-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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
- * 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.
- *
- * 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
- */
-package jalview.datamodel;
-
-import jalview.util.ShiftList;
-
-import java.util.*;
-
-/**
- * NOTE: Columns are zero based.
- */
-public class ColumnSelection
-{
- Vector selected = new Vector();
-
- //Vector of int [] {startCol, endCol}
- Vector hiddenColumns;
-
- /**
- * Add a column to the selection
- *
- * @param col index of column
- */
- public void addElement(int col)
- {
- Integer column = new Integer(col);
- if (!selected.contains(column))
- {
- selected.addElement(column);
- }
- }
-
- /**
- * clears column selection
- */
- public void clear()
- {
- selected.removeAllElements();
- }
-
- /**
- * removes col from selection
- *
- * @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);
- }
- }
-
- /**
- * 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 (selected.contains(colInt))
- {
- selected.removeElement(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.
- */
- public boolean contains(int col)
- {
- return selected.contains(new Integer(col));
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int columnAt(int i)
- {
- return ((Integer) selected.elementAt(i)).intValue();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int size()
- {
- return selected.size();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getMax()
- {
- int max = -1;
-
- for (int i = 0; i < selected.size(); i++)
- {
- if (columnAt(i) > max)
- {
- max = columnAt(i);
- }
- }
-
- return max;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getMin()
- {
- int min = 1000000000;
-
- for (int i = 0; i < selected.size(); i++)
- {
- if (columnAt(i) < min)
- {
- min = columnAt(i);
- }
- }
-
- return min;
- }
-
-
- /**
- * propagate shift in alignment columns to column selection
- *
- * @param start beginning of edit
- * @param change shift in edit (-ve or +ve number of columns)
- */
- public void compensateForEdit(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<hiddenColumns.size(); i++)
- {
- 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;
- }
- }
- }
- public ShiftList compensateForEdits(ShiftList shiftrecord) {
- if (shiftrecord!=null) {
- Vector shifts = shiftrecord.shifts;
- if (shifts!=null && shifts.size()>0) {
- for (int i=0,j=shifts.size(); i<j; i++) {
- int[] sh = (int[]) shifts.get(i);
- compensateForEdit(sh[0], sh[1]);
- }
- }
- return shiftrecord.getInverse();
- }
- return null;
- }
- /**
- * This Method is used to return all the HiddenColumn regions
- * less than the given index.
- * @param end int
- * @return Vector
- */
- public Vector getHiddenColumns()
- {
- 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
- */
- public int adjustForHiddenColumns(int column)
- {
- int result = column;
- if (hiddenColumns != null)
- {
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = (int[]) hiddenColumns.elementAt(i);
- if (result >= region[0])
- {
- result += region[1] - region[0] + 1;
- }
- }
- }
- 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
- */
- public int findColumnPosition(int hiddenColumn)
- {
- int result = hiddenColumn;
- if (hiddenColumns != null)
- {
- int index = 0;
- int gaps = 0;
- do
- {
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if (hiddenColumn > region[1])
- {
- result -= region[1]+1-region[0];
- }
- 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
- {
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if(hiddenRegion==0)
- {
- return region[0];
- }
-
- 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
