--- /dev/null
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 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
+ super();\r
+ }\r
+\r
+ /**\r
+ * isSeqCigarArray()\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
+ * 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
+ */\r
+ public CigarArray(CigarSimple[] cigars) {\r
+ super();\r
+ seqcigararray = true;\r
+ if (cigars != null && cigars.length > 0)\r
+ {\r
+ refCigars = new CigarSimple[cigars.length];\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
+ {\r
+ seqcigararray = false;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ /**\r
+ * @see Cigar.getSequenceAndDeletions\r
+ * @param GapChar char\r
+ * @return Object[][]\r
+ */\r
+ protected Object[][] getArrayofSequenceAndDeletions(char GapChar) {\r
+ if (refCigars == null || refCigars.length == 0 || length == 0) {\r
+ return null;\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
+ }\r
+ return sqanddels;\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
+ * @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
+ return "";\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
+ sqanddels[c][0] = null;\r
+ }\r
+ seqStrings.append('\n');\r
+ }\r
+ return seqStrings.toString();\r
+ }\r
+ /**\r
+ * return string results of applying cigar string to all reference cigars\r
+ * @param GapChar char\r
+ * @return String[]\r
+ */\r
+ public String[] getSequenceStrings(char GapChar) {\r
+\r
+ if (length==0 || refCigars==null || refCigars.length==0)\r
+ return null;\r
+ Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);\r
+ String[] seqs = new String[sqanddels.length];\r
+ for (int c=0; c<refCigars.length; c++) {\r
+ seqs[c] = (String) sqanddels[c][0];\r
+ }\r
+ return seqs;\r
+ }\r
+ /**\r
+ * Combines the CigarArray cigar operations with the operations in each\r
+ * reference cigar - creating a new reference cigar\r
+ * @return Cigar[]\r
+\r
+ public CigarBase[] getEditedCigars() {\r
+\r
+ return new CigarBase[] {};\r
+ }\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
+ */\r
+ public int[] applyDeletions()\r
+ {\r
+ java.util.Vector delpos=null;\r
+ if (length==0)\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
+ 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
+ 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
+ for (int s=0; s<refCigars.length; s++) {\r
+ int d = refCigars[s].deleteRange(delstart, delend);\r
+ }\r
+\r
+ }\r
+ }\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[] dr = ((int[]) delpos.elementAt(k));\r
+ pos[k*2] = dr[0];\r
+ pos[k*2+1] = dr[1];\r
+ delpos.setElementAt(null,k);\r
+ }\r
+ delpos=null;\r
+ return pos;\r
+ }\r
+ return null;\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
+ public SeqCigar[] getSeqCigarArray() {\r
+ if (!isSeqCigarArray())\r
+ return null;\r
+ SeqCigar[] sa = new SeqCigar[refCigars.length];\r
+ for (int i=0; i<refCigars.length; i++)\r
+ sa[i] = (SeqCigar) refCigars[i];\r
+ return sa;\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff