/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
*/\r
package jalview.datamodel;\r
\r
-import java.util.Vector;\r
+import java.util.*;\r
\r
public abstract class CigarBase\r
{\r
*/\r
public Object[] getSequenceAndDeletions(String reference, char GapChar)\r
{\r
- int rlength=0;\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
+ int cursor = 0, alcursor = 0, start = 0, startpos = 0, end = 0, endpos = 0,\r
+ delcount = -1;\r
boolean consecutive_del = false;\r
if (length == 0)\r
{\r
return null;\r
}\r
- if (reference!=null)\r
- rlength=reference.length();\r
+ if (reference != null)\r
+ {\r
+ rlength = reference.length();\r
+ }\r
boolean modstart = true;\r
for (int i = 0; i < length; i++)\r
{\r
if (modstart)\r
{\r
start = cursor;\r
- startpos=alcursor;\r
+ startpos = alcursor;\r
modstart = false;\r
}\r
- if (reference!=null) {\r
- int sbend = cursor+range[i];\r
- if (sbend>rlength) {\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
- } else {\r
+ }\r
+ else\r
+ {\r
sq.append(reference.substring(cursor, sbend));\r
}\r
}\r
- alcursor+=range[i];\r
+ alcursor += range[i];\r
cursor += range[i];\r
end = cursor - 1;\r
endpos = alcursor;\r
deletions = null;\r
return new Object[]\r
{\r
- ((reference!=null) ? sq.toString() : null),\r
- new int[] {\r
+ ( (reference != null) ? sq.toString() : null),\r
+ new int[]\r
+ {\r
start, startpos, end, endpos}, trunc_deletions};\r
}\r
- protected void compact_operations() {\r
- int i=1;\r
- if (operation==null)\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
- if (last==operation[i]) {\r
- range[i-1]+=range[i];\r
- int r = length-i;\r
- if (r>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
- } else {\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
* @param cigarString String\r
{\r
throw new Error("Implementation error. Invalid operation string.");\r
}\r
- if (range<=0)\r
+ if (range <= 0)\r
+ {\r
throw new Error("Invalid range string (must be non-zero positive number)");\r
+ }\r
int lngth = 0;\r
if (operation == null)\r
{\r
System.arraycopy(rng, 0, this.range, 0, length);\r
rng = null;\r
}\r
- if ((length>0) && (operation[length-1]==op))\r
+ if ( (length > 0) && (operation[length - 1] == op))\r
+ {\r
length--; // modify existing operation.\r
+ }\r
else\r
- this.range[length]=0; // reset range\r
+ {\r
+ this.range[length] = 0; // reset range\r
+ }\r
this.operation[length] = op;\r
this.range[length++] += range;\r
}\r
* @param pos int -1, 0-length of visible region, or greater to append new ops (with insertions in between)\r
* @param op char\r
* @param range int\r
- public void addOperationAt(int pos, char op, int range)\r
- {\r
- int cursor = -1; // mark the position for the current operation being edited.\r
+ public void addOperationAt(int pos, char op, int range)\r
+ {\r
+ int cursor = -1; // mark the position for the current operation being edited.\r
int o = 0;\r
boolean last_d = false; // previous op was a deletion.\r
if (pos < -1)\r
}\r
break;\r
default:\r
- throw new Error("Implementation Error: Unknown operation in addOperation!");\r
+ throw new Error("Implementation Error: Unknown operation in addOperation!");\r
}\r
// finally, add remaining ops.\r
while (e_o<e_length) {\r
e_o++;\r
}\r
}\r
- }\r
-**/\r
+ }\r
+ **/\r
/**\r
* Mark residues from start to end (inclusive) as deleted from the alignment, and removes any insertions.\r
* @param start int\r
* @param end int\r
* @return deleted int - number of symbols marked as deleted\r
*/\r
- public int deleteRange(int start, int end) {\r
- int deleted=0;\r
- if (length==0) {\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
+ if (start < 0 || start > end)\r
+ {\r
throw new Error("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 rlength = 1 + end - start; // number of positions to delete\r
