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annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/aligner/SingleStateAlignerFlat.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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jpayne@68 1 package aligner;
jpayne@68 2
jpayne@68 3 import dna.AminoAcid;
jpayne@68 4 import shared.KillSwitch;
jpayne@68 5 import shared.Tools;
jpayne@68 6
jpayne@68 7 /**
jpayne@68 8 * Based on MSA9PBA, but reduced to a single matrix. */
jpayne@68 9 public final class SingleStateAlignerFlat implements Aligner {
jpayne@68 10
jpayne@68 11
jpayne@68 12 public SingleStateAlignerFlat(){}
jpayne@68 13
jpayne@68 14 private void prefillTopRow(){
jpayne@68 15 final int[] header=packed[0];
jpayne@68 16 final int qlen=rows;
jpayne@68 17 for(int i=0; i<=columns; i++){
jpayne@68 18 int x=columns-i+1;
jpayne@68 19 int qbases=qlen-x;
jpayne@68 20
jpayne@68 21 //Minimal points to prefer a leftmost alignment
jpayne@68 22 header[i]=qbases<=0 ? 0 : ((-qbases)<<STARTOFFSET);
jpayne@68 23
jpayne@68 24 //Forces consumption of query, but does not allow for insertions...
jpayne@68 25 // header[i]=qbases<=0 ? 0 : calcDelScoreOffset(qbases);
jpayne@68 26 }
jpayne@68 27 }
jpayne@68 28
jpayne@68 29 private void prefillLeftColumnStartingAt(int i){
jpayne@68 30 packed[0][0]=MODE_MATCH;
jpayne@68 31 i=Tools.max(1, i);
jpayne@68 32 for(int score=MODE_INS+(POINTSoff_INS*i); i<=maxRows; i++){//Fill column 0 with insertions
jpayne@68 33 score+=POINTSoff_INS;
jpayne@68 34 packed[i][0]=score;
jpayne@68 35 }
jpayne@68 36 }
jpayne@68 37
jpayne@68 38 // private void clearInner(){//NotmaxRows needed
jpayne@68 39 // for(int i=1; i<=maxRows; i++){
jpayne@68 40 // for(int j=1; j<=maxColumns; j++){
jpayne@68 41 // packed[i][j]=0;
jpayne@68 42 // }
jpayne@68 43 // }
jpayne@68 44 // }
jpayne@68 45 //
jpayne@68 46 // private void clearAll(){//NotmaxRows needed
jpayne@68 47 // for(int i=0; i<=maxRows; i++){
jpayne@68 48 // for(int j=0; j<=maxColumns; j++){
jpayne@68 49 // packed[i][j]=0;
jpayne@68 50 // }
jpayne@68 51 // }
jpayne@68 52 // }
jpayne@68 53
jpayne@68 54 private void initialize(int rows_, int columns_){
jpayne@68 55 rows=rows_;
jpayne@68 56 columns=columns_;
jpayne@68 57 if(rows<=maxRows && columns<=maxColumns){
jpayne@68 58 prefillTopRow();
jpayne@68 59 // prefillLeftColumn();
jpayne@68 60 return;
jpayne@68 61 }
jpayne@68 62
jpayne@68 63 final int maxRows0=maxRows;
jpayne@68 64 final int maxColumns0=maxColumns;
jpayne@68 65 final int[][] packed0=packed;
jpayne@68 66
jpayne@68 67 //Monotonic increase
jpayne@68 68 maxRows=Tools.max(maxRows, rows+10);
jpayne@68 69 maxColumns=Tools.max(maxColumns, columns+10);
jpayne@68 70
jpayne@68 71 if(packed==null || maxColumns>maxColumns0){//Make a new matrix
jpayne@68 72 packed=KillSwitch.allocInt2D(maxRows+1, maxColumns+1);
jpayne@68 73 prefillLeftColumnStartingAt(1);
jpayne@68 74 }else{//Copy old rows
jpayne@68 75 assert(maxRows0>0 && maxColumns0>0);
