/*\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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)\r
+ * Copyright (C) 2009 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
package jalview.datamodel;\r
\r
/**\r
- * <p>Title: </p>\r
- *\r
- * <p>Description: </p>\r
- *\r
- * <p>Copyright: Copyright (c) 2004</p>\r
- *\r
- * <p>Company: Dundee University</p>\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 discontinuities marked.\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("Implementation Error - can only make an alignment view from a CigarArray of sequences.");\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.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 'firstcol' column of some reference alignment\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
}\r
\r
/**\r
- * get the full alignment and a columnselection object marking the hidden regions\r
- * @param gapCharacter char\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
ColumnSelection colsel = new ColumnSelection();\r
\r
return new Object[]\r
- {\r
+ {\r
SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,\r
- contigs), colsel};\r
+ contigs), colsel };\r
}\r
\r
/**\r
* getSequenceStrings\r
- *\r
- * @param c char\r
+ * \r
+ * @param c\r
+ * char\r
* @return String[]\r
*/\r
public String[] getSequenceStrings(char c)\r
}\r
\r
/**\r
- *\r
+ * \r
* @return visible number of columns in alignment view\r
*/\r
public int getWidth()\r
\r
/**\r
* get the contiguous subalignments in an alignment view.\r
- * @param gapCharacter char\r
+ * \r
+ * @param gapCharacter\r
+ * char\r
* @return SequenceI[][]\r
*/\r
public SequenceI[][] getVisibleContigs(char gapCharacter)\r
int fwidth = width;\r
for (int contig = 0; contig < contigs.length; contig += 3)\r
{\r
- if ( (contigs[contig + 1] - start) > 0)\r
+ if ((contigs[contig + 1] - start) > 0)\r
{\r
njobs++;\r
}\r
- fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)\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
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
- contigs[contig + 1]);\r
+ mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(\r
+ start, contigs[contig + 1]);\r
}\r
smsa[j] = mseq;\r
j++;\r
for (int s = 0; s < mseq.length; s++)\r
{\r
mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,\r
- fwidth + 1);\r
+ fwidth + 1);\r
}\r
smsa[j] = mseq;\r
j++;\r
}\r
\r
/**\r
- * return full msa and hidden regions with visible blocks replaced with new sub alignments\r
- * @param nvismsa SequenceI[][]\r
- * @param orders AlignmentOrder[] corresponding to each SequenceI[] block.\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, AlignmentOrder[] orders,\r
- char gapCharacter)\r
+ public Object[] getUpdatedView(SequenceI[][] nvismsa,\r
+ AlignmentOrder[] orders, char gapCharacter)\r
{\r
if (sequences == null || width <= 0)\r
{\r
if (nvismsa == null)\r
{\r
throw new Error(\r
- "nvismsa==null. use getAlignmentAndColumnSelection() instead.");\r
+ "nvismsa==null. use getAlignmentAndColumnSelection() instead.");\r
}\r
if (contigs != null && contigs.length > 0)\r
{\r
if (mseq.length != sequences.length)\r
{\r
throw new Error(\r
- "Mismatch between number of sequences in block " + j + " (" +\r
- mseq.length + ") and the original view (" +\r
- sequences.length + ")");\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 here.\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
else\r
{\r
- alignment[s].setSequence(alignment[s].getSequenceAsString() +\r
- mseq[s].getSequenceAsString());\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
// recover input data\r
for (int s = 0; s < sequences.length; s++)\r
{\r
- SequenceI oseq = sequences[s].getSeq(gapCharacter).\r
- getSubSequence(start,\r
- contigs[contig + 1]);\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
else\r
{\r
- alignment[s].setSequence(alignment[s].getSequenceAsString() +\r
- oseq.getSequenceAsString());\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
// 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).getSubSequence(\r
- contigs[contig +\r
- 1], start);\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
+ 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
// mark hidden segment as hidden in the new alignment\r
- columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2] - 1);\r
+ columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2]\r
+ - 1);\r
nwidth += contigs[contig + 2];\r
}\r
// Do final segment - if it exists\r
}\r
else\r
{\r
- alignment[s].setSequence(alignment[s].getSequenceAsString() +\r
- mseq[s].getSequenceAsString());\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
// recover input data\r
for (int s = 0; s < sequences.length; s++)\r
{\r
- SequenceI oseq = sequences[s].getSeq(gapCharacter).\r
- getSubSequence(start,\r
- owidth + 1);\r
+ SequenceI oseq = sequences[s].getSeq(gapCharacter)\r
+ .getSubSequence(start, owidth + 1);\r
if (swidth < oseq.getLength())\r
{\r
swidth = oseq.getLength();\r
}\r
else\r
{\r
- alignment[s].setSequence(alignment[s].getSequenceAsString() +\r
- oseq.getSequenceAsString());\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
return new Object[]\r
- {\r
- alignment, columnselection};\r
+ { alignment, columnselection };\r
}\r
else\r
{\r
if (nvismsa.length != 1)\r
{\r
- throw new Error("Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks=" +\r
- nvismsa.length);\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
- {\r
- nvismsa[0], new ColumnSelection()};\r
+ { nvismsa[0], new ColumnSelection() };\r
}\r
else\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 SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence from underlying 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
int fwidth = width;\r
for (int contig = 0; contig < contigs.length; contig += 3)\r
{\r
- if ( (contigs[contig + 1] - start) > 0)\r
+ if ((contigs[contig + 1] - start) > 0)\r
{\r
nvis++;\r
}\r
- fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)\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
start = 0;\r
for (int contig = 0; contig < contigs.length; contig += 3)\r
{\r
- if ( (contigs[contig + 1] - start) > 0)\r
+ if ((contigs[contig + 1] - start) > 0)\r
{\r
viscontigs[nvis] = start;\r
viscontigs[nvis + 1] = contigs[contig + 1] - 1; // end is inclusive\r
else\r
{\r
return new int[]\r
- {\r
- 0, width};\r
+ { 0, width };\r
}\r
}\r
\r
/**\r
- *\r
- * @return position of first visible column of AlignmentView within its parent's alignment reference frame\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
git://source.jalview.org / jalview.git / blobdiff