X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=b427739ca3fc776c60e42ea6bfcf4549261092a1;hb=HEAD;hp=56d985986b62d6f08f32f0e4c77844a54b4cb17d;hpb=863529ed7d15dd5812cf280d82bfd53734b424a1;p=jalview.git diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java index 56d9859..b427739 100644 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@ -20,16 +20,14 @@ */ package jalview.datamodel; -import jalview.util.Comparison; -import jalview.util.ShiftList; -import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; -import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField; - import java.util.ArrayList; import java.util.BitSet; import java.util.Collections; import java.util.List; -import java.util.Vector; +import java.util.regex.PatternSyntaxException; + +import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; +import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField; /** * Data class holding the selected columns and hidden column ranges for a view. @@ -62,7 +60,7 @@ public class ColumnSelection */ IntList() { - order = new ArrayList(); + order = new ArrayList<>(); _uorder = Collections.unmodifiableList(order); selected = new BitSet(); } @@ -108,7 +106,7 @@ public class ColumnSelection void remove(int col) { - Integer colInt = new Integer(col); + Integer colInt = Integer.valueOf(col); if (selected.get(col)) { @@ -206,7 +204,7 @@ public class ColumnSelection // clear shifted bits and update List of selected columns selected.clear(temp); mask.set(temp - change); - order.set(i, new Integer(temp - change)); + order.set(i, Integer.valueOf(temp - change)); } } // lastly update the bitfield all at once @@ -233,7 +231,7 @@ public class ColumnSelection */ List getRanges() { - List rlist = new ArrayList(); + List rlist = new ArrayList<>(); if (selected.isEmpty()) { return rlist; @@ -266,13 +264,7 @@ 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; + private IntList selection = new IntList(); /** * Add a column to the selection @@ -286,6 +278,27 @@ public class ColumnSelection } /** + * add a series of start,end (inclusive) ranges to the column selection + * + * @param rng + * [start_0, end_0, start_1, end_1, ... ] + * @param baseOne + * - when true, ranges are base 1 and will be mapped to base 0 + */ + public void addRangeOfElements(int[] rng, boolean baseOne) + { + int base = baseOne ? -1 : 0; + for (int c = 0; c < rng.length; c += 2) + { + for (int p = rng[c]; p <= rng[c + 1]; p++) + { + selection.add(base + p); + } + } + + } + + /** * clears column selection */ public void clear() @@ -317,7 +330,7 @@ public class ColumnSelection Integer colInt; for (int i = start; i < end; i++) { - colInt = new Integer(i); + colInt = Integer.valueOf(i); if (selection.contains(colInt)) { selection.remove(colInt); @@ -327,10 +340,12 @@ public class ColumnSelection /** * Returns a read-only view of the (possibly empty) list of selected columns + * (base 1) *

- * The list contains no duplicates but is not necessarily ordered. It also may - * include columns hidden from the current view. To modify (for example sort) - * the list, you should first make a copy. + * The list contains no duplicates but is not necessarily ordered. Columns are + * reported in alignment coordinates (base 1), so may also include columns + * hidden from the current view. To modify (for example sort) the list, you + * should first make a copy. *

* The list is not thread-safe: iterating over it could result in * ConcurrentModificationException if it is modified by another thread. @@ -362,6 +377,22 @@ public class ColumnSelection } /** + * + */ + public boolean intersects(int from, int to) + { + // TODO: do this in a more efficient bitwise way + for (int f = from; f <= to; f++) + { + if (selection.isSelected(f)) + { + return true; + } + } + return false; + } + + /** * Answers true if no columns are selected, else false */ public boolean isEmpty() @@ -397,1429 +428,318 @@ public class ColumnSelection return selection.getMinColumn(); } - /** - * propagate shift in alignment columns to column selection - * - * @param start - * beginning of edit - * @param left - * shift in edit (+ve for removal, or -ve for inserts) - */ - public List compensateForEdit(int start, int change) + public void hideSelectedColumns(AlignmentI al) { - List deletedHiddenColumns = null; - selection.compensateForEdits(start, change); - - if (hiddenColumns != null) + synchronized (selection) { - deletedHiddenColumns = new ArrayList(); - int hSize = hiddenColumns.size(); - for (int i = 0; i < hSize; i++) + for (int[] selregions : selection.getRanges()) { - 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; - } - + al.getHiddenColumns().hideColumns(selregions[0], selregions[1]); } - - this.revealHiddenColumns(0); + selection.clear(); } - return deletedHiddenColumns; } /** - * propagate shift in alignment columns to column selection special version of - * compensateForEdit - allowing for edits within hidden regions + * Hides the specified column and any adjacent selected columns * - * @param start - * beginning of edit - * @param left - * shift in edit (+ve for removal, or -ve for inserts) + * @param res + * int */ - private void compensateForDelEdits(int start, int change) + public void hideSelectedColumns(int col, HiddenColumns hidden) { + /* + * deselect column (whether selected or not!) + */ + removeElement(col); - selection.compensateForEdits(start, change); + /* + * find adjacent selected columns + */ + int min = col - 1, max = col + 1; + while (contains(min)) + { + removeElement(min); + min--; + } - if (hiddenColumns != null) + while (contains(max)) { - 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--); - } + removeElement(max); + max++; + } - if (region[0] < 0) - { - region[0] = 0; - } - if (region[1] < 0) - { - region[1] = 0; - } - } + /* + * min, max are now the closest unselected columns + */ + min++; + max--; + if (min > max) + { + min = max; } + + hidden.hideColumns(min, max); } /** - * Adjust hidden column boundaries based on a series of column additions or - * deletions in visible regions. + * Copy constructor * - * @param shiftrecord - * @return + * @param copy */ - public ShiftList compensateForEdits(ShiftList shiftrecord) + public ColumnSelection(ColumnSelection copy) { - if (shiftrecord != null) + if (copy != null) { - final List shifts = shiftrecord.getShifts(); - if (shifts != null && shifts.size() > 0) - { - int shifted = 0; - 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]; - } - } - return shiftrecord.getInverse(); + selection = new IntList(copy.selection); } - return null; } /** - * removes intersection of position,length ranges in deletions from the - * start,end regions marked in intervals. + * ColumnSelection + */ + public ColumnSelection() + { + } + + /** + * Invert the column selection from first to end-1. leaves hiddenColumns + * untouched (and unselected) * - * @param shifts - * @param intervals - * @return + * @param first + * @param end */ - private boolean pruneIntervalVector(final List shifts, - Vector intervals) + public void invertColumnSelection(int first, int width, AlignmentI al) { - 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 hasHidden = al.getHiddenColumns().hasHiddenColumns(); + for (int i = first; i < width; i++) { - 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 (contains(i)) { - 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; - } + removeElement(i); } - if (!leadinghn) + else { - if (trailinghc) - { - if (trailinghn) - { - hr[1] = sr[0] - 1; - pruned = true; - } - } - else + if (!hasHidden || al.getHiddenColumns().isVisible(i)) { - // sr contained in hr - if (s < t) - { - sr = shifts.get(++s); - } - else - { - s++; - } - continue; + addElement(i); } } } - return pruned; // true if any interval was removed or modified by - // operations. } /** - * remove any hiddenColumns or selected columns and shift remaining based on a - * series of position, range deletions. + * set the selected columns to the given column selection, excluding any + * columns that are hidden. * - * @param deletions + * @param colsel */ - public void pruneDeletions(ShiftList deletions) + public void setElementsFrom(ColumnSelection colsel, + HiddenColumns hiddenColumns) { - if (deletions != null) + selection = new IntList(); + if (colsel.selection != null && colsel.selection.size() > 0) { - final List shifts = deletions.getShifts(); - if (shifts != null && shifts.size() > 0) + if (hiddenColumns.hasHiddenColumns()) { - // delete any intervals intersecting. - if (hiddenColumns != null) + // only select visible columns in this columns selection + for (Integer col : colsel.getSelected()) { - pruneIntervalVector(shifts, hiddenColumns); - if (hiddenColumns != null && hiddenColumns.size() == 0) + if (hiddenColumns != null + && hiddenColumns.isVisible(col.intValue())) { - hiddenColumns = null; + selection.add(col); } } - if (selection != null && selection.size() > 0) + } + else + { + // add everything regardless + for (Integer col : colsel.getSelected()) { - selection.pruneColumnList(shifts); - if (selection != null && selection.size() == 0) - { - selection = null; - } + addElement(col); } - // and shift the rest. - this.compensateForEdits(deletions); } } } /** - * This Method is used to return all the HiddenColumn regions * - * @return empty list or List of hidden column intervals + * @return true if there are columns marked */ - public List getHiddenColumns() + public boolean hasSelectedColumns() { - return hiddenColumns == null ? Collections. emptyList() - : hiddenColumns; + return (selection != null && selection.size() > 0); } /** - * Return absolute column index for a visible column index + * Selects columns where the given annotation matches the provided filter + * condition(s). Any existing column selections are first cleared. Answers the + * number of columns added. * - * @param column - * int column index in alignment view (count from zero) - * @return alignment column index for column + * @param annotations + * @param filterParams + * @return */ - public int adjustForHiddenColumns(int column) + public int filterAnnotations(AlignmentAnnotation ann_row, + AnnotationFilterParameter filterParams) { - int result = column; - if (hiddenColumns != null) + Annotation[] annotations = ann_row.annotations; + // JBPNote - this method needs to be refactored to become independent of + // viewmodel package + this.clear(); + + if (ann_row.graph == AlignmentAnnotation.CONTACT_MAP && (filterParams + .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD + || filterParams + .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD)) { - for (int i = 0; i < hiddenColumns.size(); i++) + float tVal = filterParams.getThresholdValue(); + if (ann_row.sequenceRef != null) { - int[] region = hiddenColumns.elementAt(i); - if (result >= region[0]) + // TODO - get ContactList from AlignmentView for non-seq-ref associatd + for (int column = 0; column < annotations.length; column++) { - result += region[1] - region[0] + 1; + if (ann_row.annotations[column] == null) + { + continue; + } + + int cpos = ann_row.sequenceRef.findPosition(column) - 1; + ContactListI clist = ann_row.sequenceRef + .getContactListFor(ann_row, cpos); + for (int row = column + 8, rowEnd = clist + .getContactHeight(); row < rowEnd; row++) + { + if (filterParams + .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD + ? (clist.getContactAt(row) > tVal) + : (clist.getContactAt(row) < tVal)) + { + addElement(column); + break; + // int column_forrowpos = ann_row.sequenceRef.findIndex(row + 1); + // addElement(column_forrowpos); + } + } } } + return selection.size(); } - 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 addedCount = 0; + int column = 0; + do { - int index = 0; - int[] region; - do + Annotation ann = annotations[column]; + if (ann != null) { - region = hiddenColumns.elementAt(index++); - if (hiddenColumn > region[1]) + float value = ann.value; + boolean matched = false; + + /* + * filter may have multiple conditions - + * these are or'd until a match is found + */ + if (filterParams + .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD + && value > filterParams.getThresholdValue()) { - result -= region[1] + 1 - region[0]; + matched = true; } - } 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) + + if (!matched && filterParams + .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD + && value < filterParams.getThresholdValue()) { - return 0; + matched = true; } - else + + if (!matched && filterParams.isFilterAlphaHelix() + && ann.secondaryStructure == 'H') { - return result - (hiddenColumn - region[0] + 1); + matched = true; } - } - } - 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 findColumnNToLeft(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; + if (!matched && filterParams.isFilterBetaSheet() + && ann.secondaryStructure == 'E') + { + matched = true; + } - // calculate the next gap - region = hiddenColumns.get(index); - gap = start - region[1]; + if (!matched && filterParams.isFilterTurn() + && ann.secondaryStructure == 'S') + { + matched = true; + } - // set start to just to left of current region - nextstart = region[0] - 1; - index--; - } + String regexSearchString = filterParams.getRegexString(); + if (!matched && regexSearchString != null) + { + List fields = filterParams + .getRegexSearchFields(); + for (SearchableAnnotationField field : fields) + { + String compareTo = field == SearchableAnnotationField.DISPLAY_STRING + ? ann.displayCharacter // match 'Label' + : ann.description; // and/or 'Description' + if (compareTo != null) + { + try + { + if (compareTo.matches(regexSearchString)) + { + matched = true; + } + } catch (PatternSyntaxException pse) + { + if (compareTo.equals(regexSearchString)) + { + matched = true; + } + } + if (matched) + { + break; + } + } + } + } - if (distance - gap > 0) - { - // fell out of loop because there are no more hidden regions - distance -= gap; - return nextstart - distance; - } - return start - distance; + if (matched) + { + this.addElement(column); + addedCount++; + } + } + column++; + } while (column < annotations.length); + return addedCount; } /** - * 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 + * Returns a hashCode built from selected columns ranges */ - public int findHiddenRegionPosition(int hiddenRegion) + @Override + public int hashCode() { - 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; + return selection.hashCode(); } /** - * THis method returns the rightmost limit of a region of an alignment with - * hidden columns. In otherwords, the next hidden column. - * - * @param index - * int + * Answers true if comparing to a ColumnSelection with the same selected + * columns and hidden columns, else false */ - public int getHiddenBoundaryRight(int alPos) + @Override + public boolean equals(Object obj) { - if (hiddenColumns != null) + if (!(obj instanceof ColumnSelection)) { - int index = 0; - do - { - int[] region = hiddenColumns.elementAt(index); - if (alPos < region[0]) - { - return region[0]; - } - - index++; - } while (index < hiddenColumns.size()); + return false; } - - 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() - { - synchronized (selection) - { - for (int[] selregions : selection.getRanges()) - { - 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 - * - * @param res - * int - */ - public void hideColumns(int col) - { - /* - * deselect column (whether selected or not!) - */ - removeElement(col); - - /* - * find adjacent selected columns - */ - int min = col - 1, max = col + 1; - while (contains(min)) - { - removeElement(min); - min--; - } - - while (contains(max)) - { - removeElement(max); - max++; - } - - /* - * min, max are now the closest unselected columns - */ - min++; - max--; - if (min > max) - { - min = max; - } - - 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 - * - * @param copy - */ - public ColumnSelection(ColumnSelection copy) - { - 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); - } - } - } - } - } - - /** - * ColumnSelection - */ - public 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 - * untouched (and unselected) - * - * @param first - * @param end - */ - public void invertColumnSelection(int first, int width) - { - boolean hasHidden = hiddenColumns != null && hiddenColumns.size() > 0; - for (int i = first; i < width; i++) - { - if (contains(i)) - { - removeElement(i); - } - else - { - if (!hasHidden || isVisible(i)) - { - addElement(i); - } - } - } - } - - /** - * add in any unselected columns from the given column selection, excluding - * any that are hidden. - * - * @param colsel - */ - public void addElementsFrom(ColumnSelection colsel) - { - if (colsel != null && !colsel.isEmpty()) - { - for (Integer col : colsel.getSelected()) - { - if (hiddenColumns != null && isVisible(col.intValue())) - { - selection.add(col); - } - } - } - } - - /** - * set the selected columns the given column selection, excluding any columns - * that are hidden. - * - * @param colsel - */ - public void setElementsFrom(ColumnSelection colsel) - { - selection = new IntList(); - if (colsel.selection != null && colsel.selection.size() > 0) - { - if (hiddenColumns != null && hiddenColumns.size() > 0) - { - // only select visible columns in this columns selection - addElementsFrom(colsel); - } - else - { - // add everything regardless - for (Integer col : colsel.getSelected()) - { - addElement(col); - } - } - } - } - - /** - * Add gaps into the sequences aligned to profileseq under the given - * AlignmentView - * - * @param profileseq - * @param al - * - alignment to have gaps inserted into it - * @param input - * - alignment view where sequence corresponding to profileseq is - * first entry - * @return new Column selection for new alignment view, with insertions into - * profileseq marked as hidden. - */ - public static ColumnSelection propagateInsertions(SequenceI profileseq, - AlignmentI al, AlignmentView input) - { - int profsqpos = 0; - - // return propagateInsertions(profileseq, al, ) - char gc = al.getGapCharacter(); - Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc); - ColumnSelection nview = (ColumnSelection) alandcolsel[1]; - SequenceI origseq = ((SequenceI[]) alandcolsel[0])[profsqpos]; - nview.propagateInsertions(profileseq, al, origseq); - return nview; - } - - /** - * - * @param profileseq - * - sequence in al which corresponds to origseq - * @param al - * - alignment which is to have gaps inserted into it - * @param origseq - * - sequence corresponding to profileseq which defines gap map for - * modifying al - */ - public 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 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) - { - if (viscontigs[v] > spos) - { - StringBuffer sb = new StringBuffer(); - for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++) - { - sb.append(gc); - } - for (int s = 0, ns = al.getHeight(); s < ns; s++) - { - SequenceI sqobj = al.getSequenceAt(s); - if (sqobj != profileseq) - { - String sq = al.getSequenceAt(s).getSequenceAsString(); - if (sq.length() <= spos + offset) - { - // pad sequence - int diff = spos + offset - sq.length() - 1; - if (diff > 0) - { - // pad gaps - sq = sq + sb; - while ((diff = spos + offset - sq.length() - 1) > 0) - { - // sq = sq - // + ((diff >= sb.length()) ? sb.toString() : sb - // .substring(0, diff)); - if (diff >= sb.length()) - { - sq += sb.toString(); - } - else - { - char[] buf = new char[diff]; - sb.getChars(0, diff, buf, 0); - sq += buf.toString(); - } - } - } - sq += sb.toString(); - } - else - { - al.getSequenceAt(s).setSequence( - sq.substring(0, spos + offset) + sb.toString() - + sq.substring(spos + offset)); - } - } - } - // offset+=sb.length(); - } - spos = viscontigs[v + 1] + 1; - } - if ((offset + spos) < profileseq.getLength()) - { - // pad the final region with gaps. - StringBuffer sb = new StringBuffer(); - for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++) - { - sb.append(gc); - } - for (int s = 0, ns = al.getHeight(); s < ns; s++) - { - SequenceI sqobj = al.getSequenceAt(s); - if (sqobj == profileseq) - { - continue; - } - String sq = sqobj.getSequenceAsString(); - // pad sequence - int diff = origseq.getLength() - sq.length(); - while (diff > 0) - { - // sq = sq - // + ((diff >= sb.length()) ? sb.toString() : sb - // .substring(0, diff)); - if (diff >= sb.length()) - { - sq += sb.toString(); - } - else - { - char[] buf = new char[diff]; - sb.getChars(0, diff, buf, 0); - sq += buf.toString(); - } - diff = origseq.getLength() - sq.length(); - } - } - } - } - - /** - * - * @return true if there are columns marked - */ - public boolean hasSelectedColumns() - { - 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(); - this.clear(); - int count = 0; - do - { - if (annotations[count] != null) - { - - boolean itemMatched = false; - - if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD - && annotations[count].value >= filterParams - .getThresholdValue()) - { - itemMatched = true; - } - if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD - && annotations[count].value <= filterParams - .getThresholdValue()) - { - itemMatched = true; - } - - if (filterParams.isFilterAlphaHelix() - && annotations[count].secondaryStructure == 'H') - { - itemMatched = true; - } - - if (filterParams.isFilterBetaSheet() - && annotations[count].secondaryStructure == 'E') - { - itemMatched = true; - } - - if (filterParams.isFilterTurn() - && annotations[count].secondaryStructure == 'S') - { - itemMatched = true; - } - - String regexSearchString = filterParams.getRegexString(); - if (regexSearchString != null - && !filterParams.getRegexSearchFields().isEmpty()) - { - List fields = filterParams - .getRegexSearchFields(); - try - { - if (fields.contains(SearchableAnnotationField.DISPLAY_STRING) - && annotations[count].displayCharacter - .matches(regexSearchString)) - { - itemMatched = true; - } - } catch (java.util.regex.PatternSyntaxException pse) - { - if (annotations[count].displayCharacter - .equals(regexSearchString)) - { - itemMatched = true; - } - } - if (fields.contains(SearchableAnnotationField.DESCRIPTION) - && annotations[count].description != null - && annotations[count].description - .matches(regexSearchString)) - { - itemMatched = true; - } - } - - if (itemMatched) - { - this.addElement(count); - } - } - count++; - } while (count < annotations.length); - return false; - } - - /** - * Returns a hashCode built from selected columns and hidden column ranges - */ - @Override - 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; - } - - /** - * Answers true if comparing to a ColumnSelection with the same selected - * columns and hidden columns, else false - */ - @Override - public boolean equals(Object obj) - { - if (!(obj instanceof ColumnSelection)) - { - return false; - } - ColumnSelection that = (ColumnSelection) obj; + ColumnSelection that = (ColumnSelection) obj; /* * check columns selected are either both null, or match @@ -1836,27 +756,6 @@ 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; } @@ -1879,8 +778,8 @@ public class ColumnSelection * * @return */ - public boolean markColumns(BitSet markedColumns, int startCol, - int endCol, boolean invert, boolean extendCurrent, boolean toggle) + public boolean markColumns(BitSet markedColumns, int startCol, int endCol, + boolean invert, boolean extendCurrent, boolean toggle) { boolean changed = false; if (!extendCurrent && !toggle)