2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.datamodel;
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20 public class CigarArray extends CigarBase
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23 * Do CIGAR operations on a set of sequences from many other cigars BAD THINGS
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24 * WILL HAPPEN IF A CIGARARRAY IS PASSED TO A CIGARARRAY or a CIGARCIGAR is
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25 * given a CIGARARRAY to insert gaps into.
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28 * array of subject cigars
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30 public CigarSimple refCigars[] = null;
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32 private boolean seqcigararray = false;
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34 private CigarArray()
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42 * @return boolean true if all refCigars resolve to a SeqCigar or a CigarCigar
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44 public boolean isSeqCigarArray()
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46 return seqcigararray;
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50 * Apply CIGAR operations to several cigars in parallel will throw an error if
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51 * any of cigar are actually CigarArrays.
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56 public CigarArray(CigarSimple[] cigars)
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59 seqcigararray = true;
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60 if (cigars != null && cigars.length > 0)
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62 refCigars = new CigarSimple[cigars.length];
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63 for (int c = 0; c < cigars.length; c++)
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65 refCigars[c] = cigars[c];
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66 if (!((cigars[c] instanceof SeqCigar) || cigars[c] instanceof CigarCigar))
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68 seqcigararray = false;
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75 * @see Cigar.getSequenceAndDeletions
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78 * @return Object[][]
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80 protected Object[][] getArrayofSequenceAndDeletions(char GapChar)
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82 if (refCigars == null || refCigars.length == 0 || length == 0)
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86 Object[][] sqanddels = new Object[refCigars.length][];
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87 for (int c = 0; c < refCigars.length; c++)
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89 String refString = refCigars[c].getSequenceString(GapChar);
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90 if (refString != null)
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92 sqanddels[c] = getSequenceAndDeletions(refString, GapChar);
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96 sqanddels[c] = null;
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103 * NOTE: this is an improper sequence string function
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105 * @return String formed by newline concatenated results of applying CIGAR
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106 * operations to each reference object in turn.
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109 * @return '\n' separated strings (empty results included as \n\n)
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111 public String getSequenceString(char GapChar)
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113 if (length == 0 || refCigars == null)
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117 StringBuffer seqStrings = new StringBuffer();
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118 Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);
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119 for (int c = 0; c < refCigars.length; c++)
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121 if (sqanddels[c] != null)
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123 seqStrings.append((String) sqanddels[c][0]);
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124 sqanddels[c][0] = null;
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126 seqStrings.append('\n');
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128 return seqStrings.toString();
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132 * return string results of applying cigar string to all reference cigars
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138 public String[] getSequenceStrings(char GapChar)
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141 if (length == 0 || refCigars == null || refCigars.length == 0)
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145 Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);
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146 String[] seqs = new String[sqanddels.length];
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147 for (int c = 0; c < refCigars.length; c++)
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149 seqs[c] = (String) sqanddels[c][0];
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155 * Combines the CigarArray cigar operations with the operations in each
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156 * reference cigar - creating a new reference cigar
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160 * public CigarBase[] getEditedCigars() {
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162 * return new CigarBase[] {}; }
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165 * applyDeletions edits underlying refCigars to propagate deleted regions, and
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166 * removes deletion operations from CigarArray operation list.
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168 * @return int[] position after deletion occured and range of deletion in
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169 * cigarArray or null if none occured
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171 public int[] applyDeletions()
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173 java.util.Vector delpos = null;
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178 int cursor = 0; // range counter for deletions
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179 int vcursor = 0; // visible column index
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180 int offset = 0; // shift in visible column index as deletions are made
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184 if (operation[i] != D)
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186 if (operation[i] == M)
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188 cursor += range[i];
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190 vcursor += range[i++];
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194 if (delpos == null)
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196 delpos = new java.util.Vector();
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198 int delstart = cursor, delend = cursor + range[i] - 1; // inclusive
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199 delpos.addElement(new int[]
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200 { vcursor + offset, range[i] }); // index of right hand column after
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201 // hidden region boundary
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202 offset += range[i] - 1; // shift in visible column coordinates
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203 System.arraycopy(operation, i + 1, operation, i, length - i);
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204 System.arraycopy(range, i + 1, range, i, length - i);
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207 * int dmax=0; for (int s=0; s<refCigars.length; s++) { int d =
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208 * refCigars[s].deleteRange(delstart, delend); if (d>dmax) dmax=d; }
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209 * offset+=dmax; // shift in visible column coordinates
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211 for (int s = 0; s < refCigars.length; s++)
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213 int d = refCigars[s].deleteRange(delstart, delend);
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218 if (delpos != null)
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220 int[] pos = new int[delpos.size() * 2];
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221 for (int k = 0, l = delpos.size(); k < l; k++)
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223 int[] dr = ((int[]) delpos.elementAt(k));
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224 pos[k * 2] = dr[0];
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225 pos[k * 2 + 1] = dr[1];
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226 delpos.setElementAt(null, k);
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236 * @return SeqCigar[] or null if CigarArray is not a SeqCigarArray (ie it does
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237 * not resolve to set of seqCigars)
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239 public SeqCigar[] getSeqCigarArray()
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241 if (!isSeqCigarArray())
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245 SeqCigar[] sa = new SeqCigar[refCigars.length];
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246 for (int i = 0; i < refCigars.length; i++)
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248 sa[i] = (SeqCigar) refCigars[i];
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