- */
- public int getHiddenBoundaryRight(int alPos)
- {
- 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;
-
- }
- /**
- * 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)
- {
- if (hiddenColumns != null)
- {
- int index = hiddenColumns.size()-1;
- do
- {
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if(alPos > region[1])
- return region[1];
-
- index--;
- }
- while(index >-1);
- }
-
- return alPos;
-
- }
-
- public void hideSelectedColumns()
- {
- while (size() > 0)
- {
- int column = ( (Integer) getSelected().firstElement()).intValue();
- hideColumns(column);
- }
-
- }
-
- public void hideColumns(int start, int end)
- {
- if(hiddenColumns==null)
- hiddenColumns = new Vector();
-
- boolean added = false;
- boolean overlap = false;
-
- 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(overlap)
- {
- hideColumns(start, end);
- }
- else if (!added)
- hiddenColumns.addElement(new int[] {start, end});
-
- }
-
- /**
- * This method will find a range of selected columns
- * around the column specified
- * @param res int
- */
- public void hideColumns(int col)
- {
- // 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);
- }
-
- public void revealAllHiddenColumns()
- {
- if(hiddenColumns!=null)
- {
- 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);
- }
- }
- }
-
- hiddenColumns = null;
- }
-
- public void revealHiddenColumns(int res)
- {
- for(int i=0; i<hiddenColumns.size(); i++)
- {
- int [] region = (int[])hiddenColumns.elementAt(i);
- if( res == 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)
- {
- for(int i=0; i<hiddenColumns.size(); i++)
- {
- int [] region = (int[])hiddenColumns.elementAt(i);
- if( column >= region[0] && column <= region[1])
- {
- 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.set(i, ((Integer) copy.selected.get(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.get(i);
- if (rh!=null) {
- cp = new int[rh.length];
- System.arraycopy(rh, 0, cp, 0, rh.length);
- hiddenColumns.set(i, cp);
- }
- }
- }
- }
- }
-
- /**
- * ColumnSelection
- */
- public ColumnSelection()
- {
- }
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 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 java.util.*;\r
+\r
+import jalview.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\r
+ * 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\r
+ * 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
+ * \r
+ * @param start\r
+ * int - first column in range to be removed\r
+ * @param end\r
+ * 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
+ * \r
+ * @return Vector containing selected columns as Integers\r
+ */\r
+ public Vector getSelected()\r
+ {\r
+ return selected;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param col\r
+ * 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
+ * Column number at position i in selection\r
+ * \r
+ * @param i\r
+ * index into selected columns\r
+ * \r
+ * @return column number in alignment\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
+ * rightmost selected column\r
+ * \r
+ * @return rightmost column in alignment that is selected\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
+ * Leftmost column in selection\r
+ * \r
+ * @return column index of leftmost column in selection\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
+ * propagate shift in alignment columns to column selection\r
+ * \r
+ * @param start\r
+ * beginning of edit\r
+ * @param left\r
+ * shift in edit (+ve for removal, or -ve for inserts)\r
+ */\r
+ public Vector compensateForEdit(int start, int change)\r
+ {\r
+ Vector deletedHiddenColumns = null;\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
+ deletedHiddenColumns = new Vector();\r
+ int hSize = hiddenColumns.size();\r
+ for (int i = 0; i < hSize; i++)\r
+ {\r
+ int[] region = (int[]) hiddenColumns.elementAt(i);\r
+ if (region[0] > start && start + change > region[1])\r
+ {\r
+ deletedHiddenColumns.addElement(hiddenColumns.elementAt(i));\r
+\r
+ hiddenColumns.removeElementAt(i);\r
+ i--;\r
+ hSize--;\r
+ continue;\r
+ }\r
+\r
+ if (region[0] > start)\r
+ {\r
+ region[0] -= change;\r
+ region[1] -= change;\r
+ }\r
+\r
+ if (region[0] < 0)\r
+ {\r
+ region[0] = 0;\r
+ }\r
+\r
+ }\r
+\r
+ this.revealHiddenColumns(0);\r
+ }\r
+\r
+ return deletedHiddenColumns;\r
+ }\r
+\r
+ /**\r
+ * propagate shift in alignment columns to column selection special version of\r
+ * compensateForEdit - allowing for edits within hidden regions\r
+ * \r
+ * @param start\r
+ * beginning of edit\r
+ * @param left\r
+ * shift in edit (+ve for removal, or -ve for inserts)\r
+ */\r
+ private void compensateForDelEdits(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
+ }\r
+ if (region[1] >= start)\r
+ {\r
+ region[1] -= change;\r
+ }\r
+ if (region[1] < region[0])\r
+ {\r
+ hiddenColumns.removeElementAt(i--);\r
+ }\r
+\r
+ if (region[0] < 0)\r
+ {\r
+ region[0] = 0;\r
+ }\r
+ if (region[1] < 0)\r
+ {\r
+ region[1] = 0;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Adjust hidden column boundaries based on a series of column additions or\r
+ * deletions in visible regions.\r
+ * \r
+ * @param shiftrecord\r
+ * @return\r
+ */\r
+ public ShiftList compensateForEdits(ShiftList shiftrecord)\r
+ {\r
+ if (shiftrecord != null)\r
+ {\r
+ Vector shifts = shiftrecord.shifts;\r
+ if (shifts != null && shifts.size() > 0)\r
+ {\r
+ int shifted = 0;\r
+ for (int i = 0, j = shifts.size(); i < j; i++)\r
+ {\r
+ int[] sh = (int[]) shifts.elementAt(i);\r
+ // compensateForEdit(shifted+sh[0], sh[1]);\r
+ compensateForDelEdits(shifted + sh[0], sh[1]);\r
+ shifted -= sh[1];\r
+ }\r
+ }\r
+ return shiftrecord.getInverse();\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * removes intersection of position,length ranges in deletions from the\r
+ * start,end regions marked in intervals.\r
+ * \r
+ * @param deletions\r
+ * @param intervals\r
+ * @return\r
+ */\r
+ private boolean pruneIntervalVector(Vector deletions, Vector intervals)\r
+ {\r
+ boolean pruned = false;\r
+ int i = 0, j = intervals.size() - 1, s = 0, t = deletions.size() - 1;\r
+ int hr[] = (int[]) intervals.elementAt(i);\r
+ int sr[] = (int[]) deletions.elementAt(s);\r
+ while (i <= j && s <= t)\r
+ {\r
+ boolean trailinghn = hr[1] >= sr[0];\r
+ if (!trailinghn)\r
+ {\r
+ if (i < j)\r
+ {\r
+ hr = (int[]) intervals.elementAt(++i);\r
+ }\r
+ else\r
+ {\r
+ i++;\r
+ }\r
+ continue;\r
+ }\r
+ int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert\r
+ if (endshift < hr[0] || endshift < sr[0])\r
+ { // leadinghc disjoint or not a deletion\r
+ if (s < t)\r
+ {\r
+ sr = (int[]) deletions.elementAt(++s);\r
+ }\r
+ else\r
+ {\r
+ s++;\r
+ }\r
+ continue;\r
+ }\r
+ boolean leadinghn = hr[0] >= sr[0];\r
+ boolean leadinghc = hr[0] < endshift;\r
+ boolean trailinghc = hr[1] < endshift;\r
+ if (leadinghn)\r
+ {\r
+ if (trailinghc)\r
+ { // deleted hidden region.\r
+ intervals.removeElementAt(i);\r
+ pruned = true;\r
+ j--;\r
+ if (i <= j)\r
+ {\r
+ hr = (int[]) intervals.elementAt(i);\r
+ }\r
+ continue;\r
+ }\r
+ if (leadinghc)\r
+ {\r
+ hr[0] = endshift; // clip c terminal region\r
+ leadinghn = !leadinghn;\r
+ pruned = true;\r
+ }\r
+ }\r
+ if (!leadinghn)\r
+ {\r
+ if (trailinghc)\r
+ {\r
+ if (trailinghn)\r
+ {\r
+ hr[1] = sr[0] - 1;\r
+ pruned = true;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // sr contained in hr\r
+ if (s < t)\r
+ {\r
+ sr = (int[]) deletions.elementAt(++s);\r
+ }\r
+ else\r
+ {\r
+ s++;\r
+ }\r
+ continue;\r
+ }\r
+ }\r
+ }\r
+ return pruned; // true if any interval was removed or modified by\r
+ // operations.\r
+ }\r
+\r
+ private boolean pruneColumnList(Vector deletion, Vector list)\r
+ {\r
+ int s = 0, t = deletion.size();\r
+ int[] sr = (int[]) list.elementAt(s++);\r
+ boolean pruned = false;\r
+ int i = 0, j = list.size();\r
+ while (i < j && s <= t)\r
+ {\r
+ int c = ((Integer) list.elementAt(i++)).intValue();\r
+ if (sr[0] <= c)\r
+ {\r
+ if (sr[1] + sr[0] >= c)\r
+ { // sr[1] -ve means inseriton.\r
+ list.removeElementAt(--i);\r
+ j--;\r
+ }\r
+ else\r
+ {\r
+ if (s < t)\r
+ {\r
+ sr = (int[]) deletion.elementAt(s);\r
+ }\r
+ s++;\r
+ }\r
+ }\r
+ }\r
+ return pruned;\r
+ }\r
+\r
+ /**\r
+ * remove any hiddenColumns or selected columns and shift remaining based on a\r
+ * series of position, range deletions.\r
+ * \r
+ * @param deletions\r
+ */\r
+ public void pruneDeletions(ShiftList deletions)\r
+ {\r
+ if (deletions != null)\r
+ {\r
+ Vector shifts = deletions.shifts;\r
+ if (shifts != null && shifts.size() > 0)\r
+ {\r
+ // delete any intervals intersecting.\r
+ if (hiddenColumns != null)\r
+ {\r
+ pruneIntervalVector(shifts, hiddenColumns);\r
+ if (hiddenColumns != null && hiddenColumns.size() == 0)\r
+ {\r
+ hiddenColumns = null;\r
+ }\r
+ }\r
+ if (selected != null && selected.size() > 0)\r
+ {\r
+ pruneColumnList(shifts, selected);\r
+ if (selected != null && selected.size() == 0)\r
+ {\r
+ selected = null;\r
+ }\r
+ }\r
+ // and shift the rest.\r
+ this.compensateForEdits(deletions);\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * This Method is used to return all the HiddenColumn regions less than the\r
+ * given index.\r
+ * \r
+ * @param end\r
+ * int\r
+ * @return Vector\r
+ */\r
+ public Vector getHiddenColumns()\r
+ {\r
+ return hiddenColumns;\r
+ }\r
+\r
+ /**\r
+ * Return absolute column index for a visible column index\r
+ * \r
+ * @param column\r
+ * 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 when\r
+ * hidden columns exist\r
+ * \r
+ * @param hiddenColumn\r
+ * 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
+ } 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
+ } 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 region of an alignment with\r
+ * hidden columns. In otherwords, the next hidden column.\r
+ * \r
+ * @param index\r
+ * 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
+ {\r
+ return region[0];\r
+ }\r
+\r
+ index++;\r
+ } while (index < hiddenColumns.size());\r
+ }\r
+\r
+ return alPos;\r
+\r
+ }\r
+\r
+ /**\r
+ * This method returns the leftmost limit of a region of an alignment with\r
+ * hidden columns. In otherwords, the previous hidden column.\r
+ * \r
+ * @param index\r
+ * 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
+ {\r
+ return region[1];\r
+ }\r
+\r
+ index--;\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
+ {\r
+ hiddenColumns = new Vector();\r
+ }\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
+ {\r
+ hiddenColumns.addElement(new int[]\r
+ { start, end });\r
+ }\r
+\r
+ }\r
+\r
+ /**\r
+ * This method will find a range of selected columns around the column\r
+ * specified\r
+ * \r
+ * @param res\r
+ * 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
+ {\r
+ removeElement(min);\r
+ min--;\r
+ }\r
+\r
+ while (contains(max))\r
+ {\r
+ removeElement(max);\r
+ max++;\r
+ }\r
+\r
+ min++;\r
+ max--;\r
+ if (min > max)\r
+ {\r
+ min = max;\r
+ }\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
+ {\r
+ hiddenColumns = null;\r
+ }\r
+ }\r
+\r
+ public boolean isVisible(int column)\r
+ {\r
+ if (hiddenColumns != null)\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
+\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * Copy constructor\r
+ * \r
+ * @param copy\r
+ */\r
+ public ColumnSelection(ColumnSelection copy)\r
+ {\r
+ if (copy != null)\r
+ {\r
+ if (copy.selected != null)\r
+ {\r
+ selected = new Vector();\r
+ for (int i = 0, j = copy.selected.size(); i < j; i++)\r
+ {\r
+ selected.addElement(copy.selected.elementAt(i));\r
+ }\r
+ }\r
+ if (copy.hiddenColumns != null)\r
+ {\r
+ hiddenColumns = new Vector(copy.hiddenColumns.size());\r
+ for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)\r
+ {\r
+ int[] rh, cp;\r
+ rh = (int[]) copy.hiddenColumns.elementAt(i);\r
+ if (rh != null)\r
+ {\r
+ cp = new int[rh.length];\r
+ System.arraycopy(rh, 0, cp, 0, rh.length);\r
+ hiddenColumns.addElement(cp);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * ColumnSelection\r
+ */\r
+ public ColumnSelection()\r
+ {\r
+ }\r
+\r
+ public String[] getVisibleSequenceStrings(int start, int end,\r
+ SequenceI[] seqs)\r
+ {\r
+ int i, iSize = seqs.length;\r
+ String selection[] = new String[iSize];\r
+ if (hiddenColumns != null && hiddenColumns.size() > 0)\r
+ {\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ StringBuffer visibleSeq = new StringBuffer();\r
+ Vector regions = getHiddenColumns();\r
+\r
+ int blockStart = start, blockEnd = end;\r
+ int[] region;\r
+ int hideStart, hideEnd;\r
+\r
+ for (int j = 0; j < regions.size(); j++)\r
+ {\r
+ region = (int[]) regions.elementAt(j);\r
+ hideStart = region[0];\r
+ hideEnd = region[1];\r
+\r
+ if (hideStart < start)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ blockStart = Math.min(blockStart, hideEnd + 1);\r
+ blockEnd = Math.min(blockEnd, hideStart);\r
+\r
+ if (blockStart > blockEnd)\r
+ {\r
+ break;\r
+ }\r
+\r
+ visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));\r
+\r
+ blockStart = hideEnd + 1;\r
+ blockEnd = end;\r
+ }\r
+\r
+ if (end > blockStart)\r
+ {\r
+ visibleSeq.append(seqs[i].getSequence(blockStart, end));\r
+ }\r
+\r
+ selection[i] = visibleSeq.toString();\r
+ }\r
+ }\r
+ else\r
+ {\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ selection[i] = seqs[i].getSequenceAsString(start, end);\r
+ }\r
+ }\r
+\r
+ return selection;\r
+ }\r
+\r
+ /**\r
+ * return all visible segments between the given start and end boundaries\r
+ * \r
+ * @param start\r
+ * (first column inclusive from 0)\r
+ * @param end\r
+ * (last column - not inclusive)\r
+ * @return int[] {i_start, i_end, ..} where intervals lie in start<=i_start<=i_end<end\r
+ */\r
+ public int[] getVisibleContigs(int start, int end)\r
+ {\r
+ if (hiddenColumns != null && hiddenColumns.size() > 0)\r
+ {\r
+ Vector visiblecontigs = new Vector();\r
+ Vector regions = getHiddenColumns();\r
+\r
+ int vstart = start;\r
+ int[] region;\r
+ int hideStart, hideEnd;\r
+\r
+ for (int j = 0; vstart < end && j < regions.size(); j++)\r
+ {\r
+ region = (int[]) regions.elementAt(j);\r
+ hideStart = region[0];\r
+ hideEnd = region[1];\r
+\r
+ if (hideEnd < vstart)\r
+ {\r
+ continue;\r
+ }\r
+ if (hideStart > vstart)\r
+ {\r
+ visiblecontigs.addElement(new int[]\r
+ { vstart, hideStart - 1 });\r
+ }\r
+ vstart = hideEnd + 1;\r
+ }\r
+\r
+ if (vstart < end)\r
+ {\r
+ visiblecontigs.addElement(new int[]\r
+ { vstart, end - 1 });\r
+ }\r
+ int[] vcontigs = new int[visiblecontigs.size() * 2];\r
+ for (int i = 0, j = visiblecontigs.size(); i < j; i++)\r
+ {\r
+ int[] vc = (int[]) visiblecontigs.elementAt(i);\r
+ visiblecontigs.setElementAt(null, i);\r
