-package jalview.datamodel;
-
-public class CigarArray extends CigarBase
-{
- /**
- * Do CIGAR operations on a set of sequences from many other cigars
- * BAD THINGS WILL HAPPEN IF A CIGARARRAY IS PASSED TO A CIGARARRAY
- * or a CIGARCIGAR is given a CIGARARRAY to insert gaps into.
- */
- /**
- * array of subject cigars
- */
- public CigarSimple refCigars[]=null;
- private boolean seqcigararray=false;
- private CigarArray() {
- super();
- }
-
- /**
- * isSeqCigarArray()
- * @return boolean true if all refCigars resolve to a SeqCigar or a CigarCigar
- */
- public boolean isSeqCigarArray()
- {
- return seqcigararray;
- }
-
- /**
- * Apply CIGAR operations to several cigars in parallel
- * will throw an error if any of cigar are actually CigarArrays.
- * @param cigar Cigar[]
- */
- public CigarArray(CigarSimple[] cigars) {
- super();
- seqcigararray = true;
- if (cigars != null && cigars.length > 0)
- {
- refCigars = new CigarSimple[cigars.length];
- for (int c = 0; c < cigars.length; c++)
- {
- refCigars[c] = cigars[c];
- if (! ( (cigars[c] instanceof SeqCigar)
- || cigars[c] instanceof CigarCigar))
- {
- seqcigararray = false;
- }
- }
- }
- }
- /**
- * @see Cigar.getSequenceAndDeletions
- * @param GapChar char
- * @return Object[][]
- */
- protected Object[][] getArrayofSequenceAndDeletions(char GapChar) {
- if (refCigars == null || refCigars.length == 0 || length == 0) {
- return null;
- }
- Object[][] sqanddels = new Object[refCigars.length][];
- for (int c=0; c<refCigars.length; c++) {
- String refString = refCigars[c].getSequenceString(GapChar);
- if (refString != null)
- {
- sqanddels[c] = getSequenceAndDeletions(refString, GapChar);
- } else {
- sqanddels[c] = null;
- }
- }
- return sqanddels;
- }
- /**
- * NOTE: this is an improper sequence string function
- * @return String formed by newline concatenated results of applying CIGAR operations to each reference object in turn.
- * @param GapChar char
- * @return '\n' separated strings (empty results included as \n\n)
- */
- public String getSequenceString(char GapChar)
- {
- if (length==0 || refCigars==null)
- return "";
- StringBuffer seqStrings = new StringBuffer();
- Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);
- for (int c=0; c<refCigars.length; c++) {
- if (sqanddels[c]!=null) {
- seqStrings.append( (String) sqanddels[c][0]);
- sqanddels[c][0] = null;
- }
- seqStrings.append('\n');
- }
- return seqStrings.toString();
- }
- /**
- * return string results of applying cigar string to all reference cigars
- * @param GapChar char
- * @return String[]
- */
- public String[] getSequenceStrings(char GapChar) {
-
- if (length==0 || refCigars==null || refCigars.length==0)
- return null;
- Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);
- String[] seqs = new String[sqanddels.length];
- for (int c=0; c<refCigars.length; c++) {
- seqs[c] = (String) sqanddels[c][0];
- }
- return seqs;
- }
- /**
- * Combines the CigarArray cigar operations with the operations in each
- * reference cigar - creating a new reference cigar
- * @return Cigar[]
- */
- public CigarBase[] getEditedCigars() {
-
- return new CigarBase[] {};
- }
-}
+/*\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 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 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
+ {\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) || cigars[c] instanceof CigarCigar))\r
+ {\r
+ seqcigararray = false;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * @see Cigar.getSequenceAndDeletions\r
+ * @param GapChar\r
+ * char\r
+ * @return Object[][]\r
+ */\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
+ else\r
+ {\r
+ sqanddels[c] = null;\r
+ }\r
+ }\r
+ return sqanddels;\r
+ }\r
+\r
+ /**\r
+ * NOTE: this is an improper sequence string function\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
+ {\r
+ return "";\r
+ }\r
+ StringBuffer seqStrings = new StringBuffer();\r
+ Object[][] sqanddels = getArrayofSequenceAndDeletions(GapChar);\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
+ * \r
+ * @param GapChar\r
+ * char\r
+ * @return String[]\r
+ */\r
+ public String[] getSequenceStrings(char GapChar)\r
+ {\r
+\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
+ {\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
+ * 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
+ {\r
+ return null;\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
+ {\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
+ /*\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
+ {\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
+ {\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
+ * \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
+ {\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
+ {\r
+ sa[i] = (SeqCigar) refCigars[i];\r
+ }\r
+ return sa;\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff