2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.datamodel;
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21 public class CigarArray extends CigarBase
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24 * Do CIGAR operations on a set of sequences from many other cigars
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25 * BAD THINGS WILL HAPPEN IF A CIGARARRAY IS PASSED TO A CIGARARRAY
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26 * or a CIGARCIGAR is given a CIGARARRAY to insert gaps into.
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29 * array of subject cigars
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31 public CigarSimple refCigars[]=null;
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32 private boolean seqcigararray=false;
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33 private CigarArray() {
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39 * @return boolean true if all refCigars resolve to a SeqCigar or a CigarCigar
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41 public boolean isSeqCigarArray()
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43 return seqcigararray;
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46 * Apply CIGAR operations to several cigars in parallel
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47 * will throw an error if any of cigar are actually CigarArrays.
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48 * @param cigar Cigar[]
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50 public CigarArray(CigarSimple[] cigars) {
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52 seqcigararray = true;
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53 if (cigars != null && cigars.length > 0)
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55 refCigars = new CigarSimple[cigars.length];
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56 for (int c = 0; c < cigars.length; c++)
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58 refCigars[c] = cigars[c];
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59 if (! ( (cigars[c] instanceof SeqCigar)
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60 || cigars[c] instanceof CigarCigar))
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62 seqcigararray = false;
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68 * @see Cigar.getSequenceAndDeletions
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69 * @param GapChar char
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70 * @return Object[][]
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72 protected Object[][] getArrayofSequenceAndDeletions(char GapChar) {
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73 if (refCigars == null || refCigars.length == 0 || length == 0) {
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76 Object[][] sqanddels = new Object[refCigars.length][];
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77 for (int c=0; c<refCigars.length; c++) {
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78 String refString = refCigars[c].getSequenceString(GapChar);
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79 if (refString != null)
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81 sqanddels[c] = getSequenceAndDeletions(refString, GapChar);
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83 sqanddels[c] = null;
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89 * NOTE: this is an improper sequence string function
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90 * @return String formed by newline concatenated results of applying CIGAR operations to each reference object in turn.
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91 * @param GapChar char
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92 * @return '\n' separated strings (empty results included as \n\n)
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94 public String getSequenceString(char GapChar)
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96 if (length==0 || refCigars==null)
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98 StringBuffer seqStrings = new StringBuffer();
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99 Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);
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100 for (int c=0; c<refCigars.length; c++) {
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101 if (sqanddels[c]!=null) {
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102 seqStrings.append( (String) sqanddels[c][0]);
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103 sqanddels[c][0] = null;
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105 seqStrings.append('\n');
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107 return seqStrings.toString();
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110 * return string results of applying cigar string to all reference cigars
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111 * @param GapChar char
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114 public String[] getSequenceStrings(char GapChar) {
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116 if (length==0 || refCigars==null || refCigars.length==0)
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118 Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);
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119 String[] seqs = new String[sqanddels.length];
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120 for (int c=0; c<refCigars.length; c++) {
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121 seqs[c] = (String) sqanddels[c][0];
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126 * Combines the CigarArray cigar operations with the operations in each
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127 * reference cigar - creating a new reference cigar
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130 public CigarBase[] getEditedCigars() {
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132 return new CigarBase[] {};
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137 * edits underlying refCigars to propagate deleted regions, and removes deletion
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138 * operations from CigarArray operation list.
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139 * @return int[] position after deletion occured and range of deletion in cigarArray or null if none occured
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141 public int[] applyDeletions()
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143 java.util.Vector delpos=null;
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146 int cursor=0; // range counter for deletions
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147 int vcursor=0; // visible column index
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148 int offset=0; // shift in visible column index as deletions are made
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151 if (operation[i]!=D) {
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152 if (operation[i]==M)
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154 vcursor+=range[i++];
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159 delpos=new java.util.Vector();
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160 int delstart=cursor, delend=cursor+range[i]-1; // inclusive
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161 delpos.addElement(new int[] { vcursor+offset, range[i]}); // index of right hand column after hidden region boundary
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162 offset+=range[i]-1; // shift in visible column coordinates
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163 System.arraycopy(operation, i+1, operation, i, length-i);
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164 System.arraycopy(range, i+1, range, i, length-i);
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167 for (int s=0; s<refCigars.length; s++) {
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168 int d = refCigars[s].deleteRange(delstart, delend);
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172 offset+=dmax; // shift in visible column coordinates
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174 for (int s=0; s<refCigars.length; s++) {
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175 int d = refCigars[s].deleteRange(delstart, delend);
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182 int[] pos=new int[delpos.size()*2];
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183 for (int k = 0, l = delpos.size(); k < l; k++) {
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184 int[] dr = ((int[]) delpos.elementAt(k));
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186 pos[k*2+1] = dr[1];
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187 delpos.setElementAt(null,k);
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196 * @return SeqCigar[] or null if CigarArray is not a SeqCigarArray (ie it does not resolve to set of seqCigars)
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198 public SeqCigar[] getSeqCigarArray() {
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199 if (!isSeqCigarArray())
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201 SeqCigar[] sa = new SeqCigar[refCigars.length];
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202 for (int i=0; i<refCigars.length; i++)
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203 sa[i] = (SeqCigar) refCigars[i];
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