+ vcontigs[i * 2] = vc[0];\r
+ vcontigs[i * 2 + 1] = vc[1];\r
+ }\r
+ visiblecontigs.removeAllElements();\r
+ return vcontigs;\r
+ }\r
+ else\r
+ {\r
+ return new int[]\r
+ { start, end - 1 };\r
+ }\r
+ }\r
+\r
+ /**\r
+ * delete any columns in alignmentAnnotation that are hidden (including\r
+ * sequence associated annotation).\r
+ * \r
+ * @param alignmentAnnotation\r
+ */\r
+ public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)\r
+ {\r
+ makeVisibleAnnotation(-1, -1, alignmentAnnotation);\r
+ }\r
+\r
+ /**\r
+ * delete any columns in alignmentAnnotation that are hidden (including\r
+ * sequence associated annotation).\r
+ * \r
+ * @param start\r
+ * remove any annotation to the right of this column\r
+ * @param end\r
+ * remove any annotation to the left of this column\r
+ * @param alignmentAnnotation\r
+ * the annotation to operate on\r
+ */\r
+ public void makeVisibleAnnotation(int start, int end,\r
+ AlignmentAnnotation alignmentAnnotation)\r
+ {\r
+ if (alignmentAnnotation.annotations == null)\r
+ {\r
+ return;\r
+ }\r
+ if (start == end && end == -1)\r
+ {\r
+ start = 0;\r
+ end = alignmentAnnotation.annotations.length;\r
+ }\r
+ if (hiddenColumns != null && hiddenColumns.size() > 0)\r
+ {\r
+ // then mangle the alignmentAnnotation annotation array\r
+ Vector annels = new Vector();\r
+ Annotation[] els = null;\r
+ Vector regions = getHiddenColumns();\r
+ int blockStart = start, blockEnd = end;\r
+ int[] region;\r
+ int hideStart, hideEnd, w = 0;\r
+\r
+ for (int j = 0; j < regions.size(); j++)\r
+ {\r
+ region = (int[]) regions.elementAt(j);\r
+ hideStart = region[0];\r
+ hideEnd = region[1];\r
+\r
+ if (hideStart < start)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ blockStart = Math.min(blockStart, hideEnd + 1);\r
+ blockEnd = Math.min(blockEnd, hideStart);\r
+\r
+ if (blockStart > blockEnd)\r
+ {\r
+ break;\r
+ }\r
+\r
+ annels.addElement(els = new Annotation[blockEnd - blockStart]);\r
+ System.arraycopy(alignmentAnnotation.annotations, blockStart, els,\r
+ 0, els.length);\r
+ w += els.length;\r
+ blockStart = hideEnd + 1;\r
+ blockEnd = end;\r
+ }\r
+\r
+ if (end > blockStart)\r
+ {\r
+ annels.addElement(els = new Annotation[end - blockStart + 1]);\r
+ if ((els.length+blockStart)<= alignmentAnnotation.annotations.length)\r
+ {\r
+ // copy just the visible segment of the annotation row\r
+ System.arraycopy(alignmentAnnotation.annotations, blockStart,\r
+ els, 0, els.length);\r
+ }\r
+ else\r
+ {\r
+ // copy to the end of the annotation row\r
+ System.arraycopy(alignmentAnnotation.annotations, blockStart,\r
+ els, 0, (alignmentAnnotation.annotations.length - blockStart));\r
+ }\r
+ w += els.length;\r
+ }\r
+ if (w == 0)\r
+ return;\r
+ Enumeration e = annels.elements();\r
+ alignmentAnnotation.annotations = new Annotation[w];\r
+ w = 0;\r
+ while (e.hasMoreElements())\r
+ {\r
+ Annotation[] chnk = (Annotation[]) e.nextElement();\r
+ System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,\r
+ chnk.length);\r
+ w += chnk.length;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ alignmentAnnotation.restrict(start, end);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Invert the column selection from first to end-1. leaves hiddenColumns\r
+ * untouched (and unselected)\r
+ * \r
+ * @param first\r
+ * @param end\r
+ */\r
+ public void invertColumnSelection(int first, int width)\r
+ {\r
+ boolean hasHidden = hiddenColumns != null && hiddenColumns.size() > 0;\r
+ for (int i = first; i < width; i++)\r
+ {\r
+ if (contains(i))\r
+ {\r
+ removeElement(i);\r
+ }\r
+ else\r
+ {\r
+ if (!hasHidden || isVisible(i))\r
+ {\r
+ addElement(i);\r
+ }\r
+ }\r
+ }\r
+ }\r
+}\r