*/
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.
*/
IntList()
{
- order = new ArrayList<Integer>();
+ order = new ArrayList<>();
_uorder = Collections.unmodifiableList(order);
selected = new BitSet();
}
void remove(int col)
{
- Integer colInt = new Integer(col);
+ Integer colInt = Integer.valueOf(col);
if (selected.get(col))
{
// 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
*/
List<int[]> getRanges()
{
- List<int[]> rlist = new ArrayList<int[]>();
+ List<int[]> rlist = new ArrayList<>();
if (selected.isEmpty())
{
return rlist;
}
}
- IntList selection = new IntList();
-
- /*
- * list of hidden column [start, end] ranges; the list is maintained in
- * ascending start column order
- */
- Vector<int[]> hiddenColumns;
+ private IntList selection = new IntList();
/**
* Add a column to the selection
}
/**
+ * 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()
Integer colInt;
for (int i = start; i < end; i++)
{
- colInt = new Integer(i);
+ colInt = Integer.valueOf(i);
if (selection.contains(colInt))
{
selection.remove(colInt);
/**
* Returns a read-only view of the (possibly empty) list of selected columns
+ * (base 1)
* <p>
- * 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.
* <p>
* The list is not thread-safe: iterating over it could result in
* ConcurrentModificationException if it is modified by another thread.
}
/**
+ *
+ */
+ 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()
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<int[]> compensateForEdit(int start, int change)
+ public void hideSelectedColumns(AlignmentI al)
{
- List<int[]> deletedHiddenColumns = null;
- selection.compensateForEdits(start, change);
-
- if (hiddenColumns != null)
+ synchronized (selection)
{
- deletedHiddenColumns = new ArrayList<int[]>();
- 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<int[]> 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<int[]> shifts,
- Vector<int[]> 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<int[]> 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<int[]> getHiddenColumns()
+ public boolean hasSelectedColumns()
{
- return hiddenColumns == null ? Collections.<int[]> 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<SearchableAnnotationField> 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<int[]>();
- }
-
- /*
- * 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<int[]>(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<int[]> 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<end
- */
- public int[] getVisibleContigs(int start, int end)
- {
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- List<int[]> visiblecontigs = new ArrayList<int[]>();
- List<int[]> 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<int[]> 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<Annotation[]> annels = new Vector<Annotation[]>();
- Annotation[] els = null;
- List<int[]> 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<int[]> 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<SearchableAnnotationField> 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
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
*/
- 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)
git://source.jalview.org / jalview.git / blobdiff