-package jalview.datamodel;
-
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-public class AlignmentView
-{
- /**
- * Transient object compactly representing a 'view' of an alignment - with discontinuities marked.
- */
- private SeqCigar[] sequences = null;
- private int[] contigs = null;
- public AlignmentView(CigarArray seqcigararray)
- {
- if (!seqcigararray.isSeqCigarArray())
- throw new Error("Implementation Error - can only make an alignment view from a CigarArray of sequences.");
- //contigs = seqcigararray.applyDeletions();
- contigs = seqcigararray.getDeletedRegions();
- sequences = seqcigararray.getSeqCigarArray();
- }
-
- public void setSequences(SeqCigar[] sequences)
- {
- this.sequences = sequences;
- }
-
- public void setContigs(int[] contigs)
- {
- this.contigs = contigs;
- }
-
- public SeqCigar[] getSequences()
- {
- return sequences;
- }
-
- public int[] getContigs()
- {
- return contigs;
- }
- public Object[] getAlignmentAndColumnSelection(char gapCharacter) {
- ColumnSelection colsel = new ColumnSelection();
-
- return new Object[] { SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel, contigs), colsel};
- }
- /**
- * getSequenceStrings
- *
- * @param c char
- * @return String[]
- */
- public String[] getSequenceStrings(char c)
- {
- String[] seqs=new String[sequences.length];
- for (int n=0; n<sequences.length; n++) {
- seqs[n] = sequences[n].getSequenceString(c);
- }
- return seqs;
- }
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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
+/**\r
+ * <p>\r
+ * Title:\r
+ * </p>\r
+ * \r
+ * <p>\r
+ * Description:\r
+ * </p>\r
+ * \r
+ * <p>\r
+ * Copyright: Copyright (c) 2004\r
+ * </p>\r
+ * \r
+ * <p>\r
+ * Company: Dundee University\r
+ * </p>\r
+ * \r
+ * @author not attributable\r
+ * @version 1.0\r
+ */\r
+public class AlignmentView\r
+{\r
+ /**\r
+ * Transient object compactly representing a 'view' of an alignment - with\r
+ * discontinuities marked.\r
+ */\r
+ private SeqCigar[] sequences = null;\r
+\r
+ private int[] contigs = null;\r
+\r
+ private int width = 0;\r
+\r
+ private int firstCol = 0;\r
+\r
+ public AlignmentView(CigarArray seqcigararray)\r
+ {\r
+ if (!seqcigararray.isSeqCigarArray())\r
+ {\r
+ throw new Error(\r
+ "Implementation Error - can only make an alignment view from a CigarArray of sequences.");\r
+ }\r
+ // contigs = seqcigararray.applyDeletions();\r
+ contigs = seqcigararray.getDeletedRegions();\r
+ sequences = seqcigararray.getSeqCigarArray();\r
+ width = seqcigararray.getWidth(); // visible width\r
+ }\r
+\r
+ /**\r
+ * Create an alignmentView where the first column corresponds with the\r
+ * 'firstcol' column of some reference alignment\r
+ * \r
+ * @param sdata\r
+ * @param firstcol\r
+ */\r
+ public AlignmentView(CigarArray sdata, int firstcol)\r
+ {\r
+ this(sdata);\r
+ firstCol = firstcol;\r
+ }\r
+\r
+ public void setSequences(SeqCigar[] sequences)\r
+ {\r
+ this.sequences = sequences;\r
+ }\r
+\r
+ public void setContigs(int[] contigs)\r
+ {\r
+ this.contigs = contigs;\r
+ }\r
+\r
+ public SeqCigar[] getSequences()\r
+ {\r
+ return sequences;\r
+ }\r
+\r
+ /**\r
+ * @see CigarArray.getDeletedRegions\r
+ * @return int[] { vis_start, sym_start, length }\r
+ */\r
+ public int[] getContigs()\r
+ {\r
+ return contigs;\r
+ }\r
+\r
+ /**\r
+ * get the full alignment and a columnselection object marking the hidden\r
+ * regions\r
+ * \r
