/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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 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
+ * This file is part of Jalview.\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
+ * 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
- * 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
+ * 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
* Add a column to the selection\r
* \r
* @param col\r
- * index of column\r
+ * index of column\r
*/\r
public void addElement(int col)\r
{\r
* removes col from selection\r
* \r
* @param col\r
- * index of column to be removed\r
+ * index of column to be removed\r
*/\r
public void removeElement(int col)\r
{\r
* removes a range of columns from the selection\r
* \r
* @param start\r
- * int - first column in range to be removed\r
+ * int - first column in range to be removed\r
* @param end\r
- * int - last col\r
+ * int - last col\r
*/\r
public void removeElements(int start, int end)\r
{\r
/**\r
* \r
* @param col\r
- * index to search for in column selection\r
+ * index to search for in column selection\r
* \r
* @return true if Integer(col) is in selection.\r
*/\r
* Column number at position i in selection\r
* \r
* @param i\r
- * index into selected columns\r
+ * index into selected columns\r
* \r
* @return column number in alignment\r
*/\r
* propagate shift in alignment columns to column selection\r
* \r
* @param start\r
- * beginning of edit\r
+ * beginning of edit\r
* @param left\r
- * shift in edit (+ve for removal, or -ve for inserts)\r
+ * shift in edit (+ve for removal, or -ve for inserts)\r
*/\r
public Vector compensateForEdit(int start, int change)\r
{\r
* compensateForEdit - allowing for edits within hidden regions\r
* \r
* @param start\r
- * beginning of edit\r
+ * beginning of edit\r
* @param left\r
- * shift in edit (+ve for removal, or -ve for inserts)\r
+ * shift in edit (+ve for removal, or -ve for inserts)\r
*/\r
private void compensateForDelEdits(int start, int change)\r
{\r
}\r
}\r
return pruned; // true if any interval was removed or modified by\r
- // operations.\r
+ // operations.\r
}\r
\r
private boolean pruneColumnList(Vector deletion, Vector list)\r
* given index.\r
* \r
* @param end\r
- * int\r
+ * int\r
* @return Vector\r
*/\r
public Vector getHiddenColumns()\r
* Return absolute column index for a visible column index\r
* \r
* @param column\r
- * int column index in alignment view\r
+ * int column index in alignment view\r
* @return alignment column index for column\r
*/\r
public int adjustForHiddenColumns(int column)\r
}\r
\r
/**\r
- * Use this method to find out where a visible column is in the alignment when\r
- * hidden columns exist\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
+ * int\r
* @return int\r
*/\r
public int findColumnPosition(int hiddenColumn)\r
if (hiddenColumns != null)\r
{\r
int index = 0;\r
- int gaps = 0;\r
+ int[] region;\r
do\r
{\r
- int[] region = (int[]) hiddenColumns.elementAt(index);\r
+ 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
+ } 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
-\r
- return result;\r
+ return result; // return the shifted position after removing hidden columns.\r
}\r
\r
/**\r
* hidden columns. In otherwords, the next hidden column.\r
* \r
* @param index\r
- * int\r
+ * int\r
*/\r
public int getHiddenBoundaryRight(int alPos)\r
{\r
* hidden columns. In otherwords, the previous hidden column.\r
* \r
* @param index\r
- * int\r
+ * int\r
*/\r
public int getHiddenBoundaryLeft(int alPos)\r
{\r
* specified\r
* \r
* @param res\r
- * int\r
+ * int\r
*/\r
public void hideColumns(int col)\r
{\r
* return all visible segments between the given start and end boundaries\r
* \r
* @param start\r
- * (first column inclusive from 0)\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
+ * (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
* sequence associated annotation).\r
* \r
* @param start\r
- * remove any annotation to the right of this column\r
+ * remove any annotation to the right of this column\r
* @param end\r
- * remove any annotation to the left of this column\r
+ * remove any annotation to the left of this column\r
* @param alignmentAnnotation\r
- * the annotation to operate on\r
+ * the annotation to operate on\r
*/\r
public void makeVisibleAnnotation(int start, int end,\r
AlignmentAnnotation alignmentAnnotation)\r
if (end > blockStart)\r
{\r
annels.addElement(els = new Annotation[end - blockStart + 1]);\r
- if ((els.length+blockStart)<= alignmentAnnotation.annotations.length)\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
{\r
// copy to the end of the annotation row\r
System.arraycopy(alignmentAnnotation.annotations, blockStart,\r
- els, 0, (alignmentAnnotation.annotations.length - blockStart));\r
+ els, 0,\r
+ (alignmentAnnotation.annotations.length - blockStart));\r
}\r
w += els.length;\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 - alignment to have gaps inserted into it\r
+ * @param input - alignment view where sequence corresponding to profileseq is first entry\r
+ * @return new Column selection for new alignment view, with insertions into 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,\r
+ al, origseq);\r
+ return nview;\r
+ }\r
+ /**\r
+ * \r
+ * @param profileseq - sequence in al which corresponds to origseq \r
+ * @param al - alignment which is to have gaps inserted into it\r
+ * @param origseq - sequence corresponding to profileseq which defines gap map for modifying al\r
+ */\r
+ public void propagateInsertions(SequenceI profileseq, AlignmentI al, 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\r
+ .parseMap(origseq\r
+ .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
+ sq+=sb.toString();\r
+ } else {\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
+ sq+=sb.toString();\r
+ } else {\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
git://source.jalview.org / jalview.git / blobdiff