/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*/
package jalview.datamodel;
-
-
/**
* <p>Title: </p>
*
*/
public class AlignmentView
{
- /**
- * Transient object compactly representing a 'view' of an alignment - with discontinuities marked.
- */
- private SeqCigar[] sequences = null;
+ /**
+ * Transient object compactly representing a 'view' of an alignment - with discontinuities marked.
+ */
+ private SeqCigar[] sequences = null;
private int[] contigs = null;
- private int width=0;
- private int firstCol=0;
+ private int width = 0;
+ private int firstCol = 0;
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();
width = seqcigararray.getWidth(); // visible width
}
+
/**
* Create an alignmentView where the first column corresponds with the 'firstcol' column of some reference alignment
* @param sdata
* @param firstcol
*/
- public AlignmentView(CigarArray sdata, int firstcol) {
+ public AlignmentView(CigarArray sdata, int firstcol)
+ {
this(sdata);
- firstCol=firstcol;
+ firstCol = firstcol;
}
public void setSequences(SeqCigar[] sequences)
{
return sequences;
}
+
/**
* @see CigarArray.getDeletedRegions
* @return int[] { vis_start, sym_start, length }
{
return contigs;
}
+
/**
* get the full alignment and a columnselection object marking the hidden regions
* @param gapCharacter char
* @return Object[] { SequenceI[], ColumnSelection}
*/
- public Object[] getAlignmentAndColumnSelection(char gapCharacter) {
+ public Object[] getAlignmentAndColumnSelection(char gapCharacter)
+ {
ColumnSelection colsel = new ColumnSelection();
- return new Object[] { SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel, contigs), colsel};
+ return new Object[]
+ {
+ SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
+ contigs), colsel};
}
+
/**
* getSequenceStrings
*
*/
public String[] getSequenceStrings(char c)
{
- String[] seqs=new String[sequences.length];
- for (int n=0; n<sequences.length; n++) {
+ String[] seqs = new String[sequences.length];
+ for (int n = 0; n < sequences.length; n++)
+ {
String fullseq = sequences[n].getSequenceString(c);
if (contigs != null)
{
p = contigs[h + 1] + contigs[h + 2];
}
seqs[n] += fullseq.substring(p);
- } else
+ }
+ else
+ {
seqs[n] = fullseq;
+ }
}
return seqs;
}
+
/**
*
* @return visible number of columns in alignment view
*/
- public int getWidth() {
+ public int getWidth()
+ {
return width;
}
- protected void setWidth(int width) {
+ protected void setWidth(int width)
+ {
this.width = width;
}
+
/**
* get the contiguous subalignments in an alignment view.
* @param gapCharacter char
* @return SequenceI[][]
*/
- public SequenceI[][] getVisibleContigs(char gapCharacter) {
+ public SequenceI[][] getVisibleContigs(char gapCharacter)
+ {
SequenceI[][] smsa;
int njobs = 1;
- if (sequences==null || width<=0)
+ if (sequences == null || width <= 0)
+ {
return null;
+ }
if (contigs != null && contigs.length > 0)
{
int start = 0;
}
return smsa;
}
+
/**
* return full msa and hidden regions with visible blocks replaced with new sub alignments
* @param nvismsa SequenceI[][]
* @param orders AlignmentOrder[] corresponding to each SequenceI[] block.
* @return Object[]
*/
- public Object[] getUpdatedView(SequenceI[][] nvismsa, AlignmentOrder[] orders, char gapCharacter) {
+ public Object[] getUpdatedView(SequenceI[][] nvismsa, AlignmentOrder[] orders,
+ char gapCharacter)
+ {
if (sequences == null || width <= 0)
{
throw new Error("empty view cannot be updated.");
}
if (nvismsa == null)
+ {
throw new Error(
"nvismsa==null. use getAlignmentAndColumnSelection() instead.");
+ }
if (contigs != null && contigs.length > 0)
{
SequenceI[] alignment = new SequenceI[sequences.length];
if (nvismsa[j] != null)
{
SequenceI mseq[] = nvismsa[j];
- AlignmentOrder order=(orders==null) ? null : orders[j];
+ AlignmentOrder order = (orders == null) ? null : orders[j];
j++;
- if (mseq.length!=sequences.length)
- throw new Error("Mismatch between number of sequences in block "+j+" ("+mseq.length+") and the original view ("+sequences.length+")");
+ if (mseq.length != sequences.length)
+ {
+ throw new Error(
+ "Mismatch between number of sequences in block " + j + " (" +
+ mseq.length + ") and the original view (" +
+ sequences.length + ")");
+ }
swidth = mseq[0].getLength(); // JBPNote: could ensure padded here.
for (int s = 0; s < mseq.length; s++)
{
{
alignment[s].setEnd(mseq[s].getEnd());
}
- if (order!=null) {
+ if (order != null)
+ {
order.updateSequence(mseq[s], alignment[s]);
}
}
// recover input data
for (int s = 0; s < sequences.length; s++)
{
- SequenceI oseq = sequences[s].getSeq(gapCharacter).getSubSequence(start,
- contigs[contig + 1]);
+ SequenceI oseq = sequences[s].getSeq(gapCharacter).
+ getSubSequence(start,
+ contigs[contig + 1]);
if (swidth < oseq.getLength())
{
swidth = oseq.getLength();
// add hidden segment to right of next region
for (int s = 0; s < sequences.length; s++)
{
- SequenceI hseq = sequences[s].getSeq(gapCharacter).getSubSequence(contigs[contig +
+ SequenceI hseq = sequences[s].getSeq(gapCharacter).getSubSequence(
+ contigs[contig +
1], start);
if (alignment[s] == null)
{
if (nvismsa[j] != null)
{
SequenceI mseq[] = nvismsa[j];
- AlignmentOrder order = (orders!=null) ? orders[j] : null;
+ AlignmentOrder order = (orders != null) ? orders[j] : null;
swidth = mseq[0].getLength();
for (int s = 0; s < mseq.length; s++)
{
{
alignment[s].setEnd(mseq[s].getEnd());
}
- if (order!=null) {
+ if (order != null)
+ {
order.updateSequence(mseq[s], alignment[s]);
}
}
// recover input data
for (int s = 0; s < sequences.length; s++)
{
- SequenceI oseq = sequences[s].getSeq(gapCharacter).getSubSequence(start,
- owidth + 1);
+ SequenceI oseq = sequences[s].getSeq(gapCharacter).
+ getSubSequence(start,
+ owidth + 1);
if (swidth < oseq.getLength())
{
swidth = oseq.getLength();
}
}
}
- return new Object[] { alignment, columnselection};
- } else {
- if (nvismsa.length!=1)
- throw new Error("Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks="+nvismsa.length);
- if (nvismsa[0]!=null)
- return new Object[] { nvismsa[0], new ColumnSelection()};
+ return new Object[]
+ {
+ alignment, columnselection};
+ }
+ else
+ {
+ if (nvismsa.length != 1)
+ {
+ throw new Error("Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks=" +
+ nvismsa.length);
+ }
+ if (nvismsa[0] != null)
+ {
+ return new Object[]
+ {
+ nvismsa[0], new ColumnSelection()};
+ }
else
+ {
return getAlignmentAndColumnSelection(gapCharacter);
+ }
}
}
+
/**
* returns simple array of start end positions of visible range on alignment.
* vis_start and vis_end are inclusive - use SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence from underlying alignment.
* @return int[] { start_i, end_i } for 1<i<n visible regions.
*/
- public int[] getVisibleContigs() {
+ public int[] getVisibleContigs()
+ {
if (contigs != null && contigs.length > 0)
{
int start = 0;
{
nvis++;
}
- int viscontigs[] = new int[nvis*2];
- nvis=0;
- start=0;
- for (int contig=0; contig<contigs.length; contig+=3) {
+ int viscontigs[] = new int[nvis * 2];
+ nvis = 0;
+ start = 0;
+ for (int contig = 0; contig < contigs.length; contig += 3)
+ {
if ( (contigs[contig + 1] - start) > 0)
{
viscontigs[nvis] = start;
- viscontigs[nvis+1]=contigs[contig+1]-1; // end is inclusive
- nvis+=2;
+ viscontigs[nvis + 1] = contigs[contig + 1] - 1; // end is inclusive
+ nvis += 2;
}
start = contigs[contig + 1] + contigs[contig + 2];
}
- if (start<fwidth) {
+ if (start < fwidth)
+ {
viscontigs[nvis] = start;
- viscontigs[nvis+1]=fwidth; // end is inclusive
- nvis+=2;
+ viscontigs[nvis + 1] = fwidth; // end is inclusive
+ nvis += 2;
}
return viscontigs;
- } else {
- return new int[] { 0, width};
+ }
+ else
+ {
+ return new int[]
+ {
+ 0, width};
}
}
+
/**
*
* @return position of first visible column of AlignmentView within its parent's alignment reference frame
*/
- public int getAlignmentOrigin() {
+ public int getAlignmentOrigin()
+ {
// TODO Auto-generated method stub
return firstCol;
}
git://source.jalview.org / jalview.git / blobdiff