jpayne@68 76 assert(maxRows>maxRows0 && maxColumns<=maxColumns0);
jpayne@68 77 packed=KillSwitch.allocInt2D(maxRows+1);
jpayne@68 78 for(int i=0; i<packed.length; i++){
jpayne@68 79 if(i<packed0.length){
jpayne@68 80 packed[i]=packed0[i];
jpayne@68 81 }else{
jpayne@68 82 packed[i]=KillSwitch.allocInt1D(maxColumns+1);
jpayne@68 83 }
jpayne@68 84 }
jpayne@68 85 //Fill column 0 with insertions
jpayne@68 86 prefillLeftColumnStartingAt(maxRows0);
jpayne@68 87 }
jpayne@68 88 prefillTopRow();
jpayne@68 89 }
jpayne@68 90
jpayne@68 91 /** return new int[] {rows, maxCol, maxState, maxScore, maxStart};
jpayne@68 92 * Will not fill areas that cannot match minScore */
jpayne@68 93 @Override
jpayne@68 94 public final int[] fillLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore){
jpayne@68 95 return fillUnlimited(read, ref, refStartLoc, refEndLoc, minScore);
jpayne@68 96 }
jpayne@68 97
jpayne@68 98 @Override
jpayne@68 99 public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc){
jpayne@68 100 return fillUnlimited(read, ref, refStartLoc, refEndLoc, -999999);
jpayne@68 101 }
jpayne@68 102
jpayne@68 103 /** return new int[] {rows, maxCol, maxState, maxScore, maxStart};
jpayne@68 104 * Min score is optional */
jpayne@68 105 @Override
jpayne@68 106 public final int[] fillUnlimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore){
jpayne@68 107 initialize(read.length, refEndLoc-refStartLoc+1);
jpayne@68 108
jpayne@68 109 //temporary, for finding a bug
jpayne@68 110 if(rows>maxRows || columns>maxColumns){
jpayne@68 111 throw new RuntimeException("rows="+rows+", maxRows="+maxRows+", cols="+columns+", maxCols="+maxColumns+"\n"+new String(read)+"\n");
jpayne@68 112 }
jpayne@68 113
jpayne@68 114 assert(rows<=maxRows) : "Check that values are in-bounds before calling this function: "+rows+", "+maxRows;
jpayne@68 115 assert(columns<=maxColumns) : "Check that values are in-bounds before calling this function: "+columns+", "+maxColumns;
jpayne@68 116
jpayne@68 117 assert(refStartLoc>=0) : "Check that values are in-bounds before calling this function: "+refStartLoc;
jpayne@68 118 assert(refEndLoc<ref.length) : "Check that values are in-bounds before calling this function: "+refEndLoc+", "+ref.length;
jpayne@68 119
jpayne@68 120 final int refOffset=refStartLoc-1;
jpayne@68 121 for(int row=1; row<=rows; row++){
jpayne@68 122
jpayne@68 123 final byte qBase=read[row-1];
jpayne@68 124 for(int col=1; col<=columns; col++){
jpayne@68 125
jpayne@68 126 final byte rBase=ref[refOffset+col];
jpayne@68 127
jpayne@68 128 final boolean match=(qBase==rBase);
jpayne@68 129 final boolean defined=(qBase!='N' && rBase!='N');
jpayne@68 130
jpayne@68 131 final int valueFromDiag=packed[row-1][col-1];
jpayne@68 132 final int valueFromDel=packed[row][col-1];
jpayne@68 133 final int valueFromIns=packed[row-1][col];
jpayne@68 134 // final int stateFromDiag=valueFromDiag&MODEMASK;
jpayne@68 135 final int scoreFromDiag=valueFromDiag&HIGHMASK;
jpayne@68 136 // final int stateFromDel=valueFromDel&MODEMASK;
jpayne@68 137 final int scoreFromDel=valueFromDel&HIGHMASK;
jpayne@68 138 // final int stateFromIns=valueFromIns&MODEMASK;
jpayne@68 139 final int scoreFromIns=valueFromIns&HIGHMASK;
jpayne@68 140
jpayne@68 141 // final boolean prevMatch=stateFromDiag==MODE_MATCH;
jpayne@68 142 // final boolean prevSub=stateFromDiag==MODE_SUB;
jpayne@68 143 // final boolean prevDel=stateFromDel==MODE_DEL;
jpayne@68 144 // final boolean prevIns=stateFromIns==MODE_INS;
jpayne@68 145
jpayne@68 146 //Old conditional code, replaced by faster arrays
jpayne@68 147 // final int diagScoreM=MODE_MATCH|(prevMatch ? POINTSoff_MATCH2 : POINTSoff_MATCH);
jpayne@68 148 // final int diagScoreS=MODE_SUB|(prevSub ? POINTSoff_SUB2 : POINTSoff_SUB);
jpayne@68 149 // final int delScore=scoreFromDel+(prevDel ? POINTSoff_DEL2 : POINTSoff_DEL)|MODE_DEL;
jpayne@68 150 // final int insScore=scoreFromIns+(prevIns ? POINTSoff_INS2 : POINTSoff_INS)|MODE_INS;
jpayne@68 151
jpayne@68 152 final int diagScoreM=POINTSoff_MATCH|MODE_MATCH;
jpayne@68 153 final int diagScoreS=POINTSoff_SUB|MODE_SUB;
jpayne@68 154 final int delScore=scoreFromDel+POINTSoff_DEL|MODE_DEL;
jpayne@68 155 final int insScore=scoreFromIns+POINTSoff_INS|MODE_INS;
jpayne@68 156
jpayne@68 157 int diagScore=(match ? diagScoreM : diagScoreS);
jpayne@68 158 diagScore=scoreFromDiag+(defined ? diagScore : POINTSoff_NOREF_MODE_SUB);
jpayne@68 159
jpayne@68 160 int score=diagScore>=delScore ? diagScore : delScore;
jpayne@68 161 score=score>=insScore ? score : insScore;
jpayne@68 162
jpayne@68 163 packed[row][col]=score;
jpayne@68 164 }
jpayne@68 165 // iterationsUnlimited+=columns;
jpayne@68 166 }
jpayne@68 167
jpayne@68 168
jpayne@68 169 int maxCol=-1;
jpayne@68 170 int maxState=-1;
jpayne@68 171 int maxStart=-1;
jpayne@68 172 int maxScore=Integer.MIN_VALUE;
jpayne@68 173
jpayne@68 174 for(int col=1; col<=columns; col++){
jpayne@68 175 int x=packed[rows][col];
jpayne@68 176 if((x&SCOREMASK)>maxScore){
jpayne@68 177 maxScore=x;
jpayne@68 178 maxCol=col;
jpayne@68 179 maxState=x&MODEMASK;
jpayne@68 180 maxStart=x&STARTMASK;
jpayne@68 181 }
jpayne@68 182 }
jpayne@68 183 maxScore>>=SCOREOFFSET;
jpayne@68 184
jpayne@68 185 // System.err.println("Returning "+rows+", "+maxCol+", "+maxState+", "+maxScore+"; minScore="+minScore);
jpayne@68 186 return maxScore<minScore ? null : new int[] {rows, maxCol, maxState, maxScore, maxStart};
jpayne@68 187 }
jpayne@68 188
jpayne@68 189 /** Generates the match string */
jpayne@68 190 @Override
jpayne@68 191 public final byte[] traceback(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, int col, int state){
jpayne@68 192 // assert(false);
jpayne@68 193 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc;
jpayne@68 194 assert(row==rows);
jpayne@68 195
jpayne@68 196 byte[] out=new byte[row+col-1]; //TODO if an out of bound crash occurs, try removing the "-1".
jpayne@68 197 int outPos=0;
jpayne@68 198
jpayne@68 199 // assert(state==(packed[row][col]&MODEMASK));
jpayne@68 200
jpayne@68 201 while(row>0 && col>0){
jpayne@68 202 byte q=query[row-1];
jpayne@68 203 byte r=ref[refStartLoc+col-1];
jpayne@68 204 boolean defined=(AminoAcid.isFullyDefined(q) && AminoAcid.isFullyDefined(r));
jpayne@68 205 state=(packed[row][col]&MODEMASK);
jpayne@68 206 if(state==MODE_MATCH){
jpayne@68 207 col--;
jpayne@68 208 row--;
jpayne@68 209 out[outPos]=defined ? (byte)'m' : (byte)'N';
jpayne@68 210 }else if(state==MODE_SUB){
jpayne@68 211 col--;
jpayne@68 212 row--;
jpayne@68 213 out[outPos]=defined ? (byte)'S' : (byte)'N';
jpayne@68 214 }else if(state==MODE_N){
jpayne@68 215 col--;
jpayne@68 216 row--;
jpayne@68 217 out[outPos]='N';
jpayne@68 218 }else if(state==MODE_DEL){
jpayne@68 219 col--;
jpayne@68 220 out[outPos]='D';
jpayne@68 221 }else if(state==MODE_INS){
jpayne@68 222 row--;
jpayne@68 223 // out[outPos]='I';
jpayne@68 224 if(col>=0 && col<columns){
jpayne@68 225 out[outPos]='I';
jpayne@68 226 }else{
jpayne@68 227 out[outPos]='C';
jpayne@68 228 col--;
jpayne@68 229 }
jpayne@68 230 }else{
jpayne@68 231 assert(false) : state;
jpayne@68 232 }
jpayne@68 233 outPos++;
jpayne@68 234 }
jpayne@68 235
jpayne@68 236 assert(row==0 || col==0);
jpayne@68 237 if(col!=row){//Not sure what this is doing
jpayne@68 238 while(row>0){
jpayne@68 239 out[outPos]='C';
jpayne@68 240 outPos++;
jpayne@68 241 row--;
jpayne@68 242 col--;
jpayne@68 243 }
jpayne@68 244 if(col>0){
jpayne@68 245 //do nothing
jpayne@68 246 }
jpayne@68 247 }
jpayne@68 248
jpayne@68 249 //Shrink and reverse the string
jpayne@68 250 byte[] out2=new byte[outPos];
jpayne@68 251 for(int i=0; i<outPos; i++){
jpayne@68 252 out2[i]=out[outPos-i-1];
jpayne@68 253 }
jpayne@68 254 out=null;
jpayne@68 255
jpayne@68 256 return out2;
jpayne@68 257 }
jpayne@68 258
jpayne@68 259 @Override
jpayne@68 260 /** Generates identity;
jpayne@68 261 * fills 'extra' with {match, sub, del, ins, N, clip} if present */
jpayne@68 262 public float tracebackIdentity(byte[] query, byte[] ref, int refStartLoc, int refEndLoc, int row, int col, int state, int[] extra){
jpayne@68 263
jpayne@68 264 // assert(false);
jpayne@68 265 assert(refStartLoc<=refEndLoc) : refStartLoc+", "+refEndLoc;
jpayne@68 266 assert(row==rows);
jpayne@68 267
jpayne@68 268 // assert(state==(packed[row][col]&MODEMASK));
jpayne@68 269 int match=0, sub=0, del=0, ins=0, noref=0, clip=0;
jpayne@68 270
jpayne@68 271 while(row>0 && col>0){
jpayne@68 272 byte q=query[row-1];
jpayne@68 273 byte r=ref[refStartLoc+col-1];
jpayne@68 274 boolean defined=(AminoAcid.isFullyDefined(q) && AminoAcid.isFullyDefined(r));
jpayne@68 275 state=(packed[row][col]&MODEMASK);
jpayne@68 276 if(state==MODE_MATCH){
jpayne@68 277 col--;
jpayne@68 278 row--;
jpayne@68 279 match+=(defined ? 1 : 0);
jpayne@68 280 noref+=(defined ? 0 : 1);
jpayne@68 281 }else if(state==MODE_SUB){
jpayne@68 282 col--;
jpayne@68 283 row--;
jpayne@68 284 sub+=(defined ? 1 : 0);
jpayne@68 285 noref+=(defined ? 0 : 1);
jpayne@68 286 }else if(state==MODE_N){//Can't currently happen
jpayne@68 287 col--;
jpayne@68 288 row--;
jpayne@68 289 noref++;
jpayne@68 290 }else if(state==MODE_DEL){
jpayne@68 291 col--;
jpayne@68 292 del++;
jpayne@68 293 }else if(state==MODE_INS){
jpayne@68 294 row--;
jpayne@68 295 boolean edge=(col<=1 || col>=columns);
jpayne@68 296 ins+=(edge ? 0 : 1);
jpayne@68 297 clip+=(edge ? 1 : 0);
jpayne@68 298 }else{
jpayne@68 299 assert(false) : state;
jpayne@68 300 }
jpayne@68 301 }
jpayne@68 302
jpayne@68 303 assert(row==0 || col==0);
jpayne@68 304 if(col!=row){//Not sure what this is doing
jpayne@68 305 while(row>0){
jpayne@68 306 clip++;
jpayne@68 307 row--;
jpayne@68 308 col--;
jpayne@68 309 }
jpayne@68 310 if(col>0){
jpayne@68 311 //do nothing
jpayne@68 312 }
jpayne@68 313 }
jpayne@68 314
jpayne@68 315 if(extra!=null){
jpayne@68 316 assert(extra.length==5);
jpayne@68 317 extra[0]=match;
jpayne@68 318 extra[1]=sub;
jpayne@68 319 extra[2]=del;
jpayne@68 320 extra[3]=ins;
jpayne@68 321 extra[4]=noref;
jpayne@68 322 extra[5]=clip;
jpayne@68 323 }
jpayne@68 324
jpayne@68 325 float len=match+sub+ins+del+noref*0.1f;
jpayne@68 326 float id=match/Tools.max(1.0f, len);
jpayne@68 327 return id;
jpayne@68 328 }
jpayne@68 329
jpayne@68 330 /** @return {score, bestRefStart, bestRefStop} */
jpayne@68 331 @Override
jpayne@68 332 public final int[] score(final byte[] read, final byte[] ref, final int refStartLoc, final int refEndLoc,
jpayne@68 333 final int maxRow, final int maxCol, final int maxState/*, final int maxScore, final int maxStart*/){
jpayne@68 334
jpayne@68 335 int row=maxRow;
jpayne@68 336 int col=maxCol;
jpayne@68 337 int state=maxState;
jpayne@68 338
jpayne@68 339 assert(maxState>=0 && maxState<packed.length) :
jpayne@68 340 maxState+", "+maxRow+", "+maxCol+"\n"+new String(read)+"\n"+toString(ref, refStartLoc, refEndLoc);
jpayne@68 341 assert(maxRow>=0 && maxRow<packed.length) :
jpayne@68 342 maxState+", "+maxRow+", "+maxCol+"\n"+new String(read)+"\n"+toString(ref, refStartLoc, refEndLoc);
jpayne@68 343 assert(maxCol>=0 && maxCol<packed[0].length) :
jpayne@68 344 maxState+", "+maxRow+", "+maxCol+"\n"+new String(read)+"\n"+toString(ref, refStartLoc, refEndLoc);
jpayne@68 345
jpayne@68 346 int score=packed[maxRow][maxCol]&SCOREMASK; //Or zero, if it is to be recalculated
jpayne@68 347
jpayne@68 348 if(row<rows){
jpayne@68 349 int difR=rows-row;
jpayne@68 350 int difC=columns-col;
jpayne@68 351
jpayne@68 352 while(difR>difC){
jpayne@68 353 score+=POINTSoff_NOREF;
jpayne@68 354 difR--;
jpayne@68 355 }
jpayne@68 356
jpayne@68 357 row+=difR;
jpayne@68 358 col+=difR;
jpayne@68 359
jpayne@68 360 }
jpayne@68 361
jpayne@68 362 assert(refStartLoc<=refEndLoc);
jpayne@68 363 assert(row==rows);
jpayne@68 364
jpayne@68 365
jpayne@68 366 final int bestRefStop=refStartLoc+col-1;
jpayne@68 367
jpayne@68 368 while(row>0 && col>0){
jpayne@68 369 // final byte c=read[row-1];
jpayne@68 370 // final byte r=ref[refStartLoc+col-1];
jpayne@68 371 // final boolean defined=(AminoAcid.isFullyDefined(c) && AminoAcid.isFullyDefined(r));
jpayne@68 372 state=(packed[row][col]&MODEMASK);
jpayne@68 373 if(state==MODE_MATCH){
jpayne@68 374 col--;
jpayne@68 375 row--;
jpayne@68 376 }else if(state==MODE_SUB){
jpayne@68 377 col--;
jpayne@68 378 row--;
jpayne@68 379 }else if(state==MODE_N){
jpayne@68 380 col--;
jpayne@68 381 row--;
jpayne@68 382 }else if(state==MODE_DEL){
jpayne@68 383 col--;
jpayne@68 384 }else if(state==MODE_INS){
jpayne@68 385 row--;
jpayne@68 386 }else{
jpayne@68 387 assert(false) : state;
jpayne@68 388 }
jpayne@68 389 }
jpayne@68 390 // assert(false) : row+", "+col;
jpayne@68 391 if(row>col){
jpayne@68 392 col-=row;
jpayne@68 393 }
jpayne@68 394
jpayne@68 395 final int bestRefStart=refStartLoc+col;
jpayne@68 396
jpayne@68 397 score>>=SCOREOFFSET;
jpayne@68 398 // System.err.println("t2\t"+score+", "+maxScore+", "+maxStart+", "+bestRefStart);
jpayne@68 399 int[] rvec;
jpayne@68 400 if(bestRefStart<refStartLoc || bestRefStop>refEndLoc){ //Suggest extra padding in cases of overflow
jpayne@68 401 int padLeft=Tools.max(0, refStartLoc-bestRefStart);
jpayne@68 402 int padRight=Tools.max(0, bestRefStop-refEndLoc);
jpayne@68 403 rvec=new int[] {score, bestRefStart, bestRefStop, padLeft, padRight};
jpayne@68 404 }else{
jpayne@68 405 rvec=new int[] {score, bestRefStart, bestRefStop};
jpayne@68 406 }
jpayne@68 407 return rvec;
jpayne@68 408 }
jpayne@68 409
jpayne@68 410
jpayne@68 411 /** Will not fill areas that cannot match minScore.
jpayne@68 412 * @return {score, bestRefStart, bestRefStop} */
jpayne@68 413 @Override
jpayne@68 414 public final int[] fillAndScoreLimited(byte[] read, byte[] ref, int refStartLoc, int refEndLoc, int minScore){
jpayne@68 415 int a=Tools.max(0, refStartLoc);
jpayne@68 416 int b=Tools.min(ref.length-1, refEndLoc);
jpayne@68 417 assert(b>=a);
jpayne@68 418
jpayne@68 419 if(b-a>=maxColumns){
jpayne@68 420 System.err.println("Warning: Max alignment columns exceeded; restricting range. "+(b-a+1)+" > "+maxColumns);
jpayne@68 421 assert(false) : refStartLoc+", "+refEndLoc;
jpayne@68 422 b=Tools.min(ref.length-1, a+maxColumns-1);
jpayne@68 423 }
jpayne@68 424 int[] max=fillLimited(read, ref, a, b, minScore);
jpayne@68 425 // return max==null ? null : new int[] {max[3], 0, max[1]};
jpayne@68 426
jpayne@68 427 int[] score=(max==null ? null : score(read, ref, a, b, max[0], max[1], max[2]/*, max[3], max[4]*/));
jpayne@68 428
jpayne@68 429 return score;
jpayne@68 430 }
jpayne@68 431
jpayne@68 432 public static final String toString(byte[] ref, int startLoc, int stopLoc){
jpayne@68 433 StringBuilder sb=new StringBuilder(stopLoc-startLoc+1);
jpayne@68 434 for(int i=startLoc; i<=stopLoc; i++){sb.append((char)ref[i]);}
jpayne@68 435 return sb.toString();
jpayne@68 436 }
jpayne@68 437
jpayne@68 438 // public int maxScoreByIdentity(int len, float identity){
jpayne@68 439 // assert(identity>=0 && identity<=1);
jpayne@68 440 // return (int)(len*(identity*POINTS_MATCH+(1-identity)*POINTS_SUB));
jpayne@68 441 // }
jpayne@68 442
jpayne@68 443 @Override
jpayne@68 444 public int minScoreByIdentity(int len, float identity){
jpayne@68 445 assert(identity>=0 && identity<=1);
jpayne@68 446
jpayne@68 447 int a=(int)(len*(identity*POINTS_MATCH+(1-identity)*POINTS_SUB));
jpayne@68 448 int b=(int)(len*(identity*POINTS_MATCH+(1-identity)*POINTS_INS));
jpayne@68 449 int c=(int)(len*(1*POINTS_MATCH+((1/(Tools.max(identity, 0.000001f)))-1)*POINTS_DEL));
jpayne@68 450 return Tools.min(a, b, c);
jpayne@68 451 }
jpayne@68 452
jpayne@68 453 private static int calcDelScoreOffset(int len){
jpayne@68 454 if(len<=0){return 0;}
jpayne@68 455 int score=POINTSoff_DEL*len;
jpayne@68 456 return score;
jpayne@68 457 }
jpayne@68 458 //
jpayne@68 459 // public static int calcInsScore(int len){
jpayne@68 460 // if(len<=0){return 0;}
jpayne@68 461 // int score=POINTS_INS;
jpayne@68 462 //
jpayne@68 463 // if(len>1){
jpayne@68 464 // score+=(len-1)*POINTS_INS2;
jpayne@68 465 // }
jpayne@68 466 // return score;
jpayne@68 467 // }
jpayne@68 468 //
jpayne@68 469 // private static int calcInsScoreOffset(int len){
jpayne@68 470 // if(len<=0){return 0;}
jpayne@68 471 // int score=POINTSoff_INS;
jpayne@68 472 //
jpayne@68 473 // if(len>1){
jpayne@68 474 // score+=(len-1)*POINTSoff_INS2;
jpayne@68 475 // }
jpayne@68 476 // return score;
jpayne@68 477 // }
jpayne@68 478
jpayne@68 479 @Override
jpayne@68 480 public int rows(){return rows;}
jpayne@68 481 @Override
jpayne@68 482 public int columns(){return columns;}
jpayne@68 483
jpayne@68 484
jpayne@68 485 private int maxRows;
jpayne@68 486 private int maxColumns;
jpayne@68 487
jpayne@68 488 private int[][] packed;
jpayne@68 489
jpayne@68 490 public static final int MODEBITS=3;
jpayne@68 491 public static final int STARTBITS=9;
jpayne@68 492 public static final int LOWBITS=MODEBITS+STARTBITS;
jpayne@68 493 public static final int SCOREBITS=32-STARTBITS;
jpayne@68 494 public static final int MAX_START=((1<<STARTBITS)-1);
jpayne@68 495 public static final int MAX_SCORE=((1<<(SCOREBITS-1))-1)-2000;
jpayne@68 496 public static final int MIN_SCORE=0-MAX_SCORE; //Keeps it 1 point above "BAD".
jpayne@68 497
jpayne@68 498 public static final int STARTOFFSET=MODEBITS;
jpayne@68 499 public static final int SCOREOFFSET=LOWBITS;
jpayne@68 500
jpayne@68 501 public static final int MODEMASK=~((-1)<<MODEBITS);
jpayne@68 502 public static final int STARTMASK=(~((-1)<<STARTBITS))<<STARTOFFSET;
jpayne@68 503 public static final int SCOREMASK=(~((-1)<<SCOREBITS))<<SCOREOFFSET;
jpayne@68 504 public static final int HIGHMASK=SCOREMASK|STARTMASK;
jpayne@68 505
jpayne@68 506 //For some reason changing MODE_DEL from 1 to 0 breaks everything
jpayne@68 507 private static final byte MODE_DEL=1;
jpayne@68 508 private static final byte MODE_INS=2;
jpayne@68 509 private static final byte MODE_SUB=3;
jpayne@68 510 private static final byte MODE_MATCH=4;
jpayne@68 511 private static final byte MODE_N=5;
jpayne@68 512
jpayne@68 513 public static final int POINTS_NOREF=-15;
jpayne@68 514 public static final int POINTS_MATCH=100;
jpayne@68 515 public static final int POINTS_SUB=-50;
jpayne@68 516 public static final int POINTS_INS=-121;
jpayne@68 517 public static final int POINTS_DEL=-111;
jpayne@68 518
jpayne@68 519 public static final int BAD=MIN_SCORE-1;
jpayne@68 520
jpayne@68 521
jpayne@68 522 public static final int POINTSoff_NOREF=(POINTS_NOREF<<SCOREOFFSET);
jpayne@68 523 public static final int POINTSoff_NOREF_MODE_SUB=POINTSoff_NOREF|MODE_SUB;
jpayne@68 524 public static final int POINTSoff_MATCH=(POINTS_MATCH<<SCOREOFFSET);
jpayne@68 525 public static final int POINTSoff_SUB=(POINTS_SUB<<SCOREOFFSET);
jpayne@68 526 public static final int POINTSoff_INS=(POINTS_INS<<SCOREOFFSET);
jpayne@68 527 public static final int POINTSoff_DEL=(POINTS_DEL<<SCOREOFFSET);
jpayne@68 528 public static final int BADoff=(BAD<<SCOREOFFSET);
jpayne@68 529
jpayne@68 530 private int rows;
jpayne@68 531 private int columns;
jpayne@68 532
jpayne@68 533 // public long iterationsLimited=0;
jpayne@68 534 // public long iterationsUnlimited=0;
jpayne@68 535
jpayne@68 536 public boolean verbose=false;
jpayne@68 537 public boolean verbose2=false;
jpayne@68 538
jpayne@68 539 }