X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=79e0ba22d55f18ae04e17152b5729beacc5fee1c;hb=449db06a788539e8ea7463ff4b56f012280994d0;hp=e6684705b23d43bc0c912d534563120b562924b0;hpb=749ca2a0e792c697a23f68d2cc8d719b306b7f88;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index e668470..79e0ba2 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,6 +1,6 @@
/*
* 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
@@ -18,8 +18,6 @@
*/
package jalview.datamodel;
-
-
/**
*
Title:
*
@@ -34,30 +32,34 @@ package jalview.datamodel;
*/
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
+ * 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)
@@ -74,6 +76,7 @@ public class AlignmentView
{
return sequences;
}
+
/**
* @see CigarArray.getDeletedRegions
* @return int[] { vis_start, sym_start, length }
@@ -82,16 +85,22 @@ public class AlignmentView
{
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
*
@@ -100,8 +109,9 @@ public class AlignmentView
*/
public String[] getSequenceStrings(char c)
{
- String[] seqs=new String[sequences.length];
- for (int n=0; n 0)
{
int start = 0;
@@ -198,20 +218,25 @@ public class AlignmentView
}
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];
@@ -231,10 +256,15 @@ public class AlignmentView
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++)
{
@@ -244,13 +274,14 @@ public class AlignmentView
}
else
{
- alignment[s].setSequence(alignment[s].getSequence() +
- mseq[s].getSequence());
+ alignment[s].setSequence(alignment[s].getSequenceAsString() +
+ mseq[s].getSequenceAsString());
if (mseq[s].getStart() <= mseq[s].getEnd())
{
alignment[s].setEnd(mseq[s].getEnd());
}
- if (order!=null) {
+ if (order != null)
+ {
order.updateSequence(mseq[s], alignment[s]);
}
}
@@ -264,8 +295,9 @@ public class AlignmentView
// 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();
@@ -276,8 +308,8 @@ public class AlignmentView
}
else
{
- alignment[s].setSequence(alignment[s].getSequence() +
- oseq.getSequence());
+ alignment[s].setSequence(alignment[s].getSequenceAsString() +
+ oseq.getSequenceAsString());
if (oseq.getEnd() >= oseq.getStart())
{
alignment[s].setEnd(oseq.getEnd());
@@ -295,7 +327,8 @@ public class AlignmentView
// 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)
{
@@ -303,8 +336,8 @@ public class AlignmentView
}
else
{
- alignment[s].setSequence(alignment[s].getSequence() +
- hseq.getSequence());
+ alignment[s].setSequence(alignment[s].getSequenceAsString() +
+ hseq.getSequenceAsString());
if (hseq.getEnd() >= hseq.getStart())
{
alignment[s].setEnd(hseq.getEnd());
@@ -322,7 +355,7 @@ public class AlignmentView
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++)
{
@@ -332,13 +365,14 @@ public class AlignmentView
}
else
{
- alignment[s].setSequence(alignment[s].getSequence() +
- mseq[s].getSequence());
+ alignment[s].setSequence(alignment[s].getSequenceAsString() +
+ mseq[s].getSequenceAsString());
if (mseq[s].getEnd() >= mseq[s].getStart())
{
alignment[s].setEnd(mseq[s].getEnd());
}
- if (order!=null) {
+ if (order != null)
+ {
order.updateSequence(mseq[s], alignment[s]);
}
}
@@ -354,8 +388,9 @@ public class AlignmentView
// 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();
@@ -366,8 +401,8 @@ public class AlignmentView
}
else
{
- alignment[s].setSequence(alignment[s].getSequence() +
- oseq.getSequence());
+ alignment[s].setSequence(alignment[s].getSequenceAsString() +
+ oseq.getSequenceAsString());
if (oseq.getEnd() >= oseq.getStart())
{
alignment[s].setEnd(oseq.getEnd());
@@ -385,22 +420,37 @@ public class AlignmentView
}
}
}
- 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.
+ * 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 0)
{
int start = 0;
@@ -419,33 +469,41 @@ public class AlignmentView
{
nvis++;
}
- int viscontigs[] = new int[nvis*2];
- nvis=0;
- start=0;
- for (int contig=0; contig 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];
+ start = contigs[contig + 1] + contigs[contig + 2];
}
- if (start