+ * @param gapCharacter\r
+ * char\r
+ * @return Object[] { SequenceI[], ColumnSelection}\r
+ */\r
+ public Object[] getAlignmentAndColumnSelection(char gapCharacter)\r
+ {\r
+ ColumnSelection colsel = new ColumnSelection();\r
+\r
+ return new Object[]\r
+ {\r
+ SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,\r
+ contigs), colsel };\r
+ }\r
+\r
+ /**\r
+ * getSequenceStrings\r
+ * \r
+ * @param c\r
+ * char\r
+ * @return String[]\r
+ */\r
+ public String[] getSequenceStrings(char c)\r
+ {\r
+ String[] seqs = new String[sequences.length];\r
+ for (int n = 0; n < sequences.length; n++)\r
+ {\r
+ String fullseq = sequences[n].getSequenceString(c);\r
+ if (contigs != null)\r
+ {\r
+ seqs[n] = "";\r
+ int p = 0;\r
+ for (int h = 0; h < contigs.length; h += 3)\r
+ {\r
+ seqs[n] += fullseq.substring(p, contigs[h + 1]);\r
+ p = contigs[h + 1] + contigs[h + 2];\r
+ }\r
+ seqs[n] += fullseq.substring(p);\r
+ }\r
+ else\r
+ {\r
+ seqs[n] = fullseq;\r
+ }\r
+ }\r
+ return seqs;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return visible number of columns in alignment view\r
+ */\r
+ public int getWidth()\r
+ {\r
+ return width;\r
+ }\r
+\r
+ protected void setWidth(int width)\r
+ {\r
+ this.width = width;\r
+ }\r
+\r
+ /**\r
+ * get the contiguous subalignments in an alignment view.\r
+ * \r
+ * @param gapCharacter\r
+ * char\r
+ * @return SequenceI[][]\r
+ */\r
+ public SequenceI[][] getVisibleContigs(char gapCharacter)\r
+ {\r
+ SequenceI[][] smsa;\r
+ int njobs = 1;\r
+ if (sequences == null || width <= 0)\r
+ {\r
+ return null;\r
+ }\r
+ if (contigs != null && contigs.length > 0)\r
+ {\r
+ int start = 0;\r
+ njobs = 0;\r
+ int fwidth = width;\r
+ for (int contig = 0; contig < contigs.length; contig += 3)\r
+ {\r
+ if ((contigs[contig + 1] - start) > 0)\r
+ {\r
+ njobs++;\r
+ }\r
+ fwidth += contigs[contig + 2]; // end up with full region width\r
+ // (including hidden regions)\r
+ start = contigs[contig + 1] + contigs[contig + 2];\r
+ }\r
+ if (start < fwidth)\r
+ {\r
+ njobs++;\r
+ }\r
+ smsa = new SequenceI[njobs][];\r
+ start = 0;\r
+ int j = 0;\r
+ for (int contig = 0; contig < contigs.length; contig += 3)\r
+ {\r
+ if (contigs[contig + 1] - start > 0)\r
+ {\r
+ SequenceI mseq[] = new SequenceI[sequences.length];\r
+ for (int s = 0; s < mseq.length; s++)\r
+ {\r
+ mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(\r
+ start, contigs[contig + 1]);\r
+ }\r
+ smsa[j] = mseq;\r
+ j++;\r
+ }\r
+ start = contigs[contig + 1] + contigs[contig + 2];\r
+ }\r
+ if (start < fwidth)\r
+ {\r
+ SequenceI mseq[] = new SequenceI[sequences.length];\r
+ for (int s = 0; s < mseq.length; s++)\r
+ {\r
+ mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,\r
+ fwidth + 1);\r
+ }\r
+ smsa[j] = mseq;\r
+ j++;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ smsa = new SequenceI[1][];\r
+ smsa[0] = new SequenceI[sequences.length];\r
+ for (int s = 0; s < sequences.length; s++)\r
+ {\r
+ smsa[0][s] = sequences[s].getSeq(gapCharacter);\r
+ }\r
+ }\r
+ return smsa;\r
+ }\r
+\r
+ /**\r
+ * return full msa and hidden regions with visible blocks replaced with new\r
+ * sub alignments\r
+ * \r
+ * @param nvismsa\r
+ * SequenceI[][]\r
+ * @param orders\r
+ * AlignmentOrder[] corresponding to each SequenceI[] block.\r
+ * @return Object[]\r
+ */\r
+ public Object[] getUpdatedView(SequenceI[][] nvismsa,\r
+ AlignmentOrder[] orders, char gapCharacter)\r
+ {\r
+ if (sequences == null || width <= 0)\r
+ {\r
+ throw new Error("empty view cannot be updated.");\r
+ }\r
+ if (nvismsa == null)\r
+ {\r
+ throw new Error(\r
+ "nvismsa==null. use getAlignmentAndColumnSelection() instead.");\r
+ }\r
+ if (contigs != null && contigs.length > 0)\r
+ {\r
+ SequenceI[] alignment = new SequenceI[sequences.length];\r
+ ColumnSelection columnselection = new ColumnSelection();\r
+ if (contigs != null && contigs.length > 0)\r
+ {\r
+ int start = 0;\r
+ int nwidth = 0;\r
+ int owidth = width;\r
+ int j = 0;\r
+ for (int contig = 0; contig < contigs.length; contig += 3)\r
+ {\r
+ owidth += contigs[contig + 2]; // recover final column width\r
+ if (contigs[contig + 1] - start > 0)\r
+ {\r
+ int swidth = 0; // subalignment width\r
+ if (nvismsa[j] != null)\r
+ {\r
+ SequenceI mseq[] = nvismsa[j];\r
+ AlignmentOrder order = (orders == null) ? null : orders[j];\r
+ j++;\r
+ if (mseq.length != sequences.length)\r
+ {\r
+ throw new Error(\r
+ "Mismatch between number of sequences in block "\r
+ + j + " (" + mseq.length\r
+ + ") and the original view ("\r
+ + sequences.length + ")");\r
+ }\r
+ swidth = mseq[0].getLength(); // JBPNote: could ensure padded\r
+ // here.\r
+ for (int s = 0; s < mseq.length; s++)\r
+ {\r
+ if (alignment[s] == null)\r
+ {\r
+ alignment[s] = mseq[s];\r
+ }\r
+ else\r
+ {\r
+ alignment[s].setSequence(alignment[s]\r
+ .getSequenceAsString()\r
+ + mseq[s].getSequenceAsString());\r
+ if (mseq[s].getStart() <= mseq[s].getEnd())\r
+ {\r
+ alignment[s].setEnd(mseq[s].getEnd());\r
+ }\r
+ if (order != null)\r
+ {\r
+ order.updateSequence(mseq[s], alignment[s]);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // recover original alignment block or place gaps\r
+ if (true)\r
+ {\r
+ // recover input data\r
+ for (int s = 0; s < sequences.length; s++)\r
+ {\r
+ SequenceI oseq = sequences[s].getSeq(gapCharacter)\r
+ .getSubSequence(start, contigs[contig + 1]);\r
+ if (swidth < oseq.getLength())\r
+ {\r
+ swidth = oseq.getLength();\r
+ }\r
+ if (alignment[s] == null)\r
+ {\r
+ alignment[s] = oseq;\r
+ }\r
+ else\r
+ {\r
+ alignment[s].setSequence(alignment[s]\r
+ .getSequenceAsString()\r
+ + oseq.getSequenceAsString());\r
+ if (oseq.getEnd() >= oseq.getStart())\r
+ {\r
+ alignment[s].setEnd(oseq.getEnd());\r
+ }\r
+ }\r
+ }\r
+\r
+ }\r
+ j++;\r
+ }\r
+ nwidth += swidth;\r
+ }\r
+ // advance to begining of visible region\r
+ start = contigs[contig + 1] + contigs[contig + 2];\r
+ // add hidden segment to right of next region\r
+ for (int s = 0; s < sequences.length; s++)\r
+ {\r
+ SequenceI hseq = sequences[s].getSeq(gapCharacter)\r
+ .getSubSequence(contigs[contig + 1], start);\r
+ if (alignment[s] == null)\r
+ {\r
+ alignment[s] = hseq;\r
+ }\r
+ else\r
+ {\r
+ alignment[s].setSequence(alignment[s].getSequenceAsString()\r
+ + hseq.getSequenceAsString());\r
+ if (hseq.getEnd() >= hseq.getStart())\r
+ {\r
+ alignment[s].setEnd(hseq.getEnd());\r
+ }\r
+ }\r
+ }\r
+ // mark hidden segment as hidden in the new alignment\r
+ columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2]\r
+ - 1);\r
+ nwidth += contigs[contig + 2];\r
+ }\r
+ // Do final segment - if it exists\r
+ if (j < nvismsa.length)\r
+ {\r
+ int swidth = 0;\r
+ if (nvismsa[j] != null)\r
+ {\r
+ SequenceI mseq[] = nvismsa[j];\r
+ AlignmentOrder order = (orders != null) ? orders[j] : null;\r
+ swidth = mseq[0].getLength();\r
+ for (int s = 0; s < mseq.length; s++)\r
+ {\r
+ if (alignment[s] == null)\r
+ {\r
+ alignment[s] = mseq[s];\r
+ }\r
+ else\r
+ {\r
+ alignment[s].setSequence(alignment[s].getSequenceAsString()\r
+ + mseq[s].getSequenceAsString());\r
+ if (mseq[s].getEnd() >= mseq[s].getStart())\r
+ {\r
+ alignment[s].setEnd(mseq[s].getEnd());\r
+ }\r
+ if (order != null)\r
+ {\r
+ order.updateSequence(mseq[s], alignment[s]);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (start < owidth)\r
+ {\r
+ // recover input data or place gaps\r
+ if (true)\r
+ {\r
+ // recover input data\r
+ for (int s = 0; s < sequences.length; s++)\r
+ {\r
+ SequenceI oseq = sequences[s].getSeq(gapCharacter)\r
+ .getSubSequence(start, owidth + 1);\r
+ if (swidth < oseq.getLength())\r
+ {\r
+ swidth = oseq.getLength();\r
+ }\r
+ if (alignment[s] == null)\r
+ {\r
+ alignment[s] = oseq;\r
+ }\r
+ else\r
+ {\r
+ alignment[s].setSequence(alignment[s]\r
+ .getSequenceAsString()\r
+ + oseq.getSequenceAsString());\r
+ if (oseq.getEnd() >= oseq.getStart())\r
+ {\r
+ alignment[s].setEnd(oseq.getEnd());\r
+ }\r
+ }\r
+ }\r
+ nwidth += swidth;\r
+ }\r
+ else\r
+ {\r
+ // place gaps.\r
+ throw new Error("Padding not yet implemented.");\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ return new Object[]\r
+ { alignment, columnselection };\r
+ }\r
+ else\r
+ {\r
+ if (nvismsa.length != 1)\r
+ {\r
+ throw new Error(\r
+ "Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks="\r
+ + nvismsa.length);\r
+ }\r
+ if (nvismsa[0] != null)\r
+ {\r
+ return new Object[]\r
+ { nvismsa[0], new ColumnSelection() };\r
+ }\r
+ else\r
+ {\r
+ return getAlignmentAndColumnSelection(gapCharacter);\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * returns simple array of start end positions of visible range on alignment.\r
+ * vis_start and vis_end are inclusive - use\r
+ * SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence\r
+ * from underlying alignment.\r
+ * \r
+ * @return int[] { start_i, end_i } for 1<i<n visible regions.\r
+ */\r
+ public int[] getVisibleContigs()\r
+ {\r
+ if (contigs != null && contigs.length > 0)\r
+ {\r
+ int start = 0;\r
+ int nvis = 0;\r
+ int fwidth = width;\r
+ for (int contig = 0; contig < contigs.length; contig += 3)\r
+ {\r
+ if ((contigs[contig + 1] - start) > 0)\r
+ {\r
+ nvis++;\r
+ }\r
+ fwidth += contigs[contig + 2]; // end up with full region width\r
+ // (including hidden regions)\r
+ start = contigs[contig + 1] + contigs[contig + 2];\r
+ }\r
+ if (start < fwidth)\r
+ {\r
+ nvis++;\r
+ }\r
+ int viscontigs[] = new int[nvis * 2];\r
+ nvis = 0;\r
+ start = 0;\r
+ for (int contig = 0; contig < contigs.length; contig += 3)\r
+ {\r
+ if ((contigs[contig + 1] - start) > 0)\r
+ {\r
+ viscontigs[nvis] = start;\r
+ viscontigs[nvis + 1] = contigs[contig + 1] - 1; // end is inclusive\r
+ nvis += 2;\r
+ }\r
+ start = contigs[contig + 1] + contigs[contig + 2];\r
+ }\r
+ if (start < fwidth)\r
+ {\r
+ viscontigs[nvis] = start;\r
+ viscontigs[nvis + 1] = fwidth; // end is inclusive\r
+ nvis += 2;\r
+ }\r
+ return viscontigs;\r
+ }\r
+ else\r
+ {\r
+ return new int[]\r
+ { 0, width };\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return position of first visible column of AlignmentView within its\r
+ * parent's alignment reference frame\r
+ */\r
+ public int getAlignmentOrigin()\r
+ {\r
+ // TODO Auto-generated method stub\r
+ return firstCol;\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff