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package jalview.commands; |
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import java.util.List; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.ContiguousI; |
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import jalview.datamodel.SequenceI; |
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import jalview.util.Comparison; |
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| 0% |
Uncovered Elements: 39 (39) |
Complexity: 10 |
Complexity Density: 0.42 |
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public class JustifyLeftOrRightCommand extends EditCommand |
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{ |
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@param |
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@param |
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@param |
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@param |
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@param |
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@param |
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| 0% |
Uncovered Elements: 38 (38) |
Complexity: 10 |
Complexity Density: 0.42 |
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public JustifyLeftOrRightCommand(String description, boolean left,... |
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List<SequenceI> seqs, int from, int to, AlignmentI al) |
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{ |
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this.description = description; |
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for (SequenceI seq : seqs) |
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{ |
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ContiguousI cont = seq.findPositions(from + 1, to + 1); |
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if (cont == null) |
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{ |
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continue; |
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} |
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char[] range = seq.getSequence(from, to + 1); |
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if (range == null || range.length == 0) |
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{ |
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continue; |
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} |
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int dsstart = seq.getDatasetSequence().getStart(); |
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char[] sqchar = seq.getDatasetSequence().getSequence( |
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-dsstart + cont.getBegin(), -dsstart + cont.getEnd() + 1); |
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char[] alseq = new char[to - from + 1]; |
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int sqstart = left ? 0 : alseq.length - sqchar.length; |
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int gaps = alseq.length - sqchar.length; |
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int gapstart = left ? sqchar.length : 0; |
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char gc = al.getGapCharacter(); |
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for (int gp = 0; gp < gaps; gp++) |
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{ |
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alseq[gapstart + gp] = gc; |
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} |
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for (int sqp = 0, insp = 0; sqp < alseq.length; sqp++) |
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{ |
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if (sqp < range.length && !Comparison.isGap(range[sqp])) |
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{ |
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alseq[insp++ + sqstart] = range[sqp]; |
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} |
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} |
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SequenceI[] sqa = new SequenceI[1]; |
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sqa[0] = seq; |
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addEdit(new jalview.commands.EditCommand.Edit( |
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jalview.commands.EditCommand.Action.REPLACE, sqa, from, |
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to + 1, al, new String(alseq))); |
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} |
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performEdit(0, null); |
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} |
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} |