/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import jalview.util.ShiftList;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Collections;
+import java.util.List;
+import java.util.regex.PatternSyntaxException;
-import java.util.*;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
/**
- * NOTE: Columns are zero based.
+ * Data class holding the selected columns and hidden column ranges for a view.
+ * Ranges are base 1.
*/
public class ColumnSelection
{
- Vector selected = new Vector();
+ /**
+ * A class to hold an efficient representation of selected columns
+ */
+ private class IntList
+ {
+ /*
+ * list of selected columns (ordered by selection order, not column order)
+ */
+ private List<Integer> order;
+
+ /*
+ * an unmodifiable view of the selected columns list
+ */
+ private List<Integer> _uorder;
+
+ /**
+ * bitfield for column selection - allows quick lookup
+ */
+ private BitSet selected;
+
+ /**
+ * Constructor
+ */
+ IntList()
+ {
+ order = new ArrayList<>();
+ _uorder = Collections.unmodifiableList(order);
+ selected = new BitSet();
+ }
+
+ /**
+ * Copy constructor
+ *
+ * @param other
+ */
+ IntList(IntList other)
+ {
+ this();
+ if (other != null)
+ {
+ int j = other.size();
+ for (int i = 0; i < j; i++)
+ {
+ add(other.elementAt(i));
+ }
+ }
+ }
+
+ /**
+ * adds a new column i to the selection - only if i is not already selected
+ *
+ * @param i
+ */
+ void add(int i)
+ {
+ if (!selected.get(i))
+ {
+ order.add(Integer.valueOf(i));
+ selected.set(i);
+ }
+ }
+
+ void clear()
+ {
+ order.clear();
+ selected.clear();
+ }
+
+ void remove(int col)
+ {
+
+ Integer colInt = Integer.valueOf(col);
+
+ if (selected.get(col))
+ {
+ // if this ever changes to List.remove(), ensure Integer not int
+ // argument
+ // as List.remove(int i) removes the i'th item which is wrong
+ order.remove(colInt);
+ selected.clear(col);
+ }
+ }
+
+ boolean contains(Integer colInt)
+ {
+ return selected.get(colInt);
+ }
+
+ boolean isEmpty()
+ {
+ return order.isEmpty();
+ }
+
+ /**
+ * Returns a read-only view of the selected columns list
+ *
+ * @return
+ */
+ List<Integer> getList()
+ {
+ return _uorder;
+ }
+
+ int size()
+ {
+ return order.size();
+ }
+
+ /**
+ * gets the column that was selected first, second or i'th
+ *
+ * @param i
+ * @return
+ */
+ int elementAt(int i)
+ {
+ return order.get(i);
+ }
- //Vector of int [] {startCol, endCol}
- Vector hiddenColumns;
+ protected boolean pruneColumnList(final List<int[]> shifts)
+ {
+ int s = 0, t = shifts.size();
+ int[] sr = shifts.get(s++);
+ boolean pruned = false;
+ int i = 0, j = order.size();
+ while (i < j && s <= t)
+ {
+ int c = order.get(i++).intValue();
+ if (sr[0] <= c)
+ {
+ if (sr[1] + sr[0] >= c)
+ { // sr[1] -ve means inseriton.
+ order.remove(--i);
+ selected.clear(c);
+ j--;
+ }
+ else
+ {
+ if (s < t)
+ {
+ sr = shifts.get(s);
+ }
+ s++;
+ }
+ }
+ }
+ return pruned;
+ }
+
+ /**
+ * shift every selected column at or above start by change
+ *
+ * @param start
+ * - leftmost column to be shifted
+ * @param change
+ * - delta for shift
+ */
+ void compensateForEdits(int start, int change)
+ {
+ BitSet mask = new BitSet();
+ for (int i = 0; i < order.size(); i++)
+ {
+ int temp = order.get(i);
+
+ if (temp >= start)
+ {
+ // clear shifted bits and update List of selected columns
+ selected.clear(temp);
+ mask.set(temp - change);
+ order.set(i, Integer.valueOf(temp - change));
+ }
+ }
+ // lastly update the bitfield all at once
+ selected.or(mask);
+ }
+
+ boolean isSelected(int column)
+ {
+ return selected.get(column);
+ }
+
+ int getMaxColumn()
+ {
+ return selected.length() - 1;
+ }
+
+ int getMinColumn()
+ {
+ return selected.get(0) ? 0 : selected.nextSetBit(0);
+ }
+
+ /**
+ * @return a series of selection intervals along the range
+ */
+ List<int[]> getRanges()
+ {
+ List<int[]> rlist = new ArrayList<>();
+ if (selected.isEmpty())
+ {
+ return rlist;
+ }
+ int next = selected.nextSetBit(0), clear = -1;
+ while (next != -1)
+ {
+ clear = selected.nextClearBit(next);
+ rlist.add(new int[] { next, clear - 1 });
+ next = selected.nextSetBit(clear);
+ }
+ return rlist;
+ }
+
+ @Override
+ public int hashCode()
+ {
+ // TODO Auto-generated method stub
+ return selected.hashCode();
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj instanceof IntList)
+ {
+ return ((IntList) obj).selected.equals(selected);
+ }
+ return false;
+ }
+ }
+
+ private IntList selection = new IntList();
/**
* Add a column to the selection
- *
- * @param col index of column
+ *
+ * @param col
+ * index of column
*/
public void addElement(int col)
{
- Integer column = new Integer(col);
- if (!selected.contains(column))
- {
- selected.addElement(column);
- }
+ selection.add(col);
}
/**
*/
public void clear()
{
- selected.removeAllElements();
+ selection.clear();
}
/**
- * removes col from selection
- *
- * @param col index of column to be removed
+ * Removes value 'col' from the selection (not the col'th item)
+ *
+ * @param col
+ * index of column to be removed
*/
public void removeElement(int col)
{
- Integer colInt = new Integer(col);
-
- if (selected.contains(colInt))
- {
- selected.removeElement(colInt);
- }
+ selection.remove(col);
}
/**
* removes a range of columns from the selection
- * @param start int - first column in range to be removed
- * @param end int - last col
+ *
+ * @param start
+ * int - first column in range to be removed
+ * @param end
+ * int - last col
*/
public void removeElements(int start, int end)
{
Integer colInt;
- for(int i=start; i<end; i++)
+ for (int i = start; i < end; i++)
{
- colInt = new Integer(i);
- if (selected.contains(colInt))
+ colInt = Integer.valueOf(i);
+ if (selection.contains(colInt))
{
- selected.removeElement(colInt);
+ selection.remove(colInt);
}
}
}
- /**
- *
- * @return Vector containing selected columns as Integers
- */
- public Vector getSelected()
- {
- return selected;
- }
/**
- *
- * @param col index to search for in column selection
- *
- * @return true if Integer(col) is in selection.
+ * Returns a read-only view of the (possibly empty) list of selected columns
+ * <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.
+ * <p>
+ * The list is not thread-safe: iterating over it could result in
+ * ConcurrentModificationException if it is modified by another thread.
*/
- public boolean contains(int col)
+ public List<Integer> getSelected()
{
- return selected.contains(new Integer(col));
+ return selection.getList();
}
/**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @return list of int arrays containing start and end column position for
+ * runs of selected columns ordered from right to left.
*/
- public int columnAt(int i)
+ public List<int[]> getSelectedRanges()
{
- return ((Integer) selected.elementAt(i)).intValue();
+ return selection.getRanges();
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ *
+ * @param col
+ * index to search for in column selection
+ *
+ * @return true if col is selected
*/
- public int size()
+ public boolean contains(int col)
{
- return selected.size();
+ return (col > -1) ? selection.isSelected(col) : false;
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ *
*/
- public int getMax()
+ public boolean intersects(int from, int to)
{
- int max = -1;
-
- for (int i = 0; i < selected.size(); i++)
+ // TODO: do this in a more efficient bitwise way
+ for (int f = from; f <= to; f++)
{
- if (columnAt(i) > max)
+ if (selection.isSelected(f))
{
- max = columnAt(i);
+ return true;
}
}
-
- return max;
+ return false;
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Answers true if no columns are selected, else false
*/
- public int getMin()
+ public boolean isEmpty()
{
- int min = 1000000000;
+ return selection == null || selection.isEmpty();
+ }
- for (int i = 0; i < selected.size(); i++)
+ /**
+ * rightmost selected column
+ *
+ * @return rightmost column in alignment that is selected
+ */
+ public int getMax()
+ {
+ if (selection.isEmpty())
{
- if (columnAt(i) < min)
- {
- min = columnAt(i);
- }
+ return -1;
}
-
- return min;
+ return selection.getMaxColumn();
}
-
/**
- * 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)
+ * Leftmost column in selection
+ *
+ * @return column index of leftmost column in selection
*/
- public void compensateForEdit(int start, int change)
+ public int getMin()
{
- for (int i = 0; i < size(); i++)
+ if (selection.isEmpty())
{
- int temp = columnAt(i);
-
- if (temp >= start)
- {
- selected.setElementAt(new Integer(temp - change), i);
- }
+ return 1000000000;
}
+ return selection.getMinColumn();
+ }
- if(hiddenColumns!=null)
+ public void hideSelectedColumns(AlignmentI al)
+ {
+ synchronized (selection)
{
- for(int i=0; i<hiddenColumns.size(); i++)
+ for (int[] selregions : selection.getRanges())
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
- if(region[0] > start)
- {
- region[0] -= change;
- region[1] -= change;
- }
- if(region[0]<0)
- region[0] = 0;
- if(region[1] <0)
- region[1] = 0;
+ al.getHiddenColumns().hideColumns(selregions[0], selregions[1]);
}
+ selection.clear();
}
+
}
+
/**
- * propagate shift in alignment columns to column selection
- * special version of compensateForEdit - allowing for edits within hidden regions
- * @param start beginning of edit
- * @param left shift in edit (+ve for removal, or -ve for inserts)
+ * Hides the specified column and any adjacent selected columns
+ *
+ * @param res
+ * int
*/
- private void compensateForDelEdits(int start, int change)
+ public void hideSelectedColumns(int col, HiddenColumns hidden)
{
- for (int i = 0; i < size(); i++)
+ /*
+ * deselect column (whether selected or not!)
+ */
+ removeElement(col);
+
+ /*
+ * find adjacent selected columns
+ */
+ int min = col - 1, max = col + 1;
+ while (contains(min))
{
- int temp = columnAt(i);
-
- if (temp >= start)
- {
- selected.setElementAt(new Integer(temp - change), i);
- }
+ removeElement(min);
+ min--;
}
- if(hiddenColumns!=null)
+ while (contains(max))
{
- for(int i=0; i<hiddenColumns.size(); i++)
- {
- int[] region = (int[]) 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;
- }
- }
- }
- /**
- * Adjust hidden column boundaries based on a series of column
- * additions or deletions in visible regions.
- * @param shiftrecord
- * @return
- */
- public ShiftList compensateForEdits(ShiftList shiftrecord) {
- if (shiftrecord!=null) {
- Vector shifts = shiftrecord.shifts;
- if (shifts!=null && shifts.size()>0) {
- int shifted=0;
- for (int i=0,j=shifts.size(); i<j; i++) {
- int[] sh = (int[]) shifts.elementAt(i);
- //compensateForEdit(shifted+sh[0], sh[1]);
- compensateForDelEdits(shifted+sh[0], sh[1]);
- shifted-=sh[1];
- }
- }
- return shiftrecord.getInverse();
+ removeElement(max);
+ max++;
}
- return null;
- }
- /**
- * removes intersection of position,length ranges in deletions
- * from the start,end regions marked in intervals.
- * @param deletions
- * @param intervals
- * @return
- */
- private boolean pruneIntervalVector(Vector deletions, Vector intervals) {
- boolean pruned=false;
- int i=0,j=intervals.size()-1, s=0, t=deletions.size()-1;
- int hr[]=(int[]) intervals.elementAt(i);
- int sr[]=(int[]) deletions.elementAt(s);
- while (i<=j && s<=t) {
- boolean trailinghn=hr[1]>=sr[0];
- if (!trailinghn) {
- if (i<j)
- hr=(int[]) 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=(int[]) deletions.elementAt(++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=(int[]) 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=(int[]) deletions.elementAt(++s);
- else
- s++;
- continue;
- }
- }
- }
- return pruned; // true if any interval was removed or modified by operations.
- }
- private boolean pruneColumnList(Vector deletion, Vector list) {
- int s=0,t=deletion.size();
- int[] sr=(int[])list.elementAt(s++);
- boolean pruned=false;
- int i=0, j=list.size();
- while (i<j && s<=t) {
- int c=((Integer)list.elementAt(i++)).intValue();
- if (sr[0]<=c) {
- if (sr[1]+sr[0]>=c) { // sr[1] -ve means inseriton.
- list.removeElementAt(--i);
- j--;
- } else {
- if (s<t)
- sr = (int[])deletion.elementAt(s);
- s++;
- }
- }
+
+ /*
+ * min, max are now the closest unselected columns
+ */
+ min++;
+ max--;
+ if (min > max)
+ {
+ min = max;
}
- return pruned;
+
+ hidden.hideColumns(min, max);
}
+
/**
- * remove any hiddenColumns or selected columns and shift remaining
- * based on a series of position, range deletions.
- * @param deletions
+ * Copy constructor
+ *
+ * @param copy
*/
- public void pruneDeletions(ShiftList deletions) {
- if (deletions!=null) {
- Vector shifts=deletions.shifts;
- if (shifts!=null && shifts.size()>0) {
- // delete any intervals intersecting.
- if (hiddenColumns!=null) {
- pruneIntervalVector(shifts, hiddenColumns);
- if (hiddenColumns!=null && hiddenColumns.size()==0) {
- hiddenColumns=null;
- }
- }
- if (selected!=null && selected.size()>0) {
- pruneColumnList(shifts, selected);
- if (selected!=null && selected.size()==0)
- selected=null;
- }
- // and shift the rest.
- this.compensateForEdits(deletions);
- }
+ public ColumnSelection(ColumnSelection copy)
+ {
+ if (copy != null)
+ {
+ selection = new IntList(copy.selection);
}
}
+
/**
- * This Method is used to return all the HiddenColumn regions
- * less than the given index.
- * @param end int
- * @return Vector
+ * ColumnSelection
*/
- public Vector getHiddenColumns()
+ public ColumnSelection()
{
- return hiddenColumns;
}
+
/**
- * Return absolute column index for a visible column index
- * @param column int column index in alignment view
- * @return alignment column index for column
+ * Invert the column selection from first to end-1. leaves hiddenColumns
+ * untouched (and unselected)
+ *
+ * @param first
+ * @param end
*/
- public int adjustForHiddenColumns(int column)
+ public void invertColumnSelection(int first, int width, AlignmentI al)
{
- int result = column;
- if (hiddenColumns != null)
+ boolean hasHidden = al.getHiddenColumns().hasHiddenColumns();
+ for (int i = first; i < width; i++)
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ if (contains(i))
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
- if (result >= region[0])
+ removeElement(i);
+ }
+ else
+ {
+ if (!hasHidden || al.getHiddenColumns().isVisible(i))
{
- result += region[1] - region[0] + 1;
+ addElement(i);
}
}
}
- return result;
}
/**
- * Use this method to find out where a visible column is in the alignment
- * when hidden columns exist
- * @param hiddenColumn int
- * @return int
+ * set the selected columns to the given column selection, excluding any
+ * columns that are hidden.
+ *
+ * @param colsel
*/
- public int findColumnPosition(int hiddenColumn)
+ public void setElementsFrom(ColumnSelection colsel,
+ HiddenColumns hiddenColumns)
{
- int result = hiddenColumn;
- if (hiddenColumns != null)
+ selection = new IntList();
+ if (colsel.selection != null && colsel.selection.size() > 0)
{
- int index = 0;
- int gaps = 0;
- do
+ if (hiddenColumns.hasHiddenColumns())
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if (hiddenColumn > region[1])
+ // only select visible columns in this columns selection
+ for (Integer col : colsel.getSelected())
{
- result -= region[1]+1-region[0];
+ if (hiddenColumns != null
+ && hiddenColumns.isVisible(col.intValue()))
+ {
+ selection.add(col);
+ }
}
- index++;
}
- while (index < hiddenColumns.size());
-
- result -= gaps;
- }
-
- return result;
- }
-
- /**
- * Use this method to determine where the next hiddenRegion starts
- */
- public int findHiddenRegionPosition(int hiddenRegion)
- {
- int result = 0;
- if (hiddenColumns != null)
- {
- int index = 0;
- int gaps = 0;
- do
+ else
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if(hiddenRegion==0)
+ // add everything regardless
+ for (Integer col : colsel.getSelected())
{
- return region[0];
+ addElement(col);
}
-
- gaps += region[1] +1 - region[0];
- result = region[1] +1;
- index++;
}
- while(index < hiddenRegion+1);
-
- 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
+ *
+ * @return true if there are columns marked
*/
- public int getHiddenBoundaryRight(int alPos)
+ public boolean hasSelectedColumns()
{
- if (hiddenColumns != null)
- {
- int index = 0;
- do
- {
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if(alPos < region[0])
- return region[0];
-
- index++;
- }
- while(index < hiddenColumns.size());
- }
-
- return alPos;
-
+ return (selection != null && selection.size() > 0);
}
+
/**
- * THis method returns the rightmost limit of a
- * region of an alignment with hidden columns.
- * In otherwords, the next hidden column.
- * @param index int
+ * 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 annotations
+ * @param filterParams
+ * @return
*/
- public int getHiddenBoundaryLeft(int alPos)
+ public int filterAnnotations(AlignmentAnnotation ann_row,
+ AnnotationFilterParameter filterParams)
{
- 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.CUSTOMRENDERER && (filterParams
+ .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
+ || filterParams
+ .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD))
{
- int index = hiddenColumns.size()-1;
- do
+ float tVal = filterParams.getThresholdValue();
+ if (ann_row.sequenceRef != null)
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if(alPos > region[1])
- return region[1];
+ // TODO - get ContactList from AlignmentView for non-seq-ref associatd
+ for (int column = 0; column < annotations.length; column++)
+ {
+ if (ann_row.annotations[column] == null)
+ {
+ continue;
+ }
- index--;
+ 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);
+ }
+ }
+ }
}
- while(index >-1);
+ return selection.size();
}
- return alPos;
+ int addedCount = 0;
+ int column = 0;
+ do
+ {
+ Annotation ann = annotations[column];
+ if (ann != null)
+ {
+ 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())
+ {
+ matched = true;
+ }
- }
+ if (!matched && filterParams
+ .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
+ && value < filterParams.getThresholdValue())
+ {
+ matched = true;
+ }
- public void hideSelectedColumns()
- {
- while (size() > 0)
- {
- int column = ( (Integer) getSelected().firstElement()).intValue();
- hideColumns(column);
- }
+ if (!matched && filterParams.isFilterAlphaHelix()
+ && ann.secondaryStructure == 'H')
+ {
+ matched = true;
+ }
- }
+ if (!matched && filterParams.isFilterBetaSheet()
+ && ann.secondaryStructure == 'E')
+ {
+ matched = true;
+ }
- public void hideColumns(int start, int end)
- {
- if(hiddenColumns==null)
- hiddenColumns = new Vector();
+ if (!matched && filterParams.isFilterTurn()
+ && ann.secondaryStructure == 'S')
+ {
+ matched = true;
+ }
- boolean added = false;
- boolean overlap = false;
+ 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;
+ }
+ }
+ }
+ }
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = (int[]) hiddenColumns.elementAt(i);
- if ( start<=region[1] && end>=region[0])
- {
- hiddenColumns.removeElementAt(i);
- overlap = true;
- break;
- }
- else if (end < region[0] && start < region[0])
- {
- hiddenColumns.insertElementAt(new int[]
- {start, end}, i);
- added = true;
- break;
+ if (matched)
+ {
+ this.addElement(column);
+ addedCount++;
+ }
}
- }
-
- if(overlap)
- {
- hideColumns(start, end);
- }
- else if (!added)
- hiddenColumns.addElement(new int[] {start, end});
+ column++;
+ } while (column < annotations.length);
+ return addedCount;
}
/**
- * This method will find a range of selected columns
- * around the column specified
- * @param res int
+ * Returns a hashCode built from selected columns ranges
*/
- public void hideColumns(int col)
+ @Override
+ public int hashCode()
{
- // First find out range of columns to hide
- int min = col, max = col+1;
- while( contains(min) )
- { removeElement(min); min --; }
-
- while( contains(max) )
- { removeElement(max); max ++; }
-
- min++; max--;
-
- hideColumns(min, max);
+ return selection.hashCode();
}
- public void revealAllHiddenColumns()
+ /**
+ * Answers true if comparing to a ColumnSelection with the same selected
+ * columns and hidden columns, else false
+ */
+ @Override
+ public boolean equals(Object obj)
{
- if(hiddenColumns!=null)
+ if (!(obj instanceof ColumnSelection))
{
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = (int[]) hiddenColumns.elementAt(i);
- for (int j = region[0]; j < region[1]+1; j++)
- {
- addElement(j);
- }
- }
+ return false;
}
+ ColumnSelection that = (ColumnSelection) obj;
- hiddenColumns = null;
- }
-
- public void revealHiddenColumns(int res)
- {
- for(int i=0; i<hiddenColumns.size(); i++)
+ /*
+ * check columns selected are either both null, or match
+ */
+ if (this.selection == null)
{
- int [] region = (int[])hiddenColumns.elementAt(i);
- if( res == region[0])
+ if (that.selection != null)
{
- for (int j = region[0]; j < region[1]+1; j++)
- {
- addElement(j);
- }
-
- hiddenColumns.removeElement(region);
- break;
+ return false;
}
}
- if(hiddenColumns.size()==0)
- hiddenColumns = null;
- }
-
- public boolean isVisible(int column)
- {
- for(int i=0; i<hiddenColumns.size(); i++)
+ if (!this.selection.equals(that.selection))
{
- int [] region = (int[])hiddenColumns.elementAt(i);
- if( column >= region[0] && column <= region[1])
- {
- return false;
- }
+ return false;
}
+
return true;
}
+
/**
- * Copy constructor
- * @param copy
- */
- public ColumnSelection(ColumnSelection copy) {
- if (copy!=null) {
- if (copy.selected!=null) {
- selected = new Vector();
- for (int i=0,j=copy.selected.size(); i<j; i++) {
- selected.setElementAt( ((Integer) copy.selected.elementAt(i)), i);
- }
- }
- if (copy.hiddenColumns!=null) {
- hiddenColumns=new Vector();
- for (int i=0,j=copy.hiddenColumns.size(); i<j; i++) {
- int[] rh,cp;
- rh = (int[])copy.hiddenColumns.elementAt(i);
- if (rh!=null) {
- cp = new int[rh.length];
- System.arraycopy(rh, 0, cp, 0, rh.length);
- hiddenColumns.setElementAt(cp, i);
- }
- }
- }
- }
- }
- /**
- * ColumnSelection
+ * Updates the column selection depending on the parameters, and returns true
+ * if any change was made to the selection
+ *
+ * @param markedColumns
+ * a set identifying marked columns (base 0)
+ * @param startCol
+ * the first column of the range to operate over (base 0)
+ * @param endCol
+ * the last column of the range to operate over (base 0)
+ * @param invert
+ * if true, deselect marked columns and select unmarked
+ * @param extendCurrent
+ * if true, extend rather than replacing the current column selection
+ * @param toggle
+ * if true, toggle the selection state of marked columns
+ *
+ * @return
*/
- public ColumnSelection()
+ public boolean markColumns(BitSet markedColumns, int startCol, int endCol,
+ boolean invert, boolean extendCurrent, boolean toggle)
{
- }
-
- public String[] getVisibleSequenceStrings(int start, int end, SequenceI[] seqs) {
- int i,iSize=seqs.length;
- String selection[] = new String[iSize];
- if (hiddenColumns!=null && hiddenColumns.size()>0)
+ boolean changed = false;
+ if (!extendCurrent && !toggle)
{
- for (i=0; i<iSize; i++) {
- StringBuffer visibleSeq = new StringBuffer();
- Vector regions = getHiddenColumns();
-
- int blockStart = start, blockEnd=end;
- int [] region;
- int hideStart, hideEnd;
-
- for (int j = 0; j < regions.size(); j++)
+ changed = !this.isEmpty();
+ clear();
+ }
+ if (invert)
+ {
+ // invert only in the currently selected sequence region
+ int i = markedColumns.nextClearBit(startCol);
+ int ibs = markedColumns.nextSetBit(startCol);
+ while (i >= startCol && i <= endCol)
+ {
+ if (ibs < 0 || i < ibs)
{
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
-
- if(hideStart < start)
+ changed = true;
+ if (toggle && contains(i))
{
- continue;
+ removeElement(i++);
}
-
- blockStart = Math.min(blockStart, hideEnd+1);
- blockEnd = Math.min(blockEnd, hideStart);
-
- if(blockStart>blockEnd)
+ else
{
- break;
+ addElement(i++);
}
-
-
- visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
-
- blockStart = hideEnd+1;
- blockEnd = end;
}
-
- if(end>blockStart)
- visibleSeq.append(seqs[i].getSequence(blockStart, end));
-
- selection[i] = visibleSeq.toString();
+ else
+ {
+ i = markedColumns.nextClearBit(ibs);
+ ibs = markedColumns.nextSetBit(i);
+ }
}
}
else
{
- for(i=0; i<iSize; i++)
+ int i = markedColumns.nextSetBit(startCol);
+ while (i >= startCol && i <= endCol)
{
- selection[i] = seqs[i].getSequence(start, end);
+ changed = true;
+ if (toggle && contains(i))
+ {
+ removeElement(i);
+ }
+ else
+ {
+ addElement(i);
+ }
+ i = markedColumns.nextSetBit(i + 1);
}
}
-
- return selection;
+ return changed;
}
+
/**
- * return all visible segments between the given start and end boundaries
+ * Adjusts column selections, and the given selection group, to match the
+ * range of a stretch (e.g. mouse drag) operation
+ * <p>
+ * Method refactored from ScalePanel.mouseDragged
*
- * @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
+ * @param res
+ * current column position, adjusted for hidden columns
+ * @param sg
+ * current selection group
+ * @param min
+ * start position of the stretch group
+ * @param max
+ * end position of the stretch group
*/
- public int[] getVisibleContigs(int start, int end) {
- if (hiddenColumns!=null && hiddenColumns.size()>0)
+ public void stretchGroup(int res, SequenceGroup sg, int min, int max)
+ {
+ if (!contains(res))
{
- Vector visiblecontigs=new Vector();
- Vector regions = getHiddenColumns();
+ addElement(res);
+ }
- int vstart = start;
- int [] region;
- int hideStart, hideEnd;
+ if (res > sg.getStartRes())
+ {
+ // expand selection group to the right
+ sg.setEndRes(res);
+ }
+ if (res < sg.getStartRes())
+ {
+ // expand selection group to the left
+ sg.setStartRes(res);
+ }
- for (int j = 0; vstart<end && j < regions.size(); j++)
+ /*
+ * expand or shrink column selection to match the
+ * range of the drag operation
+ */
+ for (int col = min; col <= max; col++)
+ {
+ if (col < sg.getStartRes() || col > sg.getEndRes())
{
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
-
- if(hideEnd < vstart)
- {
- continue;
- }
- if (hideStart>vstart) {
- visiblecontigs.addElement(new int[] {vstart, hideStart-1});
- }
- vstart=hideEnd+1;
+ // shrinking drag - remove from selection
+ removeElement(col);
}
-
- if(vstart<end)
- visiblecontigs.addElement(new int[] { vstart, end-1});
- int[] vcontigs = new int[visiblecontigs.size()*2];
- for (int i=0,j=visiblecontigs.size(); i<j; i++) {
- int [] vc = (int[]) visiblecontigs.get(i);
- visiblecontigs.setElementAt(null, i);
- vcontigs[i*2] = vc[0];
- vcontigs[i*2+1] = vc[1];
+ else
+ {
+ // expanding drag - add to selection
+ addElement(col);
}
- visiblecontigs.clear();
- return vcontigs;
- }
- else
- {
- return new int[] { start, end-1 };
}
}
}
git://source.jalview.org / jalview.git / blobdiff