-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\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
- * 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\r
- 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
- 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
- /**\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
- {\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
- /**\r
- * @see Cigar.getSequenceAndDeletions\r
- * @param GapChar 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
- * @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
- {\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
- * @param GapChar 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
- * @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
- {\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 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
- {\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 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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import java.util.List;
+
+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;
+ }
+ }
+ }
+ }
+
+ /**
+ * construct a cigar array from the current alignment, or just the subset of
+ * the current alignment specified by selectionGroup. Any columns marked as
+ * hidden in columnSelection will be marked as deleted in the array.
+ *
+ * @param alignment
+ * @param columnSelection
+ * @param selectionGroup
+ */
+ public CigarArray(AlignmentI alignment, ColumnSelection columnSelection,
+ SequenceGroup selectionGroup)
+ {
+ this(constructSeqCigarArray(alignment, selectionGroup));
+ constructFromAlignment(alignment,
+ columnSelection != null ? columnSelection.getHiddenColumns()
+ : null, selectionGroup);
+ }
+
+ private static int[] _calcStartEndBounds(AlignmentI alignment,
+ SequenceGroup selectionGroup)
+ {
+ int[] startend = new int[] { 0, 0, 0 };
+ if (selectionGroup != null)
+ {
+ startend[0] = selectionGroup.getSize();
+ startend[1] = selectionGroup.getStartRes();
+ startend[2] = selectionGroup.getEndRes(); // inclusive for start and end
+ // in
+ // SeqCigar constructor
+ }
+ else
+ {
+ startend[0] = alignment.getHeight();
+ startend[2] = alignment.getWidth() - 1;
+ }
+ return startend;
+ }
+
+ public static SeqCigar[] constructSeqCigarArray(AlignmentI alignment,
+ SequenceGroup selectionGroup)
+ {
+ SequenceI[] seqs = null;
+ int i, iSize;
+ int _startend[] = _calcStartEndBounds(alignment, selectionGroup);
+ int start = _startend[1], end = _startend[2];
+ if (selectionGroup != null)
+ {
+ iSize = selectionGroup.getSize();
+ seqs = selectionGroup.getSequencesInOrder(alignment);
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes(); // inclusive for start and end in
+ // SeqCigar constructor
+ }
+ else
+ {
+ iSize = alignment.getHeight();
+ seqs = alignment.getSequencesArray();
+ end = alignment.getWidth() - 1;
+ }
+ SeqCigar[] selseqs = new SeqCigar[iSize];
+ for (i = 0; i < iSize; i++)
+ {
+ selseqs[i] = new SeqCigar(seqs[i], start, end);
+ }
+ return selseqs;
+ }
+
+ /**
+ * internal constructor function - called by CigarArray(AlignmentI, ...);
+ *
+ * @param alignment
+ * @param list
+ * - vector of visible regions as returned from
+ * columnSelection.getHiddenColumns()
+ * @param selectionGroup
+ */
+ private void constructFromAlignment(AlignmentI alignment,
+ List<int[]> list, SequenceGroup selectionGroup)
+ {
+ int[] _startend = _calcStartEndBounds(alignment, selectionGroup);
+ int start = _startend[1], end = _startend[2];
+ // now construct the CigarArray operations
+ if (list != null)
+ {
+ int[] region;
+ int hideStart, hideEnd;
+ int last = start;
+ for (int j = 0; last < end & j < list.size(); j++)
+ {
+ region = list.get(j);
+ hideStart = region[0];
+ hideEnd = region[1];
+ // edit hidden regions to selection range
+ if (hideStart < last)
+ {
+ if (hideEnd > last)
+ {
+ hideStart = last;
+ }
+ else
+ {
+ continue;
+ }
+ }
+
+ if (hideStart > end)
+ {
+ break;
+ }
+
+ if (hideEnd > end)
+ {
+ hideEnd = end;
+ }
+
+ if (hideStart > hideEnd)
+ {
+ break;
+ }
+ /**
+ * form operations...
+ */
+ if (last < hideStart)
+ {
+ addOperation(CigarArray.M, hideStart - last);
+ }
+ addOperation(CigarArray.D, 1 + hideEnd - hideStart);
+ last = hideEnd + 1;
+ }
+ // Final match if necessary.
+ if (last < end)
+ {
+ addOperation(CigarArray.M, end - last + 1);
+ }
+ }
+ else
+ {
+ addOperation(CigarArray.M, end - start + 1);
+ }
+ }
+
+ /**
+ * @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[] {}; }
+ */
+ /**
+ * applyDeletions edits underlying refCigars to propagate deleted regions, and
+ * removes deletion operations from CigarArray operation list.
+ *
+ * @return int[] position after deletion occured and range of deletion in
+ * cigarArray or null if none occured
+ */
+ public int[] applyDeletions()
+ {
+ java.util.Vector delpos = null;
+ if (length == 0)
+ {
+ return null;
+ }
+ int cursor = 0; // range counter for deletions
+ int vcursor = 0; // visible column index
+ int offset = 0; // shift in visible column index as deletions are made
+ int i = 0;
+ while (i < length)
+ {
+ if (operation[i] != D)
+ {
+ if (operation[i] == M)
+ {
+ cursor += range[i];
+ }
+ vcursor += range[i++];
+ }
+ else
+ {
+ if (delpos == null)
+ {
+ delpos = new java.util.Vector();
+ }
+ int delstart = cursor, delend = cursor + range[i] - 1; // inclusive
+ delpos.addElement(new int[] { vcursor + offset, range[i] }); // index of
+ // right
+ // hand
+ // column
+ // after
+ // hidden region boundary
+ offset += range[i] - 1; // shift in visible column coordinates
+ System.arraycopy(operation, i + 1, operation, i, length - i);
+ System.arraycopy(range, i + 1, range, i, length - i);
+ length--;
+ /*
+ * int dmax=0; for (int s=0; s<refCigars.length; s++) { int d =
+ * refCigars[s].deleteRange(delstart, delend); if (d>dmax) dmax=d; }
+ * offset+=dmax; // shift in visible column coordinates
+ */
+ for (int s = 0; s < refCigars.length; s++)
+ {
+ int d = refCigars[s].deleteRange(delstart, delend);
+ }
+
+ }
+ }
+ if (delpos != null)
+ {
+ int[] pos = new int[delpos.size() * 2];
+ for (int k = 0, l = delpos.size(); k < l; k++)
+ {
+ int[] dr = ((int[]) delpos.elementAt(k));
+ pos[k * 2] = dr[0];
+ pos[k * 2 + 1] = dr[1];
+ delpos.setElementAt(null, k);
+ }
+ delpos = null;
+ return pos;
+ }
+ return null;
+ }
+
+ /**
+ *
+ * @return SeqCigar[] or null if CigarArray is not a SeqCigarArray (ie it does
+ * not resolve to set of seqCigars)
+ */
+ public SeqCigar[] getSeqCigarArray()
+ {
+ if (!isSeqCigarArray())
+ {
+ return null;
+ }
+ SeqCigar[] sa = new SeqCigar[refCigars.length];
+ for (int i = 0; i < refCigars.length; i++)
+ {
+ sa[i] = (SeqCigar) refCigars[i];
+ }
+ return sa;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff