-package jalview.datamodel;
-
-public abstract class CigarBase
-{
- /**
- * Base class for compact idiosyncratic representation of gaps and aligned residues
- * Regards to Tom Oldfield for his DynamicArray class.
- * 17th July 2006
- * Not thread safe.
- */
- public CigarBase()
- {
- // nothing to be done (probably)
- }
-
- protected int length = 0;
- protected int _inc_length = 10; // extension range for addition of new operations
- protected char[] operation = null;
- protected int[] range = null;
- /**
- * Range of Hidden residues in seq (translated as deleted in seq)
- */
- public static final char D = 'D'; /**
- * Range of insertions to seq
- */
- public static final char I = 'I'; /**
- * Range of aligned residues
- */
- public static final char M = 'M';
- static protected final char _case_shift = 'a' - 'A';
- /**
- * Ugly function to get edited sequence string, start and end symbol positions and the deletion regions as an array of int pairs
- * May return null for an empty cigar string.
- * May return null for deletion ranges if there are none.
- * @param reference - the symbol sequence to apply the cigar operations to (or null if no sequence)
- * @param GapChar - the symbol to use for Insert operations
- * @return Object[] { String, int[] {start, startcol, end, endcol}, int[][3] {start, end, col} or null} the gapped sequence, first and last residue index, and the deletion ranges on the reference sequence
- */
- public Object[] getSequenceAndDeletions(String reference, char GapChar)
- {
- int rlength=0;
- int[][] deletions = new int[length][];
- int[][] trunc_deletions = null;
- StringBuffer sq = new StringBuffer();
- int cursor = 0, alcursor=0,start = 0, startpos=0, end = 0, endpos=0, delcount = -1;
- boolean consecutive_del = false;
- if (length == 0)
- {
- return null;
- }
- if (reference!=null)
- rlength=reference.length();
- boolean modstart = true;
- for (int i = 0; i < length; i++)
- {
- switch (operation[i])
- {
- case D:
- if (!consecutive_del)
- {
- deletions[++delcount] = new int[]
- {
- cursor, 0, alcursor};
- }
- cursor += range[i];
- deletions[delcount][1] = cursor - 1;
- consecutive_del = true;
- break;
- case I:
- consecutive_del = false;
- for (int r = 0; r < range[i]; r++)
- {
- sq.append(GapChar);
- alcursor++;
- }
- break;
- case M:
- consecutive_del = false;
- if (modstart)
- {
- start = cursor;
- startpos=alcursor;
- modstart = false;
- }
- if (reference!=null) {
- int sbend = cursor+range[i];
- if (sbend>rlength) {
- sq.append(reference.substring(cursor, rlength));
- while (sbend-- >= rlength)
- {
- sq.append(GapChar);
- }
- } else {
- sq.append(reference.substring(cursor, sbend));
- }
- }
- alcursor+=range[i];
- cursor += range[i];
- end = cursor - 1;
- endpos = alcursor;
- break;
- default:
- throw new Error("Unknown SeqCigar operation '" + operation[i] + "'");
- }
- }
- if (++delcount > 0)
- {
- trunc_deletions = new int[delcount][];
- System.arraycopy(deletions, 0, trunc_deletions, 0, delcount);
- }
- deletions = null;
- return new Object[]
- {
- ((reference!=null) ? sq.toString() : null),
- new int[] {
- start, startpos, end, endpos}, trunc_deletions};
- }
-
- /**
- * turn a cigar string into a series of operation range pairs
- * @param cigarString String
- * @return object[] {char[] operation, int[] range}
- * @throws java.lang.Exception for improperly formated cigar strings or ones with unknown operations
- */
- public static Object[] parseCigarString(String cigarString)
- throws Exception
- {
- int ops = 0;
- for (int i = 0, l = cigarString.length(); i < l; i++)
- {
- char c = cigarString.charAt(i);
- if (c == M || c == (M - _case_shift) || c == I || c == (I - _case_shift) ||
- c == D || c == (D - _case_shift))
- {
- ops++;
- }
- }
- char[] operation = new char[ops];
- int[] range = new int[ops];
- int op = 0;
- int i = 0, l = cigarString.length();
- while (i < l)
- {
- char c;
- int j = i;
- do
- {
- c = cigarString.charAt(j++);
- }
- while (c >= '0' && c <= '9' && j < l);
- if (j >= l && c >= '0' && c <= '9')
- {
- throw new Exception("Unterminated cigar string.");
- }
- try
- {
- String rangeint = cigarString.substring(i, j - 1);
- range[op] = Integer.parseInt(rangeint);
- i = j;
- }
- catch (Exception e)
- {
- throw new Error("Implementation bug in parseCigarString");
- }
- if (c >= 'a' && c <= 'z')
- {
- c -= _case_shift;
- }
- if ( (c == M || c == I || c == D))
- {
- operation[op++] = c;
- }
- else
- {
- throw new Exception("Unexpected operation '" + c +
- "' in cigar string (position " + i + " in '" +
- cigarString + "'");
- }
- }
- return new Object[]
- {
- operation, range};
- }
-
- /**
- * add an operation to cigar string
- * @param op char
- * @param range int
- */
- public void addOperation(char op, int range)
- {
- if (op >= 'a' && op <= 'z')
- {
- op -= _case_shift;
- }
- if (op != M && op != D && op != I)
- {
- throw new Error("Implementation error. Invalid operation string.");
- }
- if (range<=0)
- throw new Error("Invalid range string (must be non-zero positive number)");
- int lngth = 0;
- if (operation == null)
- {
- this.operation = new char[_inc_length];
- this.range = new int[_inc_length];
- }
- if (length + 1 == operation.length)
- {
- char[] ops = this.operation;
- this.operation = new char[length + 1 + _inc_length];
- System.arraycopy(ops, 0, this.operation, 0, length);
- ops = null;
- int[] rng = this.range;
- this.range = new int[length + 1 + _inc_length];
- System.arraycopy(rng, 0, this.range, 0, length);
- rng = null;
- }
- if ((length>0) && (operation[length-1]==op))
- length--; // modify existing operation.
- else
- this.range[length]=0; // reset range
- this.operation[length] = op;
- this.range[length++] += range;
- }
-
- /**
- * semi-efficient insert an operation on the current cigar string set at column pos (from 1)
- * NOTE: Insertion operations simply extend width of cigar result - affecting registration of alignment
- * Deletion ops will shorten length of result - and affect registration of alignment
- * Match ops will also affect length of result - affecting registration of alignment
- * (ie "10M".insert(4,I,3)->"4M3I3M") - (replace?)
- * (ie "10M".insert(4,D,3)->"4M3D3M") - (shortens alignment)
- * (ie "5I5M".insert(4,I,3)->"8I5M") - real insertion
- * (ie "5I5M".insert(4,D,3)->"4I2D3M") - shortens aligment - I's are removed, Ms changed to Ds
- * (ie "10M".insert(4,M,3)->"13M") - lengthens - Is changed to M, Ds changed to M.
- * (ie "5I5M".insert(4,M,3)->"4I8M") - effectively shifts sequence left by 1 residue and extends it by 3
- * ( "10D5M".insert(-1,M,3)->"3M7D5M")
- * ( "10D5M".insert(0,M,3)->"7D8M")
- * ( "10D5M".insert(1,M,3)->"10D8M")
- *
- * ( "1M10D5M".insert(0,M,3)->"1M10D8M")
- * ( "1M10D5M".insert(1,M,3)->"
- *
- * if pos is beyond width - I operations are added before the operation
- * @param pos int -1, 0-length of visible region, or greater to append new ops (with insertions in between)
- * @param op char
- * @param range int
- public void addOperationAt(int pos, char op, int range)
- {
- int cursor = -1; // mark the position for the current operation being edited.
- int o = 0;
- boolean last_d = false; // previous op was a deletion.
- if (pos < -1)
- throw new Error("pos<-1 is not supported.");
- while (o<length) {
- if (operation[o] != D)
- {
- if ( (cursor + this.range[o]) < pos)
- {
- cursor += this.range[o];
- o++;
- last_d=false;
- }
- else
- {
- break;
- }
- }
- else {
- last_d=true;
- o++;
- }
- }
- if (o==length) {
- // must insert more operations before pos
- if (pos-cursor>0)
- addInsertion(pos-cursor);
- // then just add the new operation. Regardless of what it is.
- addOperation(op, range);
- } else {
- int diff = pos - cursor;
-
- int e_length = length-o; // new edit operation array length.
- // diff<0 - can only happen before first insertion or match. - affects op and all following
- // dif==0 - only when at first position of existing op -
- // diff>0 - must preserve some existing operations
- int[] e_range = new int[e_length];
- System.arraycopy(this.range, o, e_range, 0, e_length);
- char[] e_op = new char[e_length];
- System.arraycopy(this.operation, o, e_op, 0, e_length);
- length = o; // can now use add_operation to extend list.
- int e_o=0; // current operation being edited.
- switch (op) {
- case M:
- switch (e_op[e_o])
- {
- case M:
- if (last_d && diff <= 0)
- {
- // reduce D's, if possible
- if (range<=this.range[o-1]) {
- this.range[o - 1] -= range;
- } else {
- this.range[o-1]=0;
- }
- if (this.range[o-1]==0)
- o--; // lose this op.
- }
- e_range[e_o] += range; // just add more matched residues
- break;
- case I:
- // change from insertion to match
- if (last_d && diff<=0)
- {
- // reduce D's, if possible
- if (range<=this.range[o-1]) {
- this.range[o - 1] -= range;
- } else {
- this.range[o-1]=0;
- }
- if (this.range[o-1]==0)
- o--; // lose this op.
- }
- e_range[e_o]
- break;
- default:
- throw new Inp
- }
-
- break;
- case I:
- break;
- case D:
- }
- break;
- default:
- throw new Error("Implementation Error: Unknown operation in addOperation!");
- }
- // finally, add remaining ops.
- while (e_o<e_length) {
- addOperation(e_op[e_o], e_range[e_o]);
- e_o++;
- }
- }
- }
-**/
- /**
- * Mark residues from start to end (inclusive) as deleted from the alignment, and removes any insertions.
- * @param start int
- * @param end int
- */
- public void deleteRange(int start, int end) {
- if (length==0) {
- // nothing to do here
- return;
- }
- if (start<0 || start>end)
- throw new Error("Implementation Error: deleteRange out of bounds: start must be non-negative and less than end.");
- // find beginning
- int cursor = 0; // mark the position for the current operation being edited.
- int rlength=1+end-start; // number of positions to delete
- int oldlen=length;
- int o = 0;
- boolean editing=false;
- char[] oldops = operation;
- int[] oldrange = range;
- length=0;
- operation = null;
- range = null;
- while (o<oldlen && cursor<=end && rlength>0) {
- if (oldops[o] == D) {
- // absorbed into new deleted region.
- addDeleted(oldrange[o++]);
- continue;
- }
-
- int remain = oldrange[o]; // number of op characters left to edit
- if (!editing) {
- if ( (cursor + remain) <= start)
- {
- addOperation(oldops[o],oldrange[o]);
- cursor+=oldrange[o++];
- continue; // next operation
- }
- editing=true;
- // add operations before hidden region
- if (start-cursor>0) {
- addOperation(oldops[o], start- cursor);
- remain -= start - cursor;
- }
- }
- // start inserting new ops
- if (o<oldlen && editing && rlength>0 && remain>0) {
- switch (oldops[o]) {
- case M:
- if (rlength>remain) {
- addDeleted(remain);
- } else {
- addDeleted(rlength);
- if (remain-rlength>0)
- this.addOperation(M,remain-rlength); // add remaining back.
- rlength=0;
- remain=0;
- }
- break;
- case I:
- if (remain-rlength>0) {
- // only remove some gaps
- addInsertion(remain-rlength);
- rlength=0;
- }
- break;
- case D:
- throw new Error("Implementation error."); // do nothing;
- default:
- throw new Error("Implementation Error! Unknown operation '"+oldops[o]+"'");
- }
- rlength-=remain;
- remain = oldrange[++o]; // number of op characters left to edit
- }
- }
- // add remaining
- while (o<oldlen) {
- addOperation(oldops[o],oldrange[o++]);
- }
- //if (cursor<(start+1)) {
- // ran out of ops - nothing to do here ?
- // addInsertion(start-cursor);
- //}
- }
- /**
- * sum of ranges in cigar string
- * @return int number of residues hidden, matched, or gaps inserted into sequence
- */
- public int getFullWidth()
- {
- int w = 0;
- if (range != null)
- {
- for (int i = 0; i < length; i++)
- {
- w += range[i];
- }
- }
- return w;
- }
-
- /**
- * Visible length of aligned sequence
- * @return int length of including gaps and less hidden regions
- */
- public int getWidth()
- {
- int w = 0;
- if (range != null)
- {
- for (int i = 0; i < length; i++)
- {
- if (operation[i] == M || operation[i] == I)
- {
- w += range[i];
- }
- }
- }
- return w;
- }
- /**
- * mark a range of inserted residues
- * @param range int
- */
- public void addInsertion(int range)
- {
- this.addOperation(I, range);
- }
-
- /**
- * mark the next range residues as hidden (not aligned) or deleted
- * @param range int
- */
- public void addDeleted(int range)
- {
- this.addOperation(D, range);
- }
-
- /**
- * Modifies operation list to delete columns from start to end (inclusive)
- * editing will remove insertion operations, and convert matches to deletions
- * @param start alignment column
- * @param end alignment column
- * @return boolean true if residues were marked as deleted.
- public boolean deleteRange(int start, int end)
- {
- boolean deleted = false;
- int op = 0, prevop = -1, firstm = -1,
- lastm = -1, postop = -1;
- int width = 0; // zero'th column
- if (length > 0)
- {
- // find operation bracketing start of the range
- do
- {
- if (operation[op] != D)
- {
- width += range[prevop = op];
- }
- op++;
- }
- while (op < length && width < start);
- }
- if (width < start)
- {
- // run off end - add more operations up to deletion.
- addInsertion(start - width);
- }
- else
- {
- // edit existing operations.
- op = prevop;
- width -= range[prevop];
- int[] oldrange = range;
- char[] oldops = operation;
- range = new int[oldrange.length];
- operation = new char[oldops.length];
- if (op < length)
- {
- do
- {
- if (operation[op] != D)
- {
- width += range[postop = op];
- }
- op++;
- }
- while (op < length && width <= end);
- }
- }
- if (deleted == true)
- {
- addDeleted(end - start + 1);
- }
- return deleted;
- }
-*/
- /**
- * Return an ENSEMBL style cigar string where D may indicates excluded parts of seq
- * @return String of form ([0-9]+[IMD])+
- */
- public String getCigarstring()
- {
- StringBuffer cigarString = new StringBuffer();
- for (int i = 0; i < length; i++)
- {
- cigarString.append("" + range[i]);
- cigarString.append(operation[i]);
- }
- return cigarString.toString();
- }
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package jalview.datamodel;\r
+\r
+import java.util.*;\r
+\r
+public abstract class CigarBase\r
+{\r
+ /**\r
+ * Base class for compact idiosyncratic representation of gaps and aligned\r
+ * residues Regards to Tom Oldfield for his DynamicArray class. 17th July 2006\r
+ * Not thread safe.\r
+ */\r
+ public CigarBase()\r
+ {\r
+ // nothing to be done (probably)\r
+ }\r
+\r
+ protected int length = 0;\r
+\r
+ protected int _inc_length = 10; // extension range for addition of new\r
+\r
+ // operations\r
+\r
+ protected char[] operation = null;\r
+\r
+ protected int[] range = null;\r
+\r
+ /**\r
+ * Range of Hidden residues in seq (translated as deleted in seq)\r
+ */\r
+ public static final char D = 'D';\r
+\r
+ /**\r
+ * Range of insertions to seq\r
+ */\r
+ public static final char I = 'I';\r
+\r
+ /**\r
+ * Range of aligned residues\r
+ */\r
+ public static final char M = 'M';\r
+\r
+ static protected final char _case_shift = 'a' - 'A';\r
+\r
+ /**\r
+ * Ugly function to get edited sequence string, start and end symbol positions\r
+ * and the deletion regions as an array of int pairs May return null for an\r
+ * empty cigar string. May return null for deletion ranges if there are none.\r
+ * \r
+ * @param reference\r
+ * - the symbol sequence to apply the cigar operations to (or null if\r
+ * no sequence)\r
+ * @param GapChar\r
+ * - the symbol to use for Insert operations\r
+ * @return Object[] { String, int[] {start, startcol, end, endcol}, int[][3]\r
+ * {start, end, col} or null} the gapped sequence, first and last\r
+ * residue index, and the deletion ranges on the reference sequence\r
+ */\r
+ public Object[] getSequenceAndDeletions(String reference, char GapChar)\r
+ {\r
+ int rlength = 0;\r
+ int[][] deletions = new int[length][];\r
+ int[][] trunc_deletions = null;\r
+ StringBuffer sq = new StringBuffer();\r
+ int cursor = 0, alcursor = 0, start = 0, startpos = 0, end = 0, endpos = 0, delcount = -1;\r
+ boolean consecutive_del = false;\r
+ if (length == 0)\r
+ {\r
+ return null;\r
+ }\r
+ if (reference != null)\r
+ {\r
+ rlength = reference.length();\r
+ }\r
+ boolean modstart = true;\r
+ for (int i = 0; i < length; i++)\r
+ {\r
+ switch (operation[i])\r
+ {\r
+ case D:\r
+ if (!consecutive_del)\r
+ {\r
+ deletions[++delcount] = new int[]\r
+ { cursor, 0, alcursor };\r
+ }\r
+ cursor += range[i];\r
+ deletions[delcount][1] = cursor - 1;\r
+ consecutive_del = true;\r
+ break;\r
+ case I:\r
+ consecutive_del = false;\r
+ for (int r = 0; r < range[i]; r++)\r
+ {\r
+ sq.append(GapChar);\r
+ alcursor++;\r
+ }\r
+ break;\r
+ case M:\r
+ consecutive_del = false;\r
+ if (modstart)\r
+ {\r
+ start = cursor;\r
+ startpos = alcursor;\r
+ modstart = false;\r
+ }\r
+ if (reference != null)\r
+ {\r
+ int sbend = cursor + range[i];\r
+ if (sbend > rlength)\r
+ {\r
+ sq.append(reference.substring(cursor, rlength));\r
+ while (sbend-- >= rlength)\r
+ {\r
+ sq.append(GapChar);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ sq.append(reference.substring(cursor, sbend));\r
+ }\r
+ }\r
+ alcursor += range[i];\r
+ cursor += range[i];\r
+ end = cursor - 1;\r
+ endpos = alcursor;\r
+ break;\r
+ default:\r
+ throw new Error("Unknown SeqCigar operation '" + operation[i] + "'");\r
+ }\r
+ }\r
+ if (++delcount > 0)\r
+ {\r
+ trunc_deletions = new int[delcount][];\r
+ System.arraycopy(deletions, 0, trunc_deletions, 0, delcount);\r
+ }\r
+ deletions = null;\r
+ return new Object[]\r
+ { ((reference != null) ? sq.toString() : null), new int[]\r
+ { start, startpos, end, endpos }, trunc_deletions };\r
+ }\r
+\r
+ protected void compact_operations()\r
+ {\r
+ int i = 1;\r
+ if (operation == null)\r
+ {\r
+ return;\r
+ }\r
+ char last = operation[0];\r
+ while (i < length)\r
+ {\r
+ if (last == operation[i])\r
+ {\r
+ range[i - 1] += range[i];\r
+ int r = length - i;\r
+ if (r > 0)\r
+ {\r
+ System.arraycopy(range, i + 1, range, i, r);\r
+ System.arraycopy(operation, i + 1, operation, i, r);\r
+ }\r
+ length--;\r
+ }\r
+ else\r
+ {\r
+ last = operation[i++];\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * turn a cigar string into a series of operation range pairs\r
+ * \r
+ * @param cigarString\r
+ * String\r
+ * @return object[] {char[] operation, int[] range}\r
+ * @throws java.lang.Exception\r
+ * for improperly formated cigar strings or ones with unknown\r
+ * operations\r
+ */\r
+ public static Object[] parseCigarString(String cigarString)\r
+ throws Exception\r
+ {\r
+ int ops = 0;\r
+ for (int i = 0, l = cigarString.length(); i < l; i++)\r
+ {\r
+ char c = cigarString.charAt(i);\r
+ if (c == M || c == (M - _case_shift) || c == I\r
+ || c == (I - _case_shift) || c == D || c == (D - _case_shift))\r
+ {\r
+ ops++;\r
+ }\r
+ }\r
+ char[] operation = new char[ops];\r
+ int[] range = new int[ops];\r
+ int op = 0;\r
+ int i = 0, l = cigarString.length();\r
+ while (i < l)\r
+ {\r
+ char c;\r
+ int j = i;\r
+ do\r
+ {\r
+ c = cigarString.charAt(j++);\r
+ } while (c >= '0' && c <= '9' && j < l);\r
+ if (j >= l && c >= '0' && c <= '9')\r
+ {\r
+ throw new Exception("Unterminated cigar string.");\r
+ }\r
+ try\r
+ {\r
+ String rangeint = cigarString.substring(i, j - 1);\r
+ range[op] = Integer.parseInt(rangeint);\r
+ i = j;\r
+ } catch (Exception e)\r
+ {\r
+ throw new Error("Implementation bug in parseCigarString");\r
+ }\r
+ if (c >= 'a' && c <= 'z')\r
+ {\r
+ c -= _case_shift;\r
+ }\r
+ if ((c == M || c == I || c == D))\r
+ {\r
+ operation[op++] = c;\r
+ }\r
+ else\r
+ {\r
+ throw new Exception("Unexpected operation '" + c\r
+ + "' in cigar string (position " + i + " in '"\r
+ + cigarString + "'");\r
+ }\r
+ }\r
+ return new Object[]\r
+ { operation, range };\r
+ }\r
+\r
+ /**\r
+ * add an operation to cigar string\r
+ * \r
+ * @param op\r
+ * char\r
+ * @param range\r
+ * int\r
+ */\r
+ public void addOperation(char op, int range)\r
+ {\r
+ if (op >= 'a' && op <= 'z')\r
+ {\r
+ op -= _case_shift;\r
+ }\r
+ if (op != M && op != D && op != I)\r
+ {\r
+ throw new Error("Implementation error. Invalid operation string.");\r
+ }\r
+ if (range==0)\r
+ {\r
+ return; // No Operation to add.\r
+ }\r
+ if (range < 0)\r
+ {\r
+ throw new Error(\r
+ "Invalid range string (must be zero or positive number)");\r
+ }\r
+ int lngth = 0;\r
+ if (operation == null)\r
+ {\r
+ this.operation = new char[_inc_length];\r
+ this.range = new int[_inc_length];\r
+ }\r
+ if (length + 1 == operation.length)\r
+ {\r
+ char[] ops = this.operation;\r
+ this.operation = new char[length + 1 + _inc_length];\r
+ System.arraycopy(ops, 0, this.operation, 0, length);\r
+ ops = null;\r
+ int[] rng = this.range;\r
+ this.range = new int[length + 1 + _inc_length];\r
+ System.arraycopy(rng, 0, this.range, 0, length);\r
+ rng = null;\r
+ }\r
+ if ((length > 0) && (operation[length - 1] == op))\r
+ {\r
+ length--; // modify existing operation.\r
+ }\r
+ else\r
+ {\r
+ this.range[length] = 0; // reset range\r
+ }\r
+ this.operation[length] = op;\r
+ this.range[length++] += range;\r
+ }\r
+\r
+ /**\r
+ * semi-efficient insert an operation on the current cigar string set at\r
+ * column pos (from 1) NOTE: Insertion operations simply extend width of cigar\r
+ * result - affecting registration of alignment Deletion ops will shorten\r
+ * length of result - and affect registration of alignment Match ops will also\r
+ * affect length of result - affecting registration of alignment (ie\r
+ * "10M".insert(4,I,3)->"4M3I3M") - (replace?) (ie\r
+ * "10M".insert(4,D,3)->"4M3D3M") - (shortens alignment) (ie\r
+ * "5I5M".insert(4,I,3)->"8I5M") - real insertion (ie\r
+ * "5I5M".insert(4,D,3)->"4I2D3M") - shortens aligment - I's are removed, Ms\r
+ * changed to Ds (ie "10M".insert(4,M,3)->"13M") - lengthens - Is changed to\r
+ * M, Ds changed to M. (ie "5I5M".insert(4,M,3)->"4I8M") - effectively shifts\r
+ * sequence left by 1 residue and extends it by 3 (\r
+ * "10D5M".insert(-1,M,3)->"3M7D5M") ( "10D5M".insert(0,M,3)->"7D8M") (\r
+ * "10D5M".insert(1,M,3)->"10D8M") ( "1M10D5M".insert(0,M,3)->"1M10D8M") (\r
+ * "1M10D5M".insert(1,M,3)->"\r
+ * \r
+ * if pos is beyond width - I operations are added before the operation\r
+ * \r
+ * @param pos\r
+ * int -1, 0-length of visible region, or greater to append new ops\r
+ * (with insertions in between)\r
+ * @param op\r
+ * char\r
+ * @param range\r
+ * int public void addOperationAt(int pos, char op, int range) { int\r
+ * cursor = -1; // mark the position for the current operation being\r
+ * edited. int o = 0; boolean last_d = false; // previous op was a\r
+ * deletion. if (pos < -1) throw new\r
+ * Error("pos<-1 is not supported."); while (o<length) { if\r
+ * (operation[o] != D) { if ( (cursor + this.range[o]) < pos) {\r
+ * cursor += this.range[o]; o++; last_d=false; } else { break; } }\r
+ * else { last_d=true; o++; } } if (o==length) { // must insert more\r
+ * operations before pos if (pos-cursor>0) addInsertion(pos-cursor);\r
+ * // then just add the new operation. Regardless of what it is.\r
+ * addOperation(op, range); } else { int diff = pos - cursor;\r
+ * \r
+ * int e_length = length-o; // new edit operation array length. //\r
+ * diff<0 - can only happen before first insertion or match. -\r
+ * affects op and all following // dif==0 - only when at first\r
+ * position of existing op - // diff>0 - must preserve some existing\r
+ * operations int[] e_range = new int[e_length];\r
+ * System.arraycopy(this.range, o, e_range, 0, e_length); char[] e_op\r
+ * = new char[e_length]; System.arraycopy(this.operation, o, e_op, 0,\r
+ * e_length); length = o; // can now use add_operation to extend\r
+ * list. int e_o=0; // current operation being edited. switch (op) {\r
+ * case M: switch (e_op[e_o]) { case M: if (last_d && diff <= 0) { //\r
+ * reduce D's, if possible if (range<=this.range[o-1]) { this.range[o\r
+ * - 1] -= range; } else { this.range[o-1]=0; } if\r
+ * (this.range[o-1]==0) o--; // lose this op. } e_range[e_o] +=\r
+ * range; // just add more matched residues break; case I: // change\r
+ * from insertion to match if (last_d && diff<=0) { // reduce D's, if\r
+ * possible if (range<=this.range[o-1]) { this.range[o - 1] -= range;\r
+ * } else { this.range[o-1]=0; } if (this.range[o-1]==0) o--; // lose\r
+ * this op. } e_range[e_o] break; default: throw new Inp }\r
+ * \r
+ * break; case I: break; case D: } break; default: throw new\r
+ * Error("Implementation Error: Unknown operation in addOperation!");\r
+ * } // finally, add remaining ops. while (e_o<e_length) {\r
+ * addOperation(e_op[e_o], e_range[e_o]); e_o++; } } }\r
+ */\r
+ /**\r
+ * Mark residues from start to end (inclusive) as deleted from the alignment,\r
+ * and removes any insertions.\r
+ * \r
+ * @param start\r
+ * int\r
+ * @param end\r
+ * int\r
+ * @return deleted int - number of symbols marked as deleted\r
+ */\r
+ public int deleteRange(int start, int end)\r
+ {\r
+ int deleted = 0;\r
+ if (length == 0)\r
+ {\r
+ // nothing to do here\r
+ return deleted;\r
+ }\r
+ if (start < 0 || start > end)\r
+ {\r
+ throw new Error(\r
+ "Implementation Error: deleteRange out of bounds: start must be non-negative and less than end.");\r
+ }\r
+ // find beginning\r
+ int cursor = 0; // mark the position for the current operation being edited.\r
+ int rlength = 1 + end - start; // number of positions to delete\r
+ int oldlen = length;\r
+ int o = 0;\r
+ boolean editing = false;\r
+ char[] oldops = operation;\r
+ int[] oldrange = range;\r
+ length = 0;\r
+ operation = null;\r
+ range = null;\r
+ compact_operations();\r
+ while (o < oldlen && cursor <= end && rlength > 0)\r
+ {\r
+ if (oldops[o] == D)\r
+ {\r
+ // absorbed into new deleted region.\r
+ addDeleted(oldrange[o++]);\r
+ continue;\r
+ }\r
+\r
+ int remain = oldrange[o]; // number of op characters left to edit\r
+ if (!editing)\r
+ {\r
+ if ((cursor + remain) <= start)\r
+ {\r
+ addOperation(oldops[o], oldrange[o]);\r
+ cursor += oldrange[o++];\r
+ continue; // next operation\r
+ }\r
+ editing = true;\r
+ // add operations before hidden region\r
+ if (start - cursor > 0)\r
+ {\r
+ addOperation(oldops[o], start - cursor);\r
+ remain -= start - cursor;\r
+ }\r
+ }\r
+ // start inserting new ops\r
+ if (o < oldlen && editing && rlength > 0 && remain > 0)\r
+ {\r
+ switch (oldops[o])\r
+ {\r
+ case M:\r
+ if (rlength > remain)\r
+ {\r
+ addDeleted(remain);\r
+ deleted += remain;\r
+ }\r
+ else\r
+ {\r
+ deleted += rlength;\r
+ addDeleted(rlength);\r
+ if (remain - rlength > 0)\r
+ {\r
+ this.addOperation(M, remain - rlength); // add remaining back.\r
+ }\r
+ rlength = 0;\r
+ remain = 0;\r
+ }\r
+ break;\r
+ case I:\r
+ if (remain - rlength > 0)\r
+ {\r
+ // only remove some gaps\r
+ addInsertion(remain - rlength);\r
+ rlength = 0;\r
+ }\r
+ break;\r
+ case D:\r
+ throw new Error("Implementation error."); // do nothing;\r
+ default:\r
+ throw new Error("Implementation Error! Unknown operation '"\r
+ + oldops[o] + "'");\r
+ }\r
+ rlength -= remain;\r
+ remain = oldrange[++o]; // number of op characters left to edit\r
+ }\r
+ }\r
+ // add remaining\r
+ while (o < oldlen)\r
+ {\r
+ addOperation(oldops[o], oldrange[o++]);\r
+ }\r
+ // if (cursor<(start+1)) {\r
+ // ran out of ops - nothing to do here ?\r
+ // addInsertion(start-cursor);\r
+ // }\r
+ return deleted;\r
+ }\r
+\r
+ /**\r
+ * Deleted regions mean that there will be discontinuous sequence numbering in\r
+ * the sequence returned by getSeq(char).\r
+ * \r
+ * @return true if there deletions\r
+ */\r
+ public boolean hasDeletedRegions()\r
+ {\r
+ for (int i = 0; i < length; i++)\r
+ {\r
+ if (operation[i] == D)\r
+ {\r
+ return true;\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+\r
+ /**\r
+ * enumerate the ranges on seq that are marked as deleted in this cigar\r
+ * \r
+ * @return int[] { vis_start, sym_start, length }\r
+ */\r
+ public int[] getDeletedRegions()\r
+ {\r
+ if (length == 0)\r
+ {\r
+ return null;\r
+ }\r
+ Vector dr = new Vector();\r
+ int cursor = 0, vcursor = 0;\r
+ for (int i = 0; i < length; i++)\r
+ {\r
+ switch (operation[i])\r
+ {\r
+ case M:\r
+ cursor += range[i];\r
+ case I:\r
+ vcursor += range[i];\r
+ break;\r
+ case D:\r
+ dr.addElement(new int[]\r
+ { vcursor, cursor, range[i] });\r
+ cursor += range[i];\r
+ }\r
+ }\r
+ if (dr.size() == 0)\r
+ {\r
+ return null;\r
+ }\r
+ int[] delregions = new int[dr.size() * 3];\r
+ for (int i = 0, l = dr.size(); i < l; i++)\r
+ {\r
+ int[] reg = (int[]) dr.elementAt(i);\r
+ delregions[i * 3] = reg[0];\r
+ delregions[i * 3 + 1] = reg[1];\r
+ delregions[i * 3 + 2] = reg[2];\r
+ }\r
+ return delregions;\r
+ }\r
+\r
+ /**\r
+ * sum of ranges in cigar string\r
+ * \r
+ * @return int number of residues hidden, matched, or gaps inserted into\r
+ * sequence\r
+ */\r
+ public int getFullWidth()\r
+ {\r
+ int w = 0;\r
+ if (range != null)\r
+ {\r
+ for (int i = 0; i < length; i++)\r
+ {\r
+ w += range[i];\r
+ }\r
+ }\r
+ return w;\r
+ }\r
+\r
+ /**\r
+ * Visible length of aligned sequence\r
+ * \r
+ * @return int length of including gaps and less hidden regions\r
+ */\r
+ public int getWidth()\r
+ {\r
+ int w = 0;\r
+ if (range != null)\r
+ {\r
+ for (int i = 0; i < length; i++)\r
+ {\r
+ if (operation[i] == M || operation[i] == I)\r
+ {\r
+ w += range[i];\r
+ }\r
+ }\r
+ }\r
+ return w;\r
+ }\r
+\r
+ /**\r
+ * mark a range of inserted residues\r
+ * \r
+ * @param range\r
+ * int\r
+ */\r
+ public void addInsertion(int range)\r
+ {\r
+ this.addOperation(I, range);\r
+ }\r
+\r
+ /**\r
+ * mark the next range residues as hidden (not aligned) or deleted\r
+ * \r
+ * @param range\r
+ * int\r
+ */\r
+ public void addDeleted(int range)\r
+ {\r
+ this.addOperation(D, range);\r
+ }\r
+\r
+ /**\r
+ * Modifies operation list to delete columns from start to end (inclusive)\r
+ * editing will remove insertion operations, and convert matches to deletions\r
+ * \r
+ * @param start\r
+ * alignment column\r
+ * @param end\r
+ * alignment column\r
+ * @return boolean true if residues were marked as deleted. public boolean\r
+ * deleteRange(int start, int end) { boolean deleted = false; int op =\r
+ * 0, prevop = -1, firstm = -1, lastm = -1, postop = -1; int width =\r
+ * 0; // zero'th column if (length > 0) { // find operation bracketing\r
+ * start of the range do { if (operation[op] != D) { width +=\r
+ * range[prevop = op]; } op++; } while (op < length && width < start);\r
+ * } if (width < start) { // run off end - add more operations up to\r
+ * deletion. addInsertion(start - width); } else { // edit existing\r
+ * operations. op = prevop; width -= range[prevop]; int[] oldrange =\r
+ * range; char[] oldops = operation; range = new int[oldrange.length];\r
+ * operation = new char[oldops.length]; if (op < length) { do { if\r
+ * (operation[op] != D) { width += range[postop = op]; } op++; } while\r
+ * (op < length && width <= end); } } if (deleted == true) {\r
+ * addDeleted(end - start + 1); } return deleted; }\r
+ */\r
+ /**\r
+ * Return an ENSEMBL style cigar string where D may indicates excluded parts\r
+ * of seq\r
+ * \r
+ * @return String of form ([0-9]+[IMD])+\r
+ */\r
+ public String getCigarstring()\r
+ {\r
+ StringBuffer cigarString = new StringBuffer();\r
+ for (int i = 0; i < length; i++)\r
+ {\r
+ cigarString.append("" + range[i]);\r
+ cigarString.append(operation[i]);\r
+ }\r
+ return cigarString.toString();\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff