+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.datamodel;\r
\r
public class CigarArray extends CigarBase\r
{\r
- /**\r
- * Do CIGAR operations on a set of sequences from many other cigars\r
- * BAD THINGS WILL HAPPEN IF A CIGARARRAY IS PASSED TO A CIGARARRAY\r
- * or a CIGARCIGAR is given a CIGARARRAY to insert gaps into.\r
- */\r
- /**\r
- * array of subject cigars\r
- */\r
- public CigarSimple refCigars[]=null;\r
- private boolean seqcigararray=false;\r
- private CigarArray() {\r
+ /**\r
+ * Do CIGAR operations on a set of sequences from many other cigars BAD THINGS\r
+ * WILL HAPPEN IF A CIGARARRAY IS PASSED TO A CIGARARRAY or a CIGARCIGAR is\r
+ * given a CIGARARRAY to insert gaps into.\r
+ */\r
+ /**\r
+ * array of subject cigars\r
+ */\r
+ public CigarSimple refCigars[] = null;\r
+\r
+ private boolean seqcigararray = false;\r
+\r
+ private CigarArray()\r
+ {\r
super();\r
}\r
\r
/**\r
* isSeqCigarArray()\r
+ * \r
* @return boolean true if all refCigars resolve to a SeqCigar or a CigarCigar\r
*/\r
public boolean isSeqCigarArray()\r
{\r
return seqcigararray;\r
}\r
+\r
/**\r
- * Apply CIGAR operations to several cigars in parallel\r
- * will throw an error if any of cigar are actually CigarArrays.\r
- * @param cigar Cigar[]\r
+ * Apply CIGAR operations to several cigars in parallel will throw an error if\r
+ * any of cigar are actually CigarArrays.\r
+ * \r
+ * @param cigar\r
+ * Cigar[]\r
*/\r
- public CigarArray(CigarSimple[] cigars) {\r
+ public CigarArray(CigarSimple[] cigars)\r
+ {\r
super();\r
seqcigararray = true;\r
if (cigars != null && cigars.length > 0)\r
for (int c = 0; c < cigars.length; c++)\r
{\r
refCigars[c] = cigars[c];\r
- if (! ( (cigars[c] instanceof SeqCigar)\r
- || cigars[c] instanceof CigarCigar))\r
+ if (!((cigars[c] instanceof SeqCigar) || cigars[c] instanceof CigarCigar))\r
{\r
seqcigararray = false;\r
}\r
}\r
}\r
}\r
+\r
/**\r
* @see Cigar.getSequenceAndDeletions\r
- * @param GapChar char\r
+ * @param GapChar\r
+ * char\r
* @return Object[][]\r
*/\r
- protected Object[][] getArrayofSequenceAndDeletions(char GapChar) {\r
- if (refCigars == null || refCigars.length == 0 || length == 0) {\r
- return null;\r
+ protected Object[][] getArrayofSequenceAndDeletions(char GapChar)\r
+ {\r
+ if (refCigars == null || refCigars.length == 0 || length == 0)\r
+ {\r
+ return null;\r
+ }\r
+ Object[][] sqanddels = new Object[refCigars.length][];\r
+ for (int c = 0; c < refCigars.length; c++)\r
+ {\r
+ String refString = refCigars[c].getSequenceString(GapChar);\r
+ if (refString != null)\r
+ {\r
+ sqanddels[c] = getSequenceAndDeletions(refString, GapChar);\r
}\r
- Object[][] sqanddels = new Object[refCigars.length][];\r
- for (int c=0; c<refCigars.length; c++) {\r
- String refString = refCigars[c].getSequenceString(GapChar);\r
- if (refString != null)\r
- {\r
- sqanddels[c] = getSequenceAndDeletions(refString, GapChar);\r
- } else {\r
- sqanddels[c] = null;\r
- }\r
+ else\r
+ {\r
+ sqanddels[c] = null;\r
}\r
- return sqanddels;\r
}\r
+ return sqanddels;\r
+ }\r
+\r
/**\r
* NOTE: this is an improper sequence string function\r
- * @return String formed by newline concatenated results of applying CIGAR operations to each reference object in turn.\r
- * @param GapChar char\r
+ * \r
+ * @return String formed by newline concatenated results of applying CIGAR\r
+ * operations to each reference object in turn.\r
+ * @param GapChar\r
+ * char\r
* @return '\n' separated strings (empty results included as \n\n)\r
*/\r
public String getSequenceString(char GapChar)\r
{\r
- if (length==0 || refCigars==null)\r
+ if (length == 0 || refCigars == null)\r
+ {\r
return "";\r
+ }\r
StringBuffer seqStrings = new StringBuffer();\r
Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);\r
- for (int c=0; c<refCigars.length; c++) {\r
- if (sqanddels[c]!=null) {\r
- seqStrings.append( (String) sqanddels[c][0]);\r
+ for (int c = 0; c < refCigars.length; c++)\r
+ {\r
+ if (sqanddels[c] != null)\r
+ {\r
+ seqStrings.append((String) sqanddels[c][0]);\r
sqanddels[c][0] = null;\r
}\r
seqStrings.append('\n');\r
}\r
return seqStrings.toString();\r
}\r
+\r
/**\r
* return string results of applying cigar string to all reference cigars\r
- * @param GapChar char\r
+ * \r
+ * @param GapChar\r
+ * char\r
* @return String[]\r
*/\r
- public String[] getSequenceStrings(char GapChar) {\r
+ public String[] getSequenceStrings(char GapChar)\r
+ {\r
\r
- if (length==0 || refCigars==null || refCigars.length==0)\r
+ if (length == 0 || refCigars == null || refCigars.length == 0)\r
+ {\r
return null;\r
+ }\r
Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);\r
String[] seqs = new String[sqanddels.length];\r
- for (int c=0; c<refCigars.length; c++) {\r
+ for (int c = 0; c < refCigars.length; c++)\r
+ {\r
seqs[c] = (String) sqanddels[c][0];\r
}\r
return seqs;\r
}\r
+\r
/**\r
* Combines the CigarArray cigar operations with the operations in each\r
* reference cigar - creating a new reference cigar\r
+ * \r
* @return Cigar[]\r
-\r
- public CigarBase[] getEditedCigars() {\r
-\r
- return new CigarBase[] {};\r
- }\r
-*/\r
+ * \r
+ * public CigarBase[] getEditedCigars() {\r
+ * \r
+ * return new CigarBase[] {}; }\r
+ */\r
/**\r
- * applyDeletions\r
- * edits underlying refCigars to propagate deleted regions, and removes deletion\r
- * operations from CigarArray operation list.\r
- * @return int[] position after deletion occured and range of deletion in cigarArray or null if none occured\r
+ * applyDeletions edits underlying refCigars to propagate deleted regions, and\r
+ * removes deletion operations from CigarArray operation list.\r
+ * \r
+ * @return int[] position after deletion occured and range of deletion in\r
+ * cigarArray or null if none occured\r
*/\r
public int[] applyDeletions()\r
{\r
- java.util.Vector delpos=null;\r
- if (length==0)\r
+ java.util.Vector delpos = null;\r
+ if (length == 0)\r
+ {\r
return null;\r
- int cursor=0; // range counter for deletions\r
- int vcursor=0; // visible column index\r
- int offset=0; // shift in visible column index as deletions are made\r
- int i=0;\r
- while (i<length) {\r
- if (operation[i]!=D) {\r
- if (operation[i]==M)\r
- cursor+=range[i];\r
- vcursor+=range[i++];\r
+ }\r
+ int cursor = 0; // range counter for deletions\r
+ int vcursor = 0; // visible column index\r
+ int offset = 0; // shift in visible column index as deletions are made\r
+ int i = 0;\r
+ while (i < length)\r
+ {\r
+ if (operation[i] != D)\r
+ {\r
+ if (operation[i] == M)\r
+ {\r
+ cursor += range[i];\r
+ }\r
+ vcursor += range[i++];\r
}\r
else\r
{\r
- if (delpos==null)\r
- delpos=new java.util.Vector();\r
- int delstart=cursor, delend=cursor+range[i]-1; // inclusive\r
- delpos.addElement(new int[] { vcursor+offset, range[i]}); // index of right hand column after hidden region boundary\r
- offset+=range[i]-1; // shift in visible column coordinates\r
- System.arraycopy(operation, i+1, operation, i, length-i);\r
- System.arraycopy(range, i+1, range, i, length-i);\r
+ if (delpos == null)\r
+ {\r
+ delpos = new java.util.Vector();\r
+ }\r
+ int delstart = cursor, delend = cursor + range[i] - 1; // inclusive\r
+ delpos.addElement(new int[]\r
+ { vcursor + offset, range[i] }); // index of right hand column after\r
+ // hidden region boundary\r
+ offset += range[i] - 1; // shift in visible column coordinates\r
+ System.arraycopy(operation, i + 1, operation, i, length - i);\r
+ System.arraycopy(range, i + 1, range, i, length - i);\r
length--;\r
- /* int dmax=0;\r
- for (int s=0; s<refCigars.length; s++) {\r
- int d = refCigars[s].deleteRange(delstart, delend);\r
- if (d>dmax)\r
- dmax=d;\r
- }\r
- offset+=dmax; // shift in visible column coordinates\r
+ /*\r
+ * int dmax=0; for (int s=0; s<refCigars.length; s++) { int d =\r
+ * refCigars[s].deleteRange(delstart, delend); if (d>dmax) dmax=d; }\r
+ * offset+=dmax; // shift in visible column coordinates\r
*/\r
- for (int s=0; s<refCigars.length; s++) {\r
+ for (int s = 0; s < refCigars.length; s++)\r
+ {\r
int d = refCigars[s].deleteRange(delstart, delend);\r
}\r
\r
}\r
}\r
- if (delpos!=null)\r
+ if (delpos != null)\r
{\r
- int[] pos=new int[delpos.size()*2];\r
- for (int k = 0, l = delpos.size(); k < l; k++) {\r
+ int[] pos = new int[delpos.size() * 2];\r
+ for (int k = 0, l = delpos.size(); k < l; k++)\r
+ {\r
int[] dr = ((int[]) delpos.elementAt(k));\r
- pos[k*2] = dr[0];\r
- pos[k*2+1] = dr[1];\r
- delpos.setElementAt(null,k);\r
+ pos[k * 2] = dr[0];\r
+ pos[k * 2 + 1] = dr[1];\r
+ delpos.setElementAt(null, k);\r
}\r
- delpos=null;\r
+ delpos = null;\r
return pos;\r
}\r
return null;\r
}\r
+\r
/**\r
- *\r
- * @return SeqCigar[] or null if CigarArray is not a SeqCigarArray (ie it does not resolve to set of seqCigars)\r
+ * \r
+ * @return SeqCigar[] or null if CigarArray is not a SeqCigarArray (ie it does\r
+ * not resolve to set of seqCigars)\r
*/\r
- public SeqCigar[] getSeqCigarArray() {\r
+ public SeqCigar[] getSeqCigarArray()\r
+ {\r
if (!isSeqCigarArray())\r
+ {\r
return null;\r
+ }\r
SeqCigar[] sa = new SeqCigar[refCigars.length];\r
- for (int i=0; i<refCigars.length; i++)\r
+ for (int i = 0; i < refCigars.length; i++)\r
+ {\r
sa[i] = (SeqCigar) refCigars[i];\r
+ }\r
return sa;\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff