-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 column will appear in the visible\r
- * alignment when hidden columns exist. If the column is not visible, then the\r
- * left-most visible column will always be returned.\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[] region;\r
- do\r
- {\r
- region = (int[]) hiddenColumns.elementAt(index++);\r
- if (hiddenColumn > region[1])\r
- {\r
- result -= region[1] + 1 - region[0];\r
- }\r
- } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));\r
- if (hiddenColumn > region[0] && hiddenColumn < region[1])\r
- {\r
- return region[0] + hiddenColumn - result;\r
- }\r
- }\r
- return result; // return the shifted position after removing hidden columns.\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\r
- * 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,\r
- (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
- /**\r
- * add in any unselected columns from the given column selection, excluding\r
- * any that are hidden.\r
- * \r
- * @param colsel\r
- */\r
- public void addElementsFrom(ColumnSelection colsel)\r
- {\r
- if (colsel != null && colsel.size() > 0)\r
- {\r
- Enumeration e = colsel.getSelected().elements();\r
- while (e.hasMoreElements())\r
- {\r
- Object eo = e.nextElement();\r
- if (hiddenColumns != null && isVisible(((Integer) eo).intValue()))\r
- {\r
- if (!selected.contains(eo))\r
- {\r
- selected.addElement(eo);\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * set the selected columns the given column selection, excluding any columns\r
- * that are hidden.\r
- * \r
- * @param colsel\r
- */\r
- public void setElementsFrom(ColumnSelection colsel)\r
- {\r
- selected = new Vector();\r
- if (colsel.selected != null && colsel.selected.size() > 0)\r
- {\r
- if (hiddenColumns != null && hiddenColumns.size() > 0)\r
- {\r
- // only select visible columns in this columns selection\r
- selected = new Vector();\r
- addElementsFrom(colsel);\r
- }\r
- else\r
- {\r
- // add everything regardless\r
- Enumeration en = colsel.selected.elements();\r
- while (en.hasMoreElements())\r
- {\r
- selected.addElement(en.nextElement());\r
- }\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * Add gaps into the sequences aligned to profileseq under the given\r
- * AlignmentView\r
- * \r
- * @param profileseq\r
- * @param al\r
- * - alignment to have gaps inserted into it\r
- * @param input\r
- * - alignment view where sequence corresponding to profileseq is\r
- * first entry\r
- * @return new Column selection for new alignment view, with insertions into\r
- * profileseq marked as hidden.\r
- */\r
- public static ColumnSelection propagateInsertions(SequenceI profileseq,\r
- Alignment al, AlignmentView input)\r
- {\r
- int profsqpos = 0;\r
-\r
- // return propagateInsertions(profileseq, al, )\r
- char gc = al.getGapCharacter();\r
- Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);\r
- ColumnSelection nview = (ColumnSelection) alandcolsel[1];\r
- SequenceI origseq = ((SequenceI[]) alandcolsel[0])[profsqpos];\r
- nview.propagateInsertions(profileseq, al, origseq);\r
- return nview;\r
- }\r
-\r
- /**\r
- * \r
- * @param profileseq\r
- * - sequence in al which corresponds to origseq\r
- * @param al\r
- * - alignment which is to have gaps inserted into it\r
- * @param origseq\r
- * - sequence corresponding to profileseq which defines gap map for\r
- * modifying al\r
- */\r
- public void propagateInsertions(SequenceI profileseq, AlignmentI al,\r
- SequenceI origseq)\r
- {\r
- char gc = al.getGapCharacter();\r
- // recover mapping between sequence's non-gap positions and positions\r
- // mapping to view.\r
- pruneDeletions(ShiftList.parseMap(origseq.gapMap()));\r
- int[] viscontigs = getVisibleContigs(0, profileseq.getLength());\r
- int spos = 0;\r
- int offset = 0;\r
- // input.pruneDeletions(ShiftList.parseMap(((SequenceI[])\r
- // alandcolsel[0])[0].gapMap()))\r
- // add profile to visible contigs\r
- for (int v = 0; v < viscontigs.length; v += 2)\r
- {\r
- if (viscontigs[v] > spos)\r
- {\r
- StringBuffer sb = new StringBuffer();\r
- for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)\r
- {\r
- sb.append(gc);\r
- }\r
- for (int s = 0, ns = al.getHeight(); s < ns; s++)\r
- {\r
- SequenceI sqobj = al.getSequenceAt(s);\r
- if (sqobj != profileseq)\r
- {\r
- String sq = al.getSequenceAt(s).getSequenceAsString();\r
- if (sq.length() <= spos + offset)\r
- {\r
- // pad sequence\r
- int diff = spos + offset - sq.length() - 1;\r
- if (diff > 0)\r
- {\r
- // pad gaps\r
- sq = sq + sb;\r
- while ((diff = spos + offset - sq.length() - 1) > 0)\r
- {\r
- // sq = sq\r
- // + ((diff >= sb.length()) ? sb.toString() : sb\r
- // .substring(0, diff));\r
- if (diff >= sb.length())\r
- {\r
- sq += sb.toString();\r
- }\r
- else\r
- {\r
- char[] buf = new char[diff];\r
- sb.getChars(0, diff, buf, 0);\r
- sq += buf.toString();\r
- }\r
- }\r
- }\r
- sq += sb.toString();\r
- }\r
- else\r
- {\r
- al.getSequenceAt(s).setSequence(\r
- sq.substring(0, spos + offset) + sb.toString()\r
- + sq.substring(spos + offset));\r
- }\r
- }\r
- }\r
- // offset+=sb.length();\r
- }\r
- spos = viscontigs[v + 1] + 1;\r
- }\r
- if ((offset + spos) < profileseq.getLength())\r
- {\r
- // pad the final region with gaps.\r
- StringBuffer sb = new StringBuffer();\r
- for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)\r
- {\r
- sb.append(gc);\r
- }\r
- for (int s = 0, ns = al.getHeight(); s < ns; s++)\r
- {\r
- SequenceI sqobj = al.getSequenceAt(s);\r
- if (sqobj == profileseq)\r
- {\r
- continue;\r
- }\r
- String sq = sqobj.getSequenceAsString();\r
- // pad sequence\r
- int diff = origseq.getLength() - sq.length();\r
- while (diff > 0)\r
- {\r
- // sq = sq\r
- // + ((diff >= sb.length()) ? sb.toString() : sb\r
- // .substring(0, diff));\r
- if (diff >= sb.length())\r
- {\r
- sq += sb.toString();\r
- }\r
- else\r
- {\r
- char[] buf = new char[diff];\r
- sb.getChars(0, diff, buf, 0);\r
- sq += buf.toString();\r
- }\r
- diff = origseq.getLength() - sq.length();\r
- }\r
- }\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.datamodel;
+
+import java.util.*;
+
+import jalview.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));
+ }
+
+ /**
+ * Column number at position i in selection
+ *
+ * @param i
+ * index into selected columns
+ *
+ * @return column number in alignment
+ */
+ public int columnAt(int i)
+ {
+ return ((Integer) selected.elementAt(i)).intValue();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int size()
+ {
+ return selected.size();
+ }
+
+ /**
+ * 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 (columnAt(i) > max)
+ {
+ max = columnAt(i);
+ }
+ }
+
+ return max;
+ }
+
+ /**
+ * Leftmost column in selection
+ *
+ * @return column index of leftmost column in selection
+ */
+ 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 left
+ * shift in edit (+ve for removal, or -ve for inserts)
+ */
+ public Vector compensateForEdit(int start, int change)
+ {
+ Vector deletedHiddenColumns = null;
+ for (int i = 0; i < size(); i++)
+ {
+ int temp = columnAt(i);
+
+ if (temp >= start)
+ {
+ selected.setElementAt(new Integer(temp - change), i);
+ }
+ }
+
+ if (hiddenColumns != null)
+ {
+ deletedHiddenColumns = new Vector();
+ int hSize = hiddenColumns.size();
+ for (int i = 0; i < hSize; i++)
+ {
+ int[] region = (int[]) hiddenColumns.elementAt(i);
+ if (region[0] > start && start + change > region[1])
+ {
+ deletedHiddenColumns.addElement(hiddenColumns.elementAt(i));
+
+ hiddenColumns.removeElementAt(i);
+ i--;
+ hSize--;
+ continue;
+ }
+
+ if (region[0] > start)
+ {
+ region[0] -= change;
+ region[1] -= change;
+ }
+
+ if (region[0] < 0)
+ {
+ region[0] = 0;
+ }
+
+ }
+
+ this.revealHiddenColumns(0);
+ }
+
+ return deletedHiddenColumns;
+ }
+
+ /**
+ * 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 < 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();
+ }
+ 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++;
+ }
+ }
+ }
+ return pruned;
+ }
+
+ /**
+ * remove any hiddenColumns or selected columns and shift remaining based on a
+ * series of position, range deletions.
+ *
+ * @param deletions
+ */
+ 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);
+ }
+ }
+ }
+
+ /**
+ * 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 column will appear in the visible
+ * alignment when hidden columns exist. If the column is not visible, then the
+ * left-most visible column will always be returned.
+ *
+ * @param hiddenColumn
+ * int
+ * @return int
+ */
+ public int findColumnPosition(int hiddenColumn)
+ {
+ int result = hiddenColumn;
+ if (hiddenColumns != null)
+ {
+ int index = 0;
+ int[] region;
+ do
+ {
+ region = (int[]) hiddenColumns.elementAt(index++);
+ if (hiddenColumn > region[1])
+ {
+ result -= region[1] + 1 - region[0];
+ }
+ } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
+ if (hiddenColumn > region[0] && hiddenColumn < region[1])
+ {
+ return region[0] + hiddenColumn - result;
+ }
+ }
+ return result; // return the shifted position after removing hidden columns.
+ }
+
+ /**
+ * 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 leftmost limit of a region of an alignment with
+ * hidden columns. In otherwords, the previous hidden column.
+ *
+ * @param index
+ * int
+ */
+ public int getHiddenBoundaryLeft(int alPos)
+ {
+ if (hiddenColumns != null)
+ {
+ int index = hiddenColumns.size() - 1;
+ do
+ {
+ int[] region = (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--;
+ if (min > 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)
+ {
+ if (hiddenColumns != null)
+ 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.addElement(copy.selected.elementAt(i));
+ }
+ }
+ if (copy.hiddenColumns != null)
+ {
+ hiddenColumns = new Vector(copy.hiddenColumns.size());
+ 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.addElement(cp);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * ColumnSelection
+ */
+ public ColumnSelection()
+ {
+ }
+
+ 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)
+ {
+ 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++)
+ {
+ region = (int[]) regions.elementAt(j);
+ hideStart = region[0];
+ hideEnd = region[1];
+
+ if (hideStart < start)
+ {
+ continue;
+ }
+
+ blockStart = Math.min(blockStart, hideEnd + 1);
+ blockEnd = Math.min(blockEnd, hideStart);
+
+ if (blockStart > blockEnd)
+ {
+ break;
+ }
+
+ visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+
+ blockStart = hideEnd + 1;
+ blockEnd = end;
+ }
+
+ if (end > blockStart)
+ {
+ visibleSeq.append(seqs[i].getSequence(blockStart, end));
+ }
+
+ selection[i] = visibleSeq.toString();
+ }
+ }
+ else
+ {
+ for (i = 0; i < iSize; i++)
+ {
+ selection[i] = seqs[i].getSequenceAsString(start, end);
+ }
+ }
+
+ return selection;
+ }
+
+ /**
+ * return all visible segments between the given start and end boundaries
+ *
+ * @param start
+ * (first column inclusive from 0)
+ * @param end
+ * (last column - not inclusive)
+ * @return int[] {i_start, i_end, ..} where intervals lie in
+ * start<=i_start<=i_end<end
+ */
+ public int[] getVisibleContigs(int start, int end)
+ {
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
+ {
+ Vector visiblecontigs = new Vector();
+ Vector regions = getHiddenColumns();
+
+ int vstart = start;
+ int[] region;
+ int hideStart, hideEnd;
+
+ for (int j = 0; vstart < end && j < regions.size(); j++)
+ {
+ 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;
+ }
+
+ 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.elementAt(i);
+ visiblecontigs.setElementAt(null, i);
+ vcontigs[i * 2] = vc[0];
+ vcontigs[i * 2 + 1] = vc[1];
+ }
+ visiblecontigs.removeAllElements();
+ return vcontigs;
+ }
+ else
+ {
+ return new int[]
+ { start, end - 1 };
+ }
+ }
+
+ /**
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
+ *
+ * @param alignmentAnnotation
+ */
+ public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
+ {
+ makeVisibleAnnotation(-1, -1, alignmentAnnotation);
+ }
+
+ /**
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
+ *
+ * @param start
+ * remove any annotation to the right of this column
+ * @param end
+ * remove any annotation to the left of this column
+ * @param alignmentAnnotation
+ * the annotation to operate on
+ */
+ public void makeVisibleAnnotation(int start, int end,
+ AlignmentAnnotation alignmentAnnotation)
+ {
+ if (alignmentAnnotation.annotations == null)
+ {
+ return;
+ }
+ if (start == end && end == -1)
+ {
+ start = 0;
+ end = alignmentAnnotation.annotations.length;
+ }
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
+ {
+ // then mangle the alignmentAnnotation annotation array
+ Vector annels = new Vector();
+ Annotation[] els = null;
+ Vector regions = getHiddenColumns();
+ int blockStart = start, blockEnd = end;
+ int[] region;
+ int hideStart, hideEnd, w = 0;
+
+ for (int j = 0; j < regions.size(); j++)
+ {
+ region = (int[]) regions.elementAt(j);
+ hideStart = region[0];
+ hideEnd = region[1];
+
+ if (hideStart < start)
+ {
+ continue;
+ }
+
+ blockStart = Math.min(blockStart, hideEnd + 1);
+ blockEnd = Math.min(blockEnd, hideStart);
+
+ if (blockStart > blockEnd)
+ {
+ break;
+ }
+
+ annels.addElement(els = new Annotation[blockEnd - blockStart]);
+ System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
+ 0, els.length);
+ w += els.length;
+ blockStart = hideEnd + 1;
+ blockEnd = end;
+ }
+
+ if (end > blockStart)
+ {
+ annels.addElement(els = new Annotation[end - blockStart + 1]);
+ if ((els.length + blockStart) <= alignmentAnnotation.annotations.length)
+ {
+ // copy just the visible segment of the annotation row
+ System.arraycopy(alignmentAnnotation.annotations, blockStart,
+ els, 0, els.length);
+ }
+ else
+ {
+ // copy to the end of the annotation row
+ System.arraycopy(alignmentAnnotation.annotations, blockStart,
+ els, 0,
+ (alignmentAnnotation.annotations.length - blockStart));
+ }
+ w += els.length;
+ }
+ if (w == 0)
+ return;
+ Enumeration e = annels.elements();
+ alignmentAnnotation.annotations = new Annotation[w];
+ w = 0;
+ while (e.hasMoreElements())
+ {
+ Annotation[] chnk = (Annotation[]) e.nextElement();
+ System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
+ chnk.length);
+ w += chnk.length;
+ }
+ }
+ else
+ {
+ alignmentAnnotation.restrict(start, end);
+ }
+ }
+
+ /**
+ * Invert the column selection from first to end-1. leaves hiddenColumns
+ * untouched (and unselected)
+ *
+ * @param first
+ * @param end
+ */
+ public void invertColumnSelection(int first, int width)
+ {
+ boolean hasHidden = hiddenColumns != null && hiddenColumns.size() > 0;
+ for (int i = first; i < width; i++)
+ {
+ if (contains(i))
+ {
+ removeElement(i);
+ }
+ else
+ {
+ if (!hasHidden || isVisible(i))
+ {
+ addElement(i);
+ }
+ }
+ }
+ }
+
+ /**
+ * add in any unselected columns from the given column selection, excluding
+ * any that are hidden.
+ *
+ * @param colsel
+ */
+ public void addElementsFrom(ColumnSelection colsel)
+ {
+ if (colsel != null && colsel.size() > 0)
+ {
+ Enumeration e = colsel.getSelected().elements();
+ while (e.hasMoreElements())
+ {
+ Object eo = e.nextElement();
+ if (hiddenColumns != null && isVisible(((Integer) eo).intValue()))
+ {
+ if (!selected.contains(eo))
+ {
+ selected.addElement(eo);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * set the selected columns the given column selection, excluding any columns
+ * that are hidden.
+ *
+ * @param colsel
+ */
+ public void setElementsFrom(ColumnSelection colsel)
+ {
+ selected = new Vector();
+ if (colsel.selected != null && colsel.selected.size() > 0)
+ {
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
+ {
+ // only select visible columns in this columns selection
+ selected = new Vector();
+ addElementsFrom(colsel);
+ }
+ else
+ {
+ // add everything regardless
+ Enumeration en = colsel.selected.elements();
+ while (en.hasMoreElements())
+ {
+ selected.addElement(en.nextElement());
+ }
+ }
+ }
+ }
+
+ /**
+ * Add gaps into the sequences aligned to profileseq under the given
+ * AlignmentView
+ *
+ * @param profileseq
+ * @param al
+ * - alignment to have gaps inserted into it
+ * @param input
+ * - alignment view where sequence corresponding to profileseq is
+ * first entry
+ * @return new Column selection for new alignment view, with insertions into
+ * profileseq marked as hidden.
+ */
+ public static ColumnSelection propagateInsertions(SequenceI profileseq,
+ Alignment al, AlignmentView input)
+ {
+ int profsqpos = 0;
+
+ // return propagateInsertions(profileseq, al, )
+ char gc = al.getGapCharacter();
+ Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);
+ ColumnSelection nview = (ColumnSelection) alandcolsel[1];
+ SequenceI origseq = ((SequenceI[]) alandcolsel[0])[profsqpos];
+ nview.propagateInsertions(profileseq, al, origseq);
+ return nview;
+ }
+
+ /**
+ *
+ * @param profileseq
+ * - sequence in al which corresponds to origseq
+ * @param al
+ * - alignment which is to have gaps inserted into it
+ * @param origseq
+ * - sequence corresponding to profileseq which defines gap map for
+ * modifying al
+ */
+ public void propagateInsertions(SequenceI profileseq, AlignmentI al,
+ SequenceI origseq)
+ {
+ char gc = al.getGapCharacter();
+ // recover mapping between sequence's non-gap positions and positions
+ // mapping to view.
+ pruneDeletions(ShiftList.parseMap(origseq.gapMap()));
+ int[] viscontigs = getVisibleContigs(0, profileseq.getLength());
+ int spos = 0;
+ int offset = 0;
+ // input.pruneDeletions(ShiftList.parseMap(((SequenceI[])
+ // alandcolsel[0])[0].gapMap()))
+ // add profile to visible contigs
+ for (int v = 0; v < viscontigs.length; v += 2)
+ {
+ if (viscontigs[v] > spos)
+ {
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
+ {
+ sb.append(gc);
+ }
+ for (int s = 0, ns = al.getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = al.getSequenceAt(s);
+ if (sqobj != profileseq)
+ {
+ String sq = al.getSequenceAt(s).getSequenceAsString();
+ if (sq.length() <= spos + offset)
+ {
+ // pad sequence
+ int diff = spos + offset - sq.length() - 1;
+ if (diff > 0)
+ {
+ // pad gaps
+ sq = sq + sb;
+ while ((diff = spos + offset - sq.length() - 1) > 0)
+ {
+ // sq = sq
+ // + ((diff >= sb.length()) ? sb.toString() : sb
+ // .substring(0, diff));
+ if (diff >= sb.length())
+ {
+ sq += sb.toString();
+ }
+ else
+ {
+ char[] buf = new char[diff];
+ sb.getChars(0, diff, buf, 0);
+ sq += buf.toString();
+ }
+ }
+ }
+ sq += sb.toString();
+ }
+ else
+ {
+ al.getSequenceAt(s).setSequence(
+ sq.substring(0, spos + offset) + sb.toString()
+ + sq.substring(spos + offset));
+ }
+ }
+ }
+ // offset+=sb.length();
+ }
+ spos = viscontigs[v + 1] + 1;
+ }
+ if ((offset + spos) < profileseq.getLength())
+ {
+ // pad the final region with gaps.
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
+ {
+ sb.append(gc);
+ }
+ for (int s = 0, ns = al.getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = al.getSequenceAt(s);
+ if (sqobj == profileseq)
+ {
+ continue;
+ }
+ String sq = sqobj.getSequenceAsString();
+ // pad sequence
+ int diff = origseq.getLength() - sq.length();
+ while (diff > 0)
+ {
+ // sq = sq
+ // + ((diff >= sb.length()) ? sb.toString() : sb
+ // .substring(0, diff));
+ if (diff >= sb.length())
+ {
+ sq += sb.toString();
+ }
+ else
+ {
+ char[] buf = new char[diff];
+ sb.getChars(0, diff, buf, 0);
+ sq += buf.toString();
+ }
+ diff = origseq.getLength() - sq.length();
+ }
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff