/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.\r
* \r
}\r
\r
/**\r
- * Use this method to find out where a column will appear in the visible alignment when\r
- * hidden columns exist. If the column is not visible, then the left-most visible column will always be returned.\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
result -= region[1] + 1 - region[0];\r
}\r
} while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));\r
- if (hiddenColumn>region[0] && hiddenColumn<region[1])\r
+ if (hiddenColumn > region[0] && hiddenColumn < region[1])\r
{\r
- return region[0]+hiddenColumn-result;\r
+ return region[0] + hiddenColumn - result;\r
}\r
}\r
return result; // return the shifted position after removing hidden columns.\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