+ int oldlen = length;\r
int o = 0;\r
- boolean editing=false;\r
+ boolean editing = false;\r
char[] oldops = operation;\r
int[] oldrange = range;\r
- length=0;\r
+ length = 0;\r
operation = null;\r
range = null;\r
compact_operations();\r
- while (o<oldlen && cursor<=end && rlength>0) {\r
- if (oldops[o] == D) {\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
+ if (!editing)\r
+ {\r
if ( (cursor + remain) <= start)\r
{\r
- addOperation(oldops[o],oldrange[o]);\r
- cursor+=oldrange[o++];\r
+ addOperation(oldops[o], oldrange[o]);\r
+ cursor += oldrange[o++];\r
continue; // next operation\r
}\r
- editing=true;\r
+ editing = true;\r
// add operations before hidden region\r
- if (start-cursor>0) {\r
- addOperation(oldops[o], start- cursor);\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
- switch (oldops[o]) {\r
+ if (o < oldlen && editing && rlength > 0 && remain > 0)\r
+ {\r
+ switch (oldops[o])\r
+ {\r
case M:\r
- if (rlength>remain) {\r
+ if (rlength > remain)\r
+ {\r
addDeleted(remain);\r
- deleted+=remain;\r
- } else {\r
- deleted+=rlength;\r
+ deleted += remain;\r
+ }\r
+ else\r
+ {\r
+ deleted += rlength;\r
addDeleted(rlength);\r
- if (remain-rlength>0)\r
- this.addOperation(M,remain-rlength); // add remaining back.\r
- rlength=0;\r
- remain=0;\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
+ if (remain - rlength > 0)\r
+ {\r
// only remove some gaps\r
- addInsertion(remain-rlength);\r
- rlength=0;\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 '"+oldops[o]+"'");\r
+ throw new Error("Implementation Error! Unknown operation '" +\r
+ oldops[o] + "'");\r
}\r
- rlength-=remain;\r
+ rlength -= remain;\r
remain = oldrange[++o]; // number of op characters left to edit\r
}\r
}\r
// add remaining\r
- while (o<oldlen) {\r
- addOperation(oldops[o],oldrange[o++]);\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
+ // ran out of ops - nothing to do here ?\r
+ // addInsertion(start-cursor);\r
//}\r
return deleted;\r
}\r
*/\r
public boolean hasDeletedRegions()\r
{\r
- for (int i = 0; i<length ; i++)\r
+ for (int i = 0; i < length; i++)\r
{\r
if (operation[i] == D)\r
{\r
}\r
return false;\r
}\r
+\r
/**\r
* enumerate the ranges on seq that are marked as deleted in this cigar\r
* @return int[] { vis_start, sym_start, length }\r
*/\r
- public int[] getDeletedRegions() {\r
- if (length==0)\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
- switch (operation[i]) {\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
+ cursor += range[i];\r
case I:\r
- vcursor+=range[i];\r
+ vcursor += range[i];\r
break;\r
case D:\r
- dr.addElement(new int[] { vcursor, cursor, range[i]});\r
- cursor+=range[i];\r
+ dr.addElement(new int[]\r
+ {vcursor, cursor, range[i]});\r
+ cursor += range[i];\r
}\r
}\r
- if (dr.size()==0)\r
+ if (dr.size() == 0)\r
+ {\r
return null;\r
- int[] delregions = new int[dr.size()*3];\r
- for (int i=0,l=dr.size(); i<l; i++) {\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
+ 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
* @return int number of residues hidden, matched, or gaps inserted into sequence\r
}\r
return w;\r
}\r
+\r
/**\r
* mark a range of inserted residues\r
* @param range int\r
* @param start alignment column\r
* @param end alignment column\r
* @return boolean true if residues were marked as deleted.\r
- public boolean deleteRange(int start, int end)\r
- {\r
+ public boolean deleteRange(int start, int end)\r
+ {\r
boolean deleted = false;\r
int op = 0, prevop = -1, firstm = -1,\r
lastm = -1, postop = -1;\r
addDeleted(end - start + 1);\r
}\r
return deleted;\r
- }\r
-*/\r
+ }\r
+ */\r
/**\r
* Return an ENSEMBL style cigar string where D may indicates excluded parts of seq\r
* @return String of form ([0-9]+[IMD])+\r
git://source.jalview.org / jalview.git / blobdiff