+ * 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 is not thread-safe: iterating over it could result in
+ * ConcurrentModificationException if it is modified by another thread.
*/
- public Vector getSelected()
+ public List getSelected()
{
- return selected;
+ return selection.getList();
}
/**
- *
- * @param col index to search for in column selection
- *
- * @return true if Integer(col) is in selection.
+ * @return list of int arrays containing start and end column position for
+ * runs of selected columns ordered from right to left.
*/
- public boolean contains(int col)
+ public List getSelectedRanges()
{
- return selected.contains(new Integer(col));
+ return selection.getRanges();
}
/**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ *
+ * @param col
+ * index to search for in column selection
+ *
+ * @return true if col is selected
*/
- public int columnAt(int i)
+ public boolean contains(int col)
{
- return ((Integer) selected.elementAt(i)).intValue();
+ return (col > -1) ? selection.isSelected(col) : false;
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Answers true if no columns are selected, else false
*/
- public int size()
+ public boolean isEmpty()
{
- return selected.size();
+ return selection == null || selection.isEmpty();
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * rightmost selected column
+ *
+ * @return rightmost column in alignment that is selected
*/
public int getMax()
{
- int max = -1;
-
- for (int i = 0; i < selected.size(); i++)
+ if (selection.isEmpty())
{
- if (columnAt(i) > max)
- {
- max = columnAt(i);
- }
+ return -1;
}
-
- return max;
+ return selection.getMaxColumn();
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Leftmost column in selection
+ *
+ * @return column index of leftmost column in selection
*/
public int getMin()
{
- int min = 1000000000;
+ if (selection.isEmpty())
+ {
+ return 1000000000;
+ }
+ return selection.getMinColumn();
+ }
- for (int i = 0; i < selected.size(); i++)
+ public void hideSelectedColumns(AlignmentI al)
+ {
+ synchronized (selection)
{
- if (columnAt(i) < min)
+ for (int[] selregions : selection.getRanges())
{
- min = columnAt(i);
+ al.getHiddenColumns().hideColumns(selregions[0], selregions[1]);
}
+ selection.clear();
}
- return min;
}
/**
- * 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)
+ * Hides the specified column and any adjacent selected columns
+ *
+ * @param res
+ * int
*/
- public void compensateForEdit(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);
+ removeElement(min);
+ min--;
+ }
- if (temp >= start)
- {
- selected.setElementAt(new Integer(temp - change), i);
- }
+ while (contains(max))
+ {
+ removeElement(max);
+ max++;
}
- if(hiddenColumns!=null)
+ /*
+ * min, max are now the closest unselected columns
+ */
+ min++;
+ max--;
+ if (min > max)
{
- for(int i=0; i start)
- {
- region[0] -= change;
- region[1] -= change;
- }
- if(region[0]<0)
- region[0] = 0;
- if(region[1] <0)
- region[1] = 0;
- }
+ min = max;
}
+
+ hidden.hideColumns(min, max);
}
- /**
- * 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)
- */
- private void compensateForDelEdits(int start, int change)
- {
- for (int i = 0; i < size(); i++)
- {
- int temp = columnAt(i);
- if (temp >= start)
- {
- selected.setElementAt(new Integer(temp - change), i);
- }
- }
- if(hiddenColumns!=null)
- {
- for(int i=0; i= start)
- {
- region[0] -= change;
- }
- if (region[1]>= start) {
- region[1] -=change;
- }
- if (region[1]0) {
- int shifted=0;
- for (int i=0,j=shifts.size(); i=sr[0];
- if (!trailinghn) {
- if (i=sr[0];
- boolean leadinghc=hr[0]=c) { // sr[1] -ve means inseriton.
- list.removeElementAt(--i);
- j--;
- } else {
- if (s0) {
- // 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().hasHidden();
+ for (int i = first; i < width; i++)
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ if (contains(i))
+ {
+ removeElement(i);
+ }
+ else
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
- if (result >= region[0])
+ 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.hasHidden())
{
- 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];
+ return (selection != null && selection.size() > 0);
+ }
- index++;
- }
- while(index < hiddenColumns.size());
- }
- return alPos;
- }
- /**
- * THis method returns the rightmost limit of a
- * region of an alignment with hidden columns.
- * In otherwords, the next hidden column.
- * @param index int
- */
- public int getHiddenBoundaryLeft(int alPos)
+ public boolean filterAnnotations(Annotation[] annotations,
+ AnnotationFilterParameter filterParams)
{
- if (hiddenColumns != null)
+ // JBPNote - this method needs to be refactored to become independent of
+ // viewmodel package
+ this.clear();
+ int count = 0;
+ do
{
- int index = hiddenColumns.size()-1;
- do
+ if (annotations[count] != null)
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if(alPos > region[1])
- return region[1];
- index--;
- }
- while(index >-1);
- }
-
- return alPos;
+ 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;
+ }
- public void hideSelectedColumns()
- {
- while (size() > 0)
- {
- int column = ( (Integer) getSelected().firstElement()).intValue();
- hideColumns(column);
- }
+ if (filterParams.isFilterAlphaHelix()
+ && annotations[count].secondaryStructure == 'H')
+ {
+ itemMatched = true;
+ }
- }
+ if (filterParams.isFilterBetaSheet()
+ && annotations[count].secondaryStructure == 'E')
+ {
+ itemMatched = true;
+ }
- public void hideColumns(int start, int end)
- {
- if(hiddenColumns==null)
- hiddenColumns = new Vector();
+ if (filterParams.isFilterTurn()
+ && annotations[count].secondaryStructure == 'S')
+ {
+ itemMatched = true;
+ }
- boolean added = false;
- boolean overlap = false;
+ 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;
+ }
+ }
- 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 (itemMatched)
+ {
+ this.addElement(count);
+ }
}
- }
-
- if(overlap)
- {
- hideColumns(start, end);
- }
- else if (!added)
- hiddenColumns.addElement(new int[] {start, end});
-
+ count++;
+ } while (count < annotations.length);
+ return false;
}
/**
- * 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= 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(); i0)
+ boolean changed = false;
+ if (!extendCurrent && !toggle)
{
- for (i=0; 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= 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
+ *
+ * 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_end0)
+ 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 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