", 50); + conses[5] = new Consensus("N", 50); + conses[6] = new Consensus("QE", 50); + conses[7] = new Consensus("P", 50); + conses[8] = new Consensus("TS", 50); + + conses[26] = new Consensus("A", 85); + conses[27] = new Consensus("C", 85); + conses[10] = new Consensus("E", 85); + conses[11] = new Consensus("F", 85); + conses[12] = new Consensus("G", 85); + conses[13] = new Consensus("H", 85); + conses[14] = new Consensus("I", 85); + conses[15] = new Consensus("L", 85); + conses[16] = new Consensus("M", 85); + conses[17] = new Consensus("N", 85); + conses[18] = new Consensus("P", 85); + conses[19] = new Consensus("Q", 85); + conses[20] = new Consensus("R", 85); + conses[21] = new Consensus("S", 85); + conses[22] = new Consensus("T", 85); + conses[23] = new Consensus("V", 85); + conses[24] = new Consensus("W", 85); + conses[25] = new Consensus("Y", 85); + conses[28] = new Consensus("K", 85); + conses[29] = new Consensus("D", 85); + + conses[30] = new Consensus("G", 0); + conses[31] = new Consensus("P", 0); + + // We now construct the colours + colours = new ConsensusColour[11]; + + Consensus[] tmp8 = new Consensus[1]; + tmp8[0] = conses[30]; //G + colours[7] = new ConsensusColour( (Color) colhash.get("ORANGE"), tmp8); + + Consensus[] tmp9 = new Consensus[1]; + tmp9[0] = conses[31]; //P + colours[8] = new ConsensusColour( (Color) colhash.get("YELLOW"), tmp9); + + Consensus[] tmp10 = new Consensus[1]; + tmp10[0] = conses[27]; //C + colours[9] = new ConsensusColour( (Color) colhash.get("PINK"), tmp8); + + Consensus[] tmp1 = new Consensus[14]; + tmp1[0] = conses[0]; //% + tmp1[1] = conses[1]; //# + tmp1[2] = conses[26]; //A + tmp1[3] = conses[27]; //C + tmp1[4] = conses[11]; //F + tmp1[5] = conses[13]; //H + tmp1[6] = conses[14]; //I + tmp1[7] = conses[15]; //L + tmp1[8] = conses[16]; //M + tmp1[9] = conses[23]; //V + tmp1[10] = conses[24]; //W + tmp1[11] = conses[25]; //Y + tmp1[12] = conses[18]; //P + tmp1[13] = conses[19]; //p + colours[0] = new ConsensusColour( (Color) colhash.get("BLUE"), tmp1); + + colours[10] = new ConsensusColour( (Color) colhash.get("CYAN"), tmp1); + + Consensus[] tmp2 = new Consensus[5]; + tmp2[0] = conses[8]; //t + tmp2[1] = conses[21]; //S + tmp2[2] = conses[22]; //T + tmp2[3] = conses[0]; //% + tmp2[4] = conses[1]; //# + colours[1] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp2); + + Consensus[] tmp3 = new Consensus[3]; + + tmp3[0] = conses[17]; //N + tmp3[1] = conses[29]; //D + tmp3[2] = conses[5]; //n + colours[2] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp3); + + Consensus[] tmp4 = new Consensus[6]; + tmp4[0] = conses[6]; // q = QE + tmp4[1] = conses[19]; //Q + tmp4[2] = conses[22]; //E + tmp4[3] = conses[3]; //+ + tmp4[4] = conses[28]; //K + tmp4[5] = conses[20]; //R + colours[3] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp4); + + Consensus[] tmp5 = new Consensus[4]; + tmp5[0] = conses[3]; //+ + tmp5[1] = conses[28]; //K + tmp5[2] = conses[20]; //R + tmp5[3] = conses[19]; //Q + colours[4] = new ConsensusColour( (Color) colhash.get("RED"), tmp5); + + Consensus[] tmp6 = new Consensus[5]; + tmp6[0] = conses[3]; //- + tmp6[1] = conses[29]; //D + tmp6[2] = conses[10]; //E + tmp6[3] = conses[6]; //q + tmp6[4] = conses[19]; //Q + colours[5] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp6); + + Consensus[] tmp7 = new Consensus[5]; + tmp7[0] = conses[3]; //- + tmp7[1] = conses[29]; //D + tmp7[2] = conses[10]; //E + tmp7[3] = conses[17]; //N + tmp7[4] = conses[2]; //DE + colours[6] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp7); + + // Now attach the ConsensusColours to the residue letters + ResidueColour = new ConsensusColour[20]; + ResidueColour[0] = colours[0]; // A + ResidueColour[1] = colours[4]; // R + ResidueColour[2] = colours[2]; // N + ResidueColour[3] = colours[6]; // D + ResidueColour[4] = colours[0]; // C + ResidueColour[5] = colours[3]; // Q + ResidueColour[6] = colours[5]; // E + ResidueColour[7] = colours[7]; // G + ResidueColour[8] = colours[10]; // H + ResidueColour[9] = colours[0]; // I + ResidueColour[10] = colours[0]; // L + ResidueColour[11] = colours[4]; // K + ResidueColour[12] = colours[0]; // M + ResidueColour[13] = colours[0]; // F + ResidueColour[14] = colours[8]; // P + ResidueColour[15] = colours[1]; // S + ResidueColour[16] = colours[1]; // T + ResidueColour[17] = colours[0]; // W + ResidueColour[18] = colours[10]; // Y + ResidueColour[19] = colours[0]; // V + } + + public Color findColour(char c) + { + return Color.pink; + } + + public Color findColour(char c, int j) + { + Color currentColour; + + if (cons2.length <= j || (includeGaps && threshold != 0 && !aboveThreshold(c, j))) + { + return Color.white; + } + + int i = ResidueProperties.aaIndex[c]; + + currentColour = Color.white; + + if (i > 19) + { + return currentColour; + } + + for (int k = 0; k < ResidueColour[i].conses.length; k++) + { + if (ResidueColour[i].conses[k].isConserved(cons2, j, size, includeGaps)) + { + currentColour = ResidueColour[i].c; + } + } + + if (i == 4) + { + if (conses[27].isConserved(cons2, j, size, includeGaps)) + { + currentColour = (Color) colhash.get("PINK"); + } + } + + if (conservationColouring) + { + currentColour = applyConservation(currentColour, j); + } + + return currentColour; + } + + /** + * @return the includeGaps + */ + protected boolean isIncludeGaps() + { + return includeGaps; + } + + /** + * @param includeGaps the includeGaps to set + */ + protected void setIncludeGaps(boolean includeGaps) + { + this.includeGaps = includeGaps; + } +} + +class ConsensusColour +{ + Consensus[] conses; + Color c; + + public ConsensusColour(Color c, Consensus[] conses) + { + this.conses = conses; + + // this.list = list; + this.c = c; + } +} diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java index 8aa59e3..5cd7b52 100755 --- a/src/jalview/schemes/Consensus.java +++ b/src/jalview/schemes/Consensus.java @@ -1,79 +1,91 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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; - -//////////////////////////////////////////// -// This does nothing at all at the moment!!!!!!!!!! -// AW 15th Dec 2004 -///////////////////////////////////////// -public class Consensus -{ - int[] mask; - double threshold; - String maskstr; - - public Consensus(String mask, double threshold) - { - // this.id = id; - // this.mask = mask; - this.maskstr = mask; - setMask(mask); - this.threshold = threshold; - } - - public void setMask(String s) - { - this.mask = setNums(s); - - // for (int i=0; i < mask.length; i++) { - // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]); - // } - } - - public boolean isConserved(int[][] cons2, int col, int size) - { - int tot = 0; - - for (int i = 0; i < mask.length; i++) - { - tot += cons2[col][mask[i]]; - } - - if ( (double) tot > ( (threshold * size) / 100)) - { - return true; - } - - return false; - } - - int[] setNums(String s) - { - int[] out = new int[s.length()]; - int i = 0; - - while (i < s.length()) - { - out[i] = ResidueProperties.aaIndex[s.charAt(i)]; - i++; - } - - return out; - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 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; + +//////////////////////////////////////////// +// This does nothing at all at the moment!!!!!!!!!! +// AW 15th Dec 2004 +///////////////////////////////////////// +public class Consensus +{ + int[] mask; + double threshold; + String maskstr; + + public Consensus(String mask, double threshold) + { + // this.id = id; + // this.mask = mask; + this.maskstr = mask; + setMask(mask); + this.threshold = threshold; + } + + public void setMask(String s) + { + this.mask = setNums(s); + + // for (int i=0; i < mask.length; i++) { + // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]); + // } + } + + /** + * @deprecated Use {@link #isConserved(int[][],int,int,boolean)} instead + */ + public boolean isConserved(int[][] cons2, int col, int size) + { + return isConserved(cons2, col, size, true); + } + + public boolean isConserved(int[][] cons2, int col, int size, boolean includeGaps) + { + int tot = 0; + if (!includeGaps) + { + size -= cons2[col][cons2[col].length-1]; + } + for (int i = 0; i < mask.length; i++) + { + tot += cons2[col][mask[i]]; + } + + if ( (double) tot > ( (threshold * size) / 100)) + { + // System.out.println("True conserved "+tot+" from "+threshold+" out of "+size+" : "+maskstr); + return true; + } + + return false; + } + + int[] setNums(String s) + { + int[] out = new int[s.length()]; + int i = 0; + + while (i < s.length()) + { + out[i] = ResidueProperties.aaIndex[s.charAt(i)]; + i++; + } + + return out; + } +} -- 1.7.10.2