X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=4d69fa4ef3ea1355c83ca89ffe2454d9c4ed20d2;hb=460c037bef9ec113c2a46010c443d85e73347592;hp=97bc5a3b7e3a62edff41d05e9a6fdab98591c1cc;hpb=6d183feafe3e566501af586286bbd1d2107ee5a9;p=jalview.git diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java index 97bc5a3..4d69fa4 100644 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@ -20,7 +20,6 @@ */ package jalview.datamodel; -import jalview.util.Comparison; import jalview.util.ShiftList; import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField; @@ -29,7 +28,6 @@ import java.util.ArrayList; import java.util.BitSet; import java.util.Collections; import java.util.List; -import java.util.Vector; /** * Data class holding the selected columns and hidden column ranges for a view. @@ -268,11 +266,7 @@ public class ColumnSelection IntList selection = new IntList(); - /* - * list of hidden column [start, end] ranges; the list is maintained in - * ascending start column order - */ - Vector hiddenColumns; + HiddenColumns hiddenColumns = new HiddenColumns(); /** * Add a column to the selection @@ -405,47 +399,12 @@ public class ColumnSelection * @param left * shift in edit (+ve for removal, or -ve for inserts) */ - public List compensateForEdit(int start, int change) - { - List deletedHiddenColumns = null; - selection.compensateForEdits(start, change); - - if (hiddenColumns != null) + /* public List compensateForEdit(int start, int change) { - deletedHiddenColumns = new ArrayList(); - int hSize = hiddenColumns.size(); - for (int i = 0; i < hSize; i++) - { - int[] region = hiddenColumns.elementAt(i); - if (region[0] > start && start + change > region[1]) - { - deletedHiddenColumns.add(region); - - hiddenColumns.removeElementAt(i); - i--; - hSize--; - continue; - } - - if (region[0] > start) - { - region[0] -= change; - region[1] -= change; - } - - if (region[0] < 0) - { - region[0] = 0; - } - - } - - this.revealHiddenColumns(0); + selection.compensateForEdits(start, change); + return hiddenColumns.compensateForEdit(start, change, this); } - - return deletedHiddenColumns; - } - + */ /** * propagate shift in alignment columns to column selection special version of * compensateForEdit - allowing for edits within hidden regions @@ -457,37 +416,8 @@ public class ColumnSelection */ private void compensateForDelEdits(int start, int change) { - selection.compensateForEdits(start, change); - - if (hiddenColumns != null) - { - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = hiddenColumns.elementAt(i); - if (region[0] >= start) - { - region[0] -= change; - } - if (region[1] >= start) - { - region[1] -= change; - } - if (region[1] < region[0]) - { - hiddenColumns.removeElementAt(i--); - } - - if (region[0] < 0) - { - region[0] = 0; - } - if (region[1] < 0) - { - region[1] = 0; - } - } - } + hiddenColumns.compensateForDelEdits(start, change); } /** @@ -497,7 +427,7 @@ public class ColumnSelection * @param shiftrecord * @return */ - public ShiftList compensateForEdits(ShiftList shiftrecord) + private ShiftList compensateForEdits(ShiftList shiftrecord) { if (shiftrecord != null) { @@ -508,7 +438,6 @@ public class ColumnSelection for (int i = 0, j = shifts.size(); i < j; i++) { int[] sh = shifts.get(i); - // compensateForEdit(shifted+sh[0], sh[1]); compensateForDelEdits(shifted + sh[0], sh[1]); shifted -= sh[1]; } @@ -518,100 +447,6 @@ public class ColumnSelection return null; } - /** - * removes intersection of position,length ranges in deletions from the - * start,end regions marked in intervals. - * - * @param shifts - * @param intervals - * @return - */ - private boolean pruneIntervalVector(final List shifts, - Vector intervals) - { - boolean pruned = false; - int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1; - int hr[] = intervals.elementAt(i); - int sr[] = shifts.get(s); - while (i <= j && s <= t) - { - boolean trailinghn = hr[1] >= sr[0]; - if (!trailinghn) - { - if (i < j) - { - hr = intervals.elementAt(++i); - } - else - { - i++; - } - continue; - } - int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert - if (endshift < hr[0] || endshift < sr[0]) - { // leadinghc disjoint or not a deletion - if (s < t) - { - sr = shifts.get(++s); - } - else - { - s++; - } - continue; - } - boolean leadinghn = hr[0] >= sr[0]; - boolean leadinghc = hr[0] < endshift; - boolean trailinghc = hr[1] < endshift; - if (leadinghn) - { - if (trailinghc) - { // deleted hidden region. - intervals.removeElementAt(i); - pruned = true; - j--; - if (i <= j) - { - hr = intervals.elementAt(i); - } - continue; - } - if (leadinghc) - { - hr[0] = endshift; // clip c terminal region - leadinghn = !leadinghn; - pruned = true; - } - } - if (!leadinghn) - { - if (trailinghc) - { - if (trailinghn) - { - hr[1] = sr[0] - 1; - pruned = true; - } - } - else - { - // sr contained in hr - if (s < t) - { - sr = shifts.get(++s); - } - else - { - s++; - } - continue; - } - } - } - return pruned; // true if any interval was removed or modified by - // operations. - } /** * remove any hiddenColumns or selected columns and shift remaining based on a @@ -619,22 +454,15 @@ public class ColumnSelection * * @param deletions */ - public void pruneDeletions(ShiftList deletions) + private void pruneDeletions(ShiftList deletions) { if (deletions != null) { final List shifts = deletions.getShifts(); if (shifts != null && shifts.size() > 0) { - // delete any intervals intersecting. - if (hiddenColumns != null) - { - pruneIntervalVector(shifts, hiddenColumns); - if (hiddenColumns != null && hiddenColumns.size() == 0) - { - hiddenColumns = null; - } - } + hiddenColumns.pruneDeletions(shifts); + if (selection != null && selection.size() > 0) { selection.pruneColumnList(shifts); @@ -649,353 +477,20 @@ public class ColumnSelection } } - /** - * This Method is used to return all the HiddenColumn regions - * - * @return empty list or List of hidden column intervals - */ - public List getHiddenColumns() - { - return hiddenColumns == null ? Collections. emptyList() - : hiddenColumns; - } - /** - * Return absolute column index for a visible column index - * - * @param column - * int column index in alignment view (count from zero) - * @return alignment column index for column - */ - public int adjustForHiddenColumns(int column) - { - int result = column; - if (hiddenColumns != null) - { - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = hiddenColumns.elementAt(i); - if (result >= region[0]) - { - result += region[1] - region[0] + 1; - } - } - } - return result; - } - - /** - * Use this method to find out where a column will appear in the visible - * alignment when hidden columns exist. If the column is not visible, then the - * left-most visible column will always be returned. - * - * @param hiddenColumn - * the column index in the full alignment including hidden columns - * @return the position of the column in the visible alignment - */ - public int findColumnPosition(int hiddenColumn) - { - int result = hiddenColumn; - if (hiddenColumns != null) - { - int index = 0; - int[] region; - do - { - region = hiddenColumns.elementAt(index++); - if (hiddenColumn > region[1]) - { - result -= region[1] + 1 - region[0]; - } - } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size())); - - if (hiddenColumn >= region[0] && hiddenColumn <= region[1]) - { - // Here the hidden column is within a region, so - // we want to return the position of region[0]-1, adjusted for any - // earlier hidden columns. - // Calculate the difference between the actual hidden col position - // and region[0]-1, and then subtract from result to convert result from - // the adjusted hiddenColumn value to the adjusted region[0]-1 value - - // However, if the region begins at 0 we cannot return region[0]-1 - // just return 0 - if (region[0] == 0) - { - return 0; - } - else - { - return result - (hiddenColumn - region[0] + 1); - } - } - } - return result; // return the shifted position after removing hidden columns. - } - - /** - * Find the visible column which is a given visible number of columns to the - * left of another visible column. i.e. for a startColumn x, the column which - * is distance 1 away will be column x-1. - * - * @param visibleDistance - * the number of visible columns to offset by - * @param startColumn - * the column to start from - * @return the position of the column in the visible alignment - */ - public int subtractVisibleColumns(int visibleDistance, int startColumn) - { - int distance = visibleDistance; - - // in case startColumn is in a hidden region, move it to the left - int start = adjustForHiddenColumns(findColumnPosition(startColumn)); - - // get index of hidden region to left of start - int index = getHiddenIndexLeft(start); - if (index == -1) - { - // no hidden regions to left of startColumn - return start - distance; - } - - // walk backwards through the alignment subtracting the counts of visible - // columns from distance - int[] region; - int gap = 0; - int nextstart = start; - - while ((index > -1) && (distance - gap > 0)) - { - // subtract the gap to right of region from distance - distance -= gap; - start = nextstart; - - // calculate the next gap - region = hiddenColumns.get(index); - gap = start - region[1]; - - // set start to just to left of current region - nextstart = region[0] - 1; - index--; - } - - if (distance - gap > 0) - { - // fell out of loop because there are no more hidden regions - distance -= gap; - return nextstart - distance; - } - return start - distance; - - } - - /** - * Use this method to determine where the next hiddenRegion starts - * - * @param hiddenRegion - * index of hidden region (counts from 0) - * @return column number in visible view - */ - public int findHiddenRegionPosition(int hiddenRegion) - { - int result = 0; - if (hiddenColumns != null) - { - int index = 0; - int gaps = 0; - do - { - int[] region = hiddenColumns.elementAt(index); - if (hiddenRegion == 0) - { - return region[0]; - } - - gaps += region[1] + 1 - region[0]; - result = region[1] + 1; - index++; - } while (index <= hiddenRegion); - - result -= gaps; - } - - return result; - } - - /** - * THis method returns the rightmost limit of a region of an alignment with - * hidden columns. In otherwords, the next hidden column. - * - * @param index - * int - */ - public int getHiddenBoundaryRight(int alPos) - { - if (hiddenColumns != null) - { - int index = 0; - do - { - int[] region = hiddenColumns.elementAt(index); - if (alPos < region[0]) - { - return region[0]; - } - - index++; - } while (index < hiddenColumns.size()); - } - - return alPos; - - } - - /** - * This method returns the leftmost limit of a region of an alignment with - * hidden columns. In otherwords, the previous hidden column. - * - * @param index - * int - */ - public int getHiddenBoundaryLeft(int alPos) - { - if (hiddenColumns != null) - { - int index = hiddenColumns.size() - 1; - do - { - int[] region = hiddenColumns.elementAt(index); - if (alPos > region[1]) - { - return region[1]; - } - - index--; - } while (index > -1); - } - - return alPos; - - } - - /** - * This method returns the index of the hidden region to the left of a column - * position. If the column is in a hidden region it returns the index of the - * region to the left. If there is no hidden region to the left it returns -1. - * - * @param pos - * int - */ - private int getHiddenIndexLeft(int pos) - { - if (hiddenColumns != null) - { - int index = hiddenColumns.size() - 1; - do - { - int[] region = hiddenColumns.elementAt(index); - if (pos > region[1]) - { - return index; - } - - index--; - } while (index > -1); - } - - return -1; - - } - - public void hideSelectedColumns() + public void hideSelectedColumns(AlignmentI al) { synchronized (selection) { for (int[] selregions : selection.getRanges()) { - hideColumns(selregions[0], selregions[1]); + al.getHiddenColumns().hideColumns(selregions[0], selregions[1]); } selection.clear(); } } - /** - * Adds the specified column range to the hidden columns - * - * @param start - * @param end - */ - public void hideColumns(int start, int end) - { - if (hiddenColumns == null) - { - hiddenColumns = new Vector(); - } - - /* - * traverse existing hidden ranges and insert / amend / append as - * appropriate - */ - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = hiddenColumns.elementAt(i); - - if (end < region[0] - 1) - { - /* - * insert discontiguous preceding range - */ - hiddenColumns.insertElementAt(new int[] { start, end }, i); - return; - } - - if (end <= region[1]) - { - /* - * new range overlaps existing, or is contiguous preceding it - adjust - * start column - */ - region[0] = Math.min(region[0], start); - return; - } - - if (start <= region[1] + 1) - { - /* - * new range overlaps existing, or is contiguous following it - adjust - * start and end columns - */ - region[0] = Math.min(region[0], start); - region[1] = Math.max(region[1], end); - - /* - * also update or remove any subsequent ranges - * that are overlapped - */ - while (i < hiddenColumns.size() - 1) - { - int[] nextRegion = hiddenColumns.get(i + 1); - if (nextRegion[0] > end + 1) - { - /* - * gap to next hidden range - no more to update - */ - break; - } - region[1] = Math.max(nextRegion[1], end); - hiddenColumns.remove(i + 1); - } - return; - } - } - - /* - * remaining case is that the new range follows everything else - */ - hiddenColumns.addElement(new int[] { start, end }); - } /** * Hides the specified column and any adjacent selected columns @@ -1003,7 +498,7 @@ public class ColumnSelection * @param res * int */ - public void hideColumns(int col) + public void hideSelectedColumns(int col, HiddenColumns hidden) { /* * deselect column (whether selected or not!) @@ -1036,72 +531,12 @@ public class ColumnSelection min = max; } - hideColumns(min, max); + hidden.hideColumns(min, max); } - /** - * Unhides, and adds to the selection list, all hidden columns - */ - public void revealAllHiddenColumns() - { - if (hiddenColumns != null) - { - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = hiddenColumns.elementAt(i); - for (int j = region[0]; j < region[1] + 1; j++) - { - addElement(j); - } - } - } - - hiddenColumns = null; - } - - /** - * Reveals, and marks as selected, the hidden column range with the given - * start column - * - * @param start - */ - public void revealHiddenColumns(int start) - { - for (int i = 0; i < hiddenColumns.size(); i++) - { - int[] region = hiddenColumns.elementAt(i); - if (start == region[0]) - { - for (int j = region[0]; j < region[1] + 1; j++) - { - addElement(j); - } - hiddenColumns.removeElement(region); - break; - } - } - if (hiddenColumns.size() == 0) - { - hiddenColumns = null; - } - } - public boolean isVisible(int column) - { - if (hiddenColumns != null) - { - for (int[] region : hiddenColumns) - { - if (column >= region[0] && column <= region[1]) - { - return false; - } - } - } - return true; - } /** * Copy constructor @@ -1113,21 +548,6 @@ public class ColumnSelection if (copy != null) { selection = new IntList(copy.selection); - if (copy.hiddenColumns != null) - { - hiddenColumns = new Vector(copy.hiddenColumns.size()); - for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++) - { - int[] rh, cp; - rh = copy.hiddenColumns.elementAt(i); - if (rh != null) - { - cp = new int[rh.length]; - System.arraycopy(rh, 0, cp, 0, rh.length); - hiddenColumns.addElement(cp); - } - } - } } } @@ -1138,312 +558,10 @@ public class ColumnSelection { } - public String[] getVisibleSequenceStrings(int start, int end, - SequenceI[] seqs) - { - int i, iSize = seqs.length; - String selections[] = new String[iSize]; - if (hiddenColumns != null && hiddenColumns.size() > 0) - { - for (i = 0; i < iSize; i++) - { - StringBuffer visibleSeq = new StringBuffer(); - List regions = getHiddenColumns(); - - int blockStart = start, blockEnd = end; - int[] region; - int hideStart, hideEnd; - - for (int j = 0; j < regions.size(); j++) - { - region = regions.get(j); - hideStart = region[0]; - hideEnd = region[1]; - - if (hideStart < start) - { - continue; - } - - blockStart = Math.min(blockStart, hideEnd + 1); - blockEnd = Math.min(blockEnd, hideStart); - - if (blockStart > blockEnd) - { - break; - } - - visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd)); - - blockStart = hideEnd + 1; - blockEnd = end; - } - - if (end > blockStart) - { - visibleSeq.append(seqs[i].getSequence(blockStart, end)); - } - - selections[i] = visibleSeq.toString(); - } - } - else - { - for (i = 0; i < iSize; i++) - { - selections[i] = seqs[i].getSequenceAsString(start, end); - } - } - - return selections; - } - - /** - * return all visible segments between the given start and end boundaries - * - * @param start - * (first column inclusive from 0) - * @param end - * (last column - not inclusive) - * @return int[] {i_start, i_end, ..} where intervals lie in - * start<=i_start<=i_end 0) - { - List visiblecontigs = new ArrayList(); - List regions = getHiddenColumns(); - - int vstart = start; - int[] region; - int hideStart, hideEnd; - - for (int j = 0; vstart < end && j < regions.size(); j++) - { - region = regions.get(j); - hideStart = region[0]; - hideEnd = region[1]; - - if (hideEnd < vstart) - { - continue; - } - if (hideStart > vstart) - { - visiblecontigs.add(new int[] { vstart, hideStart - 1 }); - } - vstart = hideEnd + 1; - } - - if (vstart < end) - { - visiblecontigs.add(new int[] { vstart, end - 1 }); - } - int[] vcontigs = new int[visiblecontigs.size() * 2]; - for (int i = 0, j = visiblecontigs.size(); i < j; i++) - { - int[] vc = visiblecontigs.get(i); - visiblecontigs.set(i, null); - vcontigs[i * 2] = vc[0]; - vcontigs[i * 2 + 1] = vc[1]; - } - visiblecontigs.clear(); - return vcontigs; - } - else - { - return new int[] { start, end - 1 }; - } - } - - /** - * Locate the first and last position visible for this sequence. if seq isn't - * visible then return the position of the left and right of the hidden - * boundary region, and the corresponding alignment column indices for the - * extent of the sequence - * - * @param seq - * @return int[] { visible start, visible end, first seqpos, last seqpos, - * alignment index for seq start, alignment index for seq end } - */ - public int[] locateVisibleBoundsOfSequence(SequenceI seq) - { - int fpos = seq.getStart(), lpos = seq.getEnd(); - int start = 0; - - if (hiddenColumns == null || hiddenColumns.size() == 0) - { - int ifpos = seq.findIndex(fpos) - 1, ilpos = seq.findIndex(lpos) - 1; - return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos }; - } - - // Simply walk along the sequence whilst watching for hidden column - // boundaries - List regions = getHiddenColumns(); - int spos = fpos, lastvispos = -1, rcount = 0, hideStart = seq - .getLength(), hideEnd = -1; - int visPrev = 0, visNext = 0, firstP = -1, lastP = -1; - boolean foundStart = false; - for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd() - && p < pLen; p++) - { - if (!Comparison.isGap(seq.getCharAt(p))) - { - // keep track of first/last column - // containing sequence data regardless of visibility - if (firstP == -1) - { - firstP = p; - } - lastP = p; - // update hidden region start/end - while (hideEnd < p && rcount < regions.size()) - { - int[] region = regions.get(rcount++); - visPrev = visNext; - visNext += region[0] - visPrev; - hideStart = region[0]; - hideEnd = region[1]; - } - if (hideEnd < p) - { - hideStart = seq.getLength(); - } - // update visible boundary for sequence - if (p < hideStart) - { - if (!foundStart) - { - fpos = spos; - start = p; - foundStart = true; - } - lastvispos = p; - lpos = spos; - } - // look for next sequence position - spos++; - } - } - if (foundStart) - { - return new int[] { findColumnPosition(start), - findColumnPosition(lastvispos), fpos, lpos, firstP, lastP }; - } - // otherwise, sequence was completely hidden - return new int[] { visPrev, visNext, 0, 0, firstP, lastP }; - } - - /** - * delete any columns in alignmentAnnotation that are hidden (including - * sequence associated annotation). - * - * @param alignmentAnnotation - */ - public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation) - { - makeVisibleAnnotation(-1, -1, alignmentAnnotation); - } - - /** - * delete any columns in alignmentAnnotation that are hidden (including - * sequence associated annotation). - * - * @param start - * remove any annotation to the right of this column - * @param end - * remove any annotation to the left of this column - * @param alignmentAnnotation - * the annotation to operate on - */ - public void makeVisibleAnnotation(int start, int end, - AlignmentAnnotation alignmentAnnotation) - { - if (alignmentAnnotation.annotations == null) - { - return; - } - if (start == end && end == -1) - { - start = 0; - end = alignmentAnnotation.annotations.length; - } - if (hiddenColumns != null && hiddenColumns.size() > 0) - { - // then mangle the alignmentAnnotation annotation array - Vector annels = new Vector(); - Annotation[] els = null; - List regions = getHiddenColumns(); - int blockStart = start, blockEnd = end; - int[] region; - int hideStart, hideEnd, w = 0; - - for (int j = 0; j < regions.size(); j++) - { - region = regions.get(j); - hideStart = region[0]; - hideEnd = region[1]; - - if (hideStart < start) - { - continue; - } - - blockStart = Math.min(blockStart, hideEnd + 1); - blockEnd = Math.min(blockEnd, hideStart); - - if (blockStart > blockEnd) - { - break; - } - annels.addElement(els = new Annotation[blockEnd - blockStart]); - System.arraycopy(alignmentAnnotation.annotations, blockStart, els, - 0, els.length); - w += els.length; - blockStart = hideEnd + 1; - blockEnd = end; - } - if (end > blockStart) - { - annels.addElement(els = new Annotation[end - blockStart + 1]); - if ((els.length + blockStart) <= alignmentAnnotation.annotations.length) - { - // copy just the visible segment of the annotation row - System.arraycopy(alignmentAnnotation.annotations, blockStart, - els, 0, els.length); - } - else - { - // copy to the end of the annotation row - System.arraycopy(alignmentAnnotation.annotations, blockStart, - els, 0, - (alignmentAnnotation.annotations.length - blockStart)); - } - w += els.length; - } - if (w == 0) - { - return; - } - alignmentAnnotation.annotations = new Annotation[w]; - w = 0; - for (Annotation[] chnk : annels) - { - System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, - chnk.length); - w += chnk.length; - } - } - else - { - alignmentAnnotation.restrict(start, end); - } - } /** * Invert the column selection from first to end-1. leaves hiddenColumns @@ -1452,9 +570,9 @@ public class ColumnSelection * @param first * @param end */ - public void invertColumnSelection(int first, int width) + public void invertColumnSelection(int first, int width, AlignmentI al) { - boolean hasHidden = hiddenColumns != null && hiddenColumns.size() > 0; + boolean hasHidden = al.getHiddenColumns().hasHidden(); for (int i = first; i < width; i++) { if (contains(i)) @@ -1463,7 +581,7 @@ public class ColumnSelection } else { - if (!hasHidden || isVisible(i)) + if (!hasHidden || al.getHiddenColumns().isVisible(i)) { addElement(i); } @@ -1483,7 +601,8 @@ public class ColumnSelection { for (Integer col : colsel.getSelected()) { - if (hiddenColumns != null && isVisible(col.intValue())) + if (hiddenColumns != null + && hiddenColumns.isVisible(col.intValue())) { selection.add(col); } @@ -1502,7 +621,7 @@ public class ColumnSelection selection = new IntList(); if (colsel.selection != null && colsel.selection.size() > 0) { - if (hiddenColumns != null && hiddenColumns.size() > 0) + if (hiddenColumns.hasHidden()) { // only select visible columns in this columns selection addElementsFrom(colsel); @@ -1538,7 +657,7 @@ public class ColumnSelection // return propagateInsertions(profileseq, al, ) char gc = al.getGapCharacter(); - Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc); + Object[] alandcolsel = input.getAlignmentAndHiddenColumns(gc); ColumnSelection nview = (ColumnSelection) alandcolsel[1]; SequenceI origseq = ((SequenceI[]) alandcolsel[0])[profsqpos]; nview.propagateInsertions(profileseq, al, origseq); @@ -1555,18 +674,18 @@ public class ColumnSelection * - sequence corresponding to profileseq which defines gap map for * modifying al */ - public void propagateInsertions(SequenceI profileseq, AlignmentI al, + private void propagateInsertions(SequenceI profileseq, AlignmentI al, SequenceI origseq) { char gc = al.getGapCharacter(); // recover mapping between sequence's non-gap positions and positions // mapping to view. pruneDeletions(ShiftList.parseMap(origseq.gapMap())); - int[] viscontigs = getVisibleContigs(0, profileseq.getLength()); + int[] viscontigs = hiddenColumns.getVisibleContigs(0, + profileseq.getLength()); int spos = 0; int offset = 0; - // input.pruneDeletions(ShiftList.parseMap(((SequenceI[]) - // alandcolsel[0])[0].gapMap())) + // add profile to visible contigs for (int v = 0; v < viscontigs.length; v += 2) { @@ -1670,45 +789,14 @@ public class ColumnSelection return (selection != null && selection.size() > 0); } - /** - * - * @return true if there are columns hidden - */ - public boolean hasHiddenColumns() - { - return hiddenColumns != null && hiddenColumns.size() > 0; - } - - /** - * - * @return true if there are more than one set of columns hidden - */ - public boolean hasManyHiddenColumns() - { - return hiddenColumns != null && hiddenColumns.size() > 1; - } - /** - * mark the columns corresponding to gap characters as hidden in the column - * selection - * - * @param sr - */ - public void hideInsertionsFor(SequenceI sr) - { - List inserts = sr.getInsertions(); - for (int[] r : inserts) - { - hideColumns(r[0], r[1]); - } - } public boolean filterAnnotations(Annotation[] annotations, AnnotationFilterParameter filterParams) { // JBPNote - this method needs to be refactored to become independent of // viewmodel package - this.revealAllHiddenColumns(); + hiddenColumns.revealAllHiddenColumns(this); this.clear(); int count = 0; do @@ -1797,15 +885,7 @@ public class ColumnSelection public int hashCode() { int hashCode = selection.hashCode(); - if (hiddenColumns != null) - { - for (int[] hidden : hiddenColumns) - { - hashCode = 31 * hashCode + hidden[0]; - hashCode = 31 * hashCode + hidden[1]; - } - } - return hashCode; + return hiddenColumns.hashCode(hashCode); } /** @@ -1836,28 +916,7 @@ public class ColumnSelection return false; } - /* - * check hidden columns are either both null, or match - */ - if (this.hiddenColumns == null) - { - return (that.hiddenColumns == null); - } - if (that.hiddenColumns == null - || that.hiddenColumns.size() != this.hiddenColumns.size()) - { - return false; - } - int i = 0; - for (int[] thisRange : hiddenColumns) - { - int[] thatRange = that.hiddenColumns.get(i++); - if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1]) - { - return false; - } - } - return true; + return this.hiddenColumns.equals(that.hiddenColumns); } /**