-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.datamodel;\r
-\r
-import jalview.util.ShiftList;\r
-\r
-import java.util.*;\r
-\r
-/**\r
- * NOTE: Columns are zero based.\r
- */\r
-public class ColumnSelection\r
-{\r
- Vector selected = new Vector();\r
-\r
- //Vector of int [] {startCol, endCol}\r
- Vector hiddenColumns;\r
-\r
- /**\r
- * Add a column to the selection\r
- *\r
- * @param col index of column\r
- */\r
- public void addElement(int col)\r
- {\r
- Integer column = new Integer(col);\r
- if (!selected.contains(column))\r
- {\r
- selected.addElement(column);\r
- }\r
- }\r
-\r
- /**\r
- * clears column selection\r
- */\r
- public void clear()\r
- {\r
- selected.removeAllElements();\r
- }\r
-\r
- /**\r
- * removes col from selection\r
- *\r
- * @param col index of column to be removed\r
- */\r
- public void removeElement(int col)\r
- {\r
- Integer colInt = new Integer(col);\r
-\r
- if (selected.contains(colInt))\r
- {\r
- selected.removeElement(colInt);\r
- }\r
- }\r
-\r
- /**\r
- * removes a range of columns from the selection\r
- * @param start int - first column in range to be removed\r
- * @param end int - last col\r
- */\r
- public void removeElements(int start, int end)\r
- {\r
- Integer colInt;\r
- for(int i=start; i<end; i++)\r
- {\r
- colInt = new Integer(i);\r
- if (selected.contains(colInt))\r
- {\r
- selected.removeElement(colInt);\r
- }\r
- }\r
- }\r
- /**\r
- *\r
- * @return Vector containing selected columns as Integers\r
- */\r
- public Vector getSelected()\r
- {\r
- return selected;\r
- }\r
-\r
- /**\r
- *\r
- * @param col index to search for in column selection\r
- *\r
- * @return true if Integer(col) is in selection.\r
- */\r
- public boolean contains(int col)\r
- {\r
- return selected.contains(new Integer(col));\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int columnAt(int i)\r
- {\r
- return ((Integer) selected.elementAt(i)).intValue();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int size()\r
- {\r
- return selected.size();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getMax()\r
- {\r
- int max = -1;\r
-\r
- for (int i = 0; i < selected.size(); i++)\r
- {\r
- if (columnAt(i) > max)\r
- {\r
- max = columnAt(i);\r
- }\r
- }\r
-\r
- return max;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getMin()\r
- {\r
- int min = 1000000000;\r
-\r
- for (int i = 0; i < selected.size(); i++)\r
- {\r
- if (columnAt(i) < min)\r
- {\r
- min = columnAt(i);\r
- }\r
- }\r
-\r
- return min;\r
- }\r
-\r
-\r
- /**\r
- * propagate shift in alignment columns to column selection\r
- *\r
- * @param start beginning of edit\r
- * @param change shift in edit (-ve or +ve number of columns)\r
- */\r
- public void compensateForEdit(int start, int change)\r
- {\r
- for (int i = 0; i < size(); i++)\r
- {\r
- int temp = columnAt(i);\r
-\r
- if (temp >= start)\r
- {\r
- selected.setElementAt(new Integer(temp - change), i);\r
- }\r
- }\r
-\r
- if(hiddenColumns!=null)\r
- {\r
- for(int i=0; i<hiddenColumns.size(); i++)\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(i);\r
- if(region[0] > start)\r
- {\r
- region[0] -= change;\r
- region[1] -= change;\r
- }\r
- if(region[0]<0)\r
- region[0] = 0;\r
- if(region[1] <0)\r
- region[1] = 0;\r
- }\r
- }\r
- }\r
- public ShiftList compensateForEdits(ShiftList shiftrecord) {\r
- if (shiftrecord!=null) {\r
- Vector shifts = shiftrecord.shifts;\r
- if (shifts!=null && shifts.size()>0) {\r
- for (int i=0,j=shifts.size(); i<j; i++) {\r
- int[] sh = (int[]) shifts.elementAt(i);\r
- compensateForEdit(sh[0], sh[1]);\r
- }\r
- }\r
- return shiftrecord.getInverse();\r
- }\r
- return null;\r
- }\r
- /**\r
- * This Method is used to return all the HiddenColumn regions\r
- * less than the given index.\r
- * @param end int\r
- * @return Vector\r
- */\r
- public Vector getHiddenColumns()\r
- {\r
- return hiddenColumns;\r
- }\r
- /**\r
- * Return absolute column index for a visible column index\r
- * @param column int column index in alignment view\r
- * @return alignment column index for column\r
- */\r
- public int adjustForHiddenColumns(int column)\r
- {\r
- int result = column;\r
- if (hiddenColumns != null)\r
- {\r
- for (int i = 0; i < hiddenColumns.size(); i++)\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(i);\r
- if (result >= region[0])\r
- {\r
- result += region[1] - region[0] + 1;\r
- }\r
- }\r
- }\r
- return result;\r
- }\r
-\r
- /**\r
- * Use this method to find out where a visible column is in the alignment\r
- * when hidden columns exist\r
- * @param hiddenColumn int\r
- * @return int\r
- */\r
- public int findColumnPosition(int hiddenColumn)\r
- {\r
- int result = hiddenColumn;\r
- if (hiddenColumns != null)\r
- {\r
- int index = 0;\r
- int gaps = 0;\r
- do\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(index);\r
- if (hiddenColumn > region[1])\r
- {\r
- result -= region[1]+1-region[0];\r
- }\r
- index++;\r
- }\r
- while (index < hiddenColumns.size());\r
-\r
- result -= gaps;\r
- }\r
-\r
- return result;\r
- }\r
-\r
- /**\r
- * Use this method to determine where the next hiddenRegion starts\r
- */\r
- public int findHiddenRegionPosition(int hiddenRegion)\r
- {\r
- int result = 0;\r
- if (hiddenColumns != null)\r
- {\r
- int index = 0;\r
- int gaps = 0;\r
- do\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(index);\r
- if(hiddenRegion==0)\r
- {\r
- return region[0];\r
- }\r
-\r
- gaps += region[1] +1 - region[0];\r
- result = region[1] +1;\r
- index++;\r
- }\r
- while(index < hiddenRegion+1);\r
-\r
- result -= gaps;\r
- }\r
-\r
- return result;\r
- }\r
-\r
- /**\r
- * THis method returns the rightmost limit of a\r
- * region of an alignment with hidden columns.\r
- * In otherwords, the next hidden column.\r
- * @param index int\r
- */\r
- public int getHiddenBoundaryRight(int alPos)\r
- {\r
- if (hiddenColumns != null)\r
- {\r
- int index = 0;\r
- do\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(index);\r
- if(alPos < region[0])\r
- return region[0];\r
-\r
- index++;\r
- }\r
- while(index < hiddenColumns.size());\r
- }\r
-\r
- return alPos;\r
-\r
- }\r
- /**\r
- * THis method returns the rightmost limit of a\r
- * region of an alignment with hidden columns.\r
- * In otherwords, the next hidden column.\r
- * @param index int\r
- */\r
- public int getHiddenBoundaryLeft(int alPos)\r
- {\r
- if (hiddenColumns != null)\r
- {\r
- int index = hiddenColumns.size()-1;\r
- do\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(index);\r
- if(alPos > region[1])\r
- return region[1];\r
-\r
- index--;\r
- }\r
- while(index >-1);\r
- }\r
-\r
- return alPos;\r
-\r
- }\r
-\r
- public void hideSelectedColumns()\r
- {\r
- while (size() > 0)\r
- {\r
- int column = ( (Integer) getSelected().firstElement()).intValue();\r
- hideColumns(column);\r
- }\r
-\r
- }\r
-\r
- public void hideColumns(int start, int end)\r
- {\r
- if(hiddenColumns==null)\r
- hiddenColumns = new Vector();\r
-\r
- boolean added = false;\r
- boolean overlap = false;\r
-\r
- for (int i = 0; i < hiddenColumns.size(); i++)\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(i);\r
- if ( start<=region[1] && end>=region[0])\r
- {\r
- hiddenColumns.removeElementAt(i);\r
- overlap = true;\r
- break;\r
- }\r
- else if (end < region[0] && start < region[0])\r
- {\r
- hiddenColumns.insertElementAt(new int[]\r
- {start, end}, i);\r
- added = true;\r
- break;\r
- }\r
- }\r
-\r
- if(overlap)\r
- {\r
- hideColumns(start, end);\r
- }\r
- else if (!added)\r
- hiddenColumns.addElement(new int[] {start, end});\r
-\r
- }\r
-\r
- /**\r
- * This method will find a range of selected columns\r
- * around the column specified\r
- * @param res int\r
- */\r
- public void hideColumns(int col)\r
- {\r
- // First find out range of columns to hide\r
- int min = col, max = col+1;\r
- while( contains(min) )\r
- { removeElement(min); min --; }\r
-\r
- while( contains(max) )\r
- { removeElement(max); max ++; }\r
-\r
- min++; max--;\r
-\r
- hideColumns(min, max);\r
- }\r
-\r
- public void revealAllHiddenColumns()\r
- {\r
- if(hiddenColumns!=null)\r
- {\r
- for (int i = 0; i < hiddenColumns.size(); i++)\r
- {\r
- int[] region = (int[]) hiddenColumns.elementAt(i);\r
- for (int j = region[0]; j < region[1]+1; j++)\r
- {\r
- addElement(j);\r
- }\r
- }\r
- }\r
-\r
- hiddenColumns = null;\r
- }\r
-\r
- public void revealHiddenColumns(int res)\r
- {\r
- for(int i=0; i<hiddenColumns.size(); i++)\r
- {\r
- int [] region = (int[])hiddenColumns.elementAt(i);\r
- if( res == region[0])\r
- {\r
- for (int j = region[0]; j < region[1]+1; j++)\r
- {\r
- addElement(j);\r
- }\r
-\r
- hiddenColumns.removeElement(region);\r
- break;\r
- }\r
- }\r
- if(hiddenColumns.size()==0)\r
- hiddenColumns = null;\r
- }\r
-\r
- public boolean isVisible(int column)\r
- {\r
- for(int i=0; i<hiddenColumns.size(); i++)\r
- {\r
- int [] region = (int[])hiddenColumns.elementAt(i);\r
- if( column >= region[0] && column <= region[1])\r
- {\r
- return false;\r
- }\r
- }\r
- return true;\r
- }\r
- /**\r
- * Copy constructor\r
- * @param copy\r
- */\r
- public ColumnSelection(ColumnSelection copy) {\r
- if (copy!=null) {\r
- if (copy.selected!=null) {\r
- selected = new Vector();\r
- for (int i=0,j=copy.selected.size(); i<j; i++) {\r
- selected.setElementAt(((Integer) copy.selected.elementAt(i)), i);\r
- }\r
- }\r
- if (copy.hiddenColumns!=null) {\r
- hiddenColumns=new Vector();\r
- for (int i=0,j=copy.hiddenColumns.size(); i<j; i++) {\r
- int[] rh,cp;\r
- rh = (int[])copy.hiddenColumns.elementAt(i);\r
- if (rh!=null) {\r
- cp = new int[rh.length];\r
- System.arraycopy(rh, 0, cp, 0, rh.length);\r
- hiddenColumns.setElementAt(cp, i);\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * ColumnSelection\r
- */\r
- public ColumnSelection()\r
- {\r
- }\r
-}\r
+/*
+ * 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.
+ *
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+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;
+
+/**
+ * Data class holding the selected columns and hidden column ranges for a view.
+ * Ranges are base 1.
+ */
+public class ColumnSelection
+{
+ /**
+ * 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<Integer>();
+ _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 = new Integer(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);
+ }
+
+ 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, new Integer(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<int[]>();
+ 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;
+ }
+ }
+
+ IntList selection = new IntList();
+
+ /**
+ * Add a column to the selection
+ *
+ * @param col
+ * index of column
+ */
+ public void addElement(int col)
+ {
+ selection.add(col);
+ }
+
+ /**
+ * clears column selection
+ */
+ public void clear()
+ {
+ selection.clear();
+ }
+
+ /**
+ * Removes value 'col' from the selection (not the col'th item)
+ *
+ * @param col
+ * index of column to be removed
+ */
+ public void removeElement(int col)
+ {
+ 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
+ */
+ public void removeElements(int start, int end)
+ {
+ Integer colInt;
+ for (int i = start; i < end; i++)
+ {
+ colInt = new Integer(i);
+ if (selection.contains(colInt))
+ {
+ selection.remove(colInt);
+ }
+ }
+ }
+
+ /**
+ * 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 List<Integer> getSelected()
+ {
+ return selection.getList();
+ }
+
+ /**
+ * @return list of int arrays containing start and end column position for
+ * runs of selected columns ordered from right to left.
+ */
+ public List<int[]> getSelectedRanges()
+ {
+ return selection.getRanges();
+ }
+
+ /**
+ *
+ * @param col
+ * index to search for in column selection
+ *
+ * @return true if col is selected
+ */
+ public boolean contains(int col)
+ {
+ return (col > -1) ? selection.isSelected(col) : false;
+ }
+
+ /**
+ * Answers true if no columns are selected, else false
+ */
+ public boolean isEmpty()
+ {
+ return selection == null || selection.isEmpty();
+ }
+
+ /**
+ * rightmost selected column
+ *
+ * @return rightmost column in alignment that is selected
+ */
+ public int getMax()
+ {
+ if (selection.isEmpty())
+ {
+ return -1;
+ }
+ return selection.getMaxColumn();
+ }
+
+ /**
+ * Leftmost column in selection
+ *
+ * @return column index of leftmost column in selection
+ */
+ public int getMin()
+ {
+ if (selection.isEmpty())
+ {
+ return 1000000000;
+ }
+ return selection.getMinColumn();
+ }
+
+ public void hideSelectedColumns(AlignmentI al)
+ {
+ synchronized (selection)
+ {
+ for (int[] selregions : selection.getRanges())
+ {
+ al.getHiddenColumns().hideColumns(selregions[0], selregions[1]);
+ }
+ selection.clear();
+ }
+
+ }
+
+
+ /**
+ * Hides the specified column and any adjacent selected columns
+ *
+ * @param res
+ * int
+ */
+ public void hideSelectedColumns(int col, HiddenColumns hidden)
+ {
+ /*
+ * 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;
+ }
+
+ hidden.hideColumns(min, max);
+ }
+
+
+
+
+
+ /**
+ * Copy constructor
+ *
+ * @param copy
+ */
+ public ColumnSelection(ColumnSelection copy)
+ {
+ if (copy != null)
+ {
+ selection = new IntList(copy.selection);
+ }
+ }
+
+ /**
+ * ColumnSelection
+ */
+ public ColumnSelection()
+ {
+ }
+
+
+
+
+
+
+ /**
+ * 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, AlignmentI al)
+ {
+ boolean hasHidden = al.getHiddenColumns().hasHidden();
+ for (int i = first; i < width; i++)
+ {
+ if (contains(i))
+ {
+ removeElement(i);
+ }
+ else
+ {
+ if (!hasHidden || al.getHiddenColumns().isVisible(i))
+ {
+ addElement(i);
+ }
+ }
+ }
+ }
+
+ /**
+ * set the selected columns to the given column selection, excluding any
+ * columns that are hidden.
+ *
+ * @param colsel
+ */
+ public void setElementsFrom(ColumnSelection colsel,
+ HiddenColumns hiddenColumns)
+ {
+ selection = new IntList();
+ if (colsel.selection != null && colsel.selection.size() > 0)
+ {
+ if (hiddenColumns.hasHidden())
+ {
+ // only select visible columns in this columns selection
+ for (Integer col : colsel.getSelected())
+ {
+ if (hiddenColumns != null
+ && hiddenColumns.isVisible(col.intValue()))
+ {
+ selection.add(col);
+ }
+ }
+ }
+ else
+ {
+ // add everything regardless
+ for (Integer col : colsel.getSelected())
+ {
+ addElement(col);
+ }
+ }
+ }
+ }
+
+
+ /**
+ *
+ * @return true if there are columns marked
+ */
+ public boolean hasSelectedColumns()
+ {
+ return (selection != null && selection.size() > 0);
+ }
+
+
+
+ public boolean filterAnnotations(Annotation[] annotations,
+ AnnotationFilterParameter filterParams)
+ {
+ // JBPNote - this method needs to be refactored to become independent of
+ // viewmodel package
+ 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 ranges
+ */
+ @Override
+ public int hashCode()
+ {
+ return selection.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;
+
+ /*
+ * check columns selected are either both null, or match
+ */
+ if (this.selection == null)
+ {
+ if (that.selection != null)
+ {
+ return false;
+ }
+ }
+ if (!this.selection.equals(that.selection))
+ {
+ return false;
+ }
+
+ return true;
+ }
+
+ /**
+ * 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 boolean markColumns(BitSet markedColumns, int startCol,
+ int endCol, boolean invert, boolean extendCurrent, boolean toggle)
+ {
+ boolean changed = false;
+ if (!extendCurrent && !toggle)
+ {
+ 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)
+ {
+ changed = true;
+ if (toggle && contains(i))
+ {
+ removeElement(i++);
+ }
+ else
+ {
+ addElement(i++);
+ }
+ }
+ else
+ {
+ i = markedColumns.nextClearBit(ibs);
+ ibs = markedColumns.nextSetBit(i);
+ }
+ }
+ }
+ else
+ {
+ int i = markedColumns.nextSetBit(startCol);
+ while (i >= startCol && i <= endCol)
+ {
+ changed = true;
+ if (toggle && contains(i))
+ {
+ removeElement(i);
+ }
+ else
+ {
+ addElement(i);
+ }
+ i = markedColumns.nextSetBit(i + 1);
+ }
+ }
+ return changed;
+ }
+
+ /**
+ * 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 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 void stretchGroup(int res, SequenceGroup sg, int min, int max)
+ {
+ if (!contains(res))
+ {
+ addElement(res);
+ }
+
+ 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);
+ }
+
+ /*
+ * 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())
+ {
+ // shrinking drag - remove from selection
+ removeElement(col);
+ }
+ else
+ {
+ // expanding drag - add to selection
+ addElement(col);
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff