+/*
+ * 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() {
+ /**
+ * 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()
}
/**
- * Apply CIGAR operations to several cigars in parallel
- * will throw an error if any of cigar are actually CigarArrays.
- * @param cigar Cigar[]
+ * 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) {
+ public CigarArray(CigarSimple[] cigars)
+ {
super();
seqcigararray = true;
if (cigars != null && cigars.length > 0)
for (int c = 0; c < cigars.length; c++)
{
refCigars[c] = cigars[c];
- if (! ( (cigars[c] instanceof SeqCigar)
- || cigars[c] instanceof CigarCigar))
+ 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
+ * @param GapChar
+ * char
* @return Object[][]
*/
- protected Object[][] getArrayofSequenceAndDeletions(char GapChar) {
- if (refCigars == null || refCigars.length == 0 || length == 0) {
- return null;
+ 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);
}
- 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;
- }
+ else
+ {
+ sqanddels[c] = null;
}
- return sqanddels;
}
+ 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 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)
+ 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]);
+ 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
+ *
+ * @param GapChar
+ * char
* @return String[]
*/
- public String[] getSequenceStrings(char GapChar) {
+ public String[] getSequenceStrings(char GapChar)
+ {
- if (length==0 || refCigars==null || refCigars.length==0)
+ 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++) {
+ 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 CigarBase[] getEditedCigars() {
+ 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);
+ }
- return new CigarBase[] {};
+ }
+ }
+ 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