X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FCigarArray.java;h=17e9ea6fc65e17faad9b7f76656fa0f1a30cdf68;hb=0ae965fc73680bdc69b06986c060ff17342c4787;hp=6fef9a41527181cce7fe7bd239d34a3c469aff8d;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index 6fef9a4..17e9ea6 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -1,252 +1,391 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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 .
- */
-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[] {}; }
- */
- /**
- * 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; sdmax) 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;
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import java.util.Iterator;
+
+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, HiddenColumns hidden,
+ SequenceGroup selectionGroup)
+ {
+ this(constructSeqCigarArray(alignment, selectionGroup));
+ constructFromAlignment(alignment, hidden, 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,
+ HiddenColumns hidden, SequenceGroup selectionGroup)
+ {
+ int[] _startend = _calcStartEndBounds(alignment, selectionGroup);
+ int start = _startend[1];
+ int end = _startend[2];
+ // now construct the CigarArray operations
+ if (hidden != null)
+ {
+ int[] region;
+ int hideStart;
+ int hideEnd;
+ int last = start;
+
+ Iterator regions = hidden.getBoundedIterator(start, end);
+ while (regions.hasNext())
+ {
+ region = regions.next();
+ hideStart = region[0];
+ hideEnd = region[1];
+
+ // truncate region at start if last falls in region
+ if ((hideStart < last) && (hideEnd >= last))
+ {
+ hideStart = last;
+ }
+
+ // truncate region at end if end falls in region
+ if (hideEnd > end) // already checked that hideStart<=end
+ {
+ hideEnd = end;
+ }
+
+ /**
+ * 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 CigarBase.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; sdmax) 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;
+ }
+}