File PaSiMapModel.java

Branches:

Statements:

Methods:

Classes:

LOC:

289

NCLOC:

185

Total complexity:

Complexity density:

0.52

Statements/Method:

3.05

Methods/Class:

Average method complexity:

1.59

Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PaSiMapModel	37	67	35	0.00%

Class PaSiMapModel

Class PaSiMapModel	Line # 37	Total Statements 67	Complexity 35	TOTAL Coverage 0.00%
PaSiMapModel(AlignmentViewport,SequenceI[],boolean,ScoreModelI) PaSiMapModel(AlignmentViewport,SequenceI[],boolean,ScoreModelI)	7272	4.04	1.01	0.0 0.00%
calculate(PairwiseAlignPanel) : void calculate(PairwiseAlignPanel) : void	8585	15.015	5.05	0.0 0.00%
updateRc(RotatableCanvasI) : void updateRc(RotatableCanvasI) : void	118118	1.01	1.01	0.0 0.00%
isNucleotide() : boolean isNucleotide() : boolean	123123	1.01	1.01	0.0 0.00%
setNucleotide(boolean) : void setNucleotide(boolean) : void	128128	1.01	1.01	0.0 0.00%
getTop() : int getTop() : int	138138	1.01	1.01	0.0 0.00%
setTop(int) : void setTop(int) : void	143143	1.01	1.01	0.0 0.00%
updateRcView(int,int,int) : void updateRcView(int,int,int) : void	159159	3.03	2.02	0.0 0.00%
getDetails() : String getDetails() : String	170170	1.01	1.01	0.0 0.00%
getAlignmentOutput() : String getAlignmentOutput() : String	175175	1.01	1.01	0.0 0.00%
getInputData() : AlignmentViewport getInputData() : AlignmentViewport	180180	1.01	1.01	0.0 0.00%
setInputData(AlignmentViewport) : void setInputData(AlignmentViewport) : void	185185	1.01	1.01	0.0 0.00%
getPointsasCsv(boolean,int,int,int) : String getPointsasCsv(boolean,int,int,int) : String	190190	25.025	6.06	0.0 0.00%
getScoreModelName() : String getScoreModelName() : String	236236	1.01	2.02	0.0 0.00%
setScoreModel(ScoreModelI) : void setScoreModel(ScoreModelI) : void	241241	1.01	1.01	0.0 0.00%
getSequencePoints() : List<SequencePoint> getSequencePoints() : List<SequencePoint>	246246	1.01	1.01	0.0 0.00%
setSequencePoints(List<SequencePoint>) : void setSequencePoints(List<SequencePoint>) : void	251251	1.01	1.01	0.0 0.00%
getPasimapData() : PaSiMap getPasimapData() : PaSiMap	261261	1.01	1.01	0.0 0.00%
setPaSiMap(PaSiMap) : void setPaSiMap(PaSiMap) : void	266266	1.01	1.01	0.0 0.00%
isCancelled() : boolean isCancelled() : boolean	271271	3.03	3.03	0.0 0.00%
cancel() : void cancel() : void	280280	1.01	1.01	0.0 0.00%
canCancel() : boolean canCancel() : boolean	285285	1.01	1.01	0.0 0.00%

Contributing tests

No tests hitting this source file were found.

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* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)

* Copyright (C) $$Year-Rel$$ The Jalview Authors

* This file is part of Jalview.

* Jalview is free software: you can redistribute it and/or

* modify it under the terms of the GNU General Public License

* as published by the Free Software Foundation, either version 3

* of the License, or (at your option) any later version.

* Jalview is distributed in the hope that it will be useful, but

* WITHOUT ANY WARRANTY; without even the implied warranty

* of MERCHANTABILITY or FITNESS FOR A PARTICULAR

* PURPOSE. See the GNU General Public License for more details.

* You should have received a copy of the GNU General Public License

* along with Jalview. If not, see <http://www.gnu.org/licenses/>.

* The Jalview Authors are detailed in the 'AUTHORS' file.

package jalview.viewmodel;

import jalview.analysis.PaSiMap;

import jalview.api.RotatableCanvasI;

import jalview.api.analysis.ScoreModelI;

import jalview.api.analysis.SimilarityParamsI;

import jalview.datamodel.AlignmentView;

import jalview.datamodel.Point;

import jalview.datamodel.SequenceI;

import jalview.datamodel.SequencePoint;

import jalview.gui.PairwiseAlignPanel;

import jalview.viewmodel.AlignmentViewport;

import java.util.List;

import java.util.Vector;

public class PaSiMapModel

{

* inputs

private AlignmentViewport inputData;

private final SequenceI[] seqs;

* options - score model, nucleotide / protein

private ScoreModelI scoreModel;

private boolean nucleotide = false;

* outputs

private PaSiMap pasimap;

int top;

private List<SequencePoint> points;

/**

* Constructor given sequence data, score model and score calculation

* parameter options.

* @param seqData

* @param sqs

* @param nuc

* @param modelName

* @param params

public PaSiMapModel(AlignmentViewport seqData, SequenceI[] sqs,

boolean nuc, ScoreModelI modelName)

{

inputData = seqData;

seqs = sqs;

nucleotide = nuc;

scoreModel = modelName;

}

/**

* Performs the PaSiMap calculation (in the same thread) and extracts result

* data needed for visualisation by PaSiMapPanel

public void calculate(PairwiseAlignPanel pap)

{

pasimap = new PaSiMap(inputData, scoreModel, pap);

pasimap.run(); // executes in same thread, wait for completion

if (pasimap.isCancelled())

{

// no more work to do

return;

}

// Now find the component coordinates

int ii = 0;

while ((ii < seqs.length) && (seqs[ii] != null))

{

ii++;

}

int width = pasimap.getWidth();

104

int height = pasimap.getHeight();

105

top = width;

106

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points = new Vector<>();

108

Point[] scores = pasimap.getComponents(width - 1, width - 2, width - 3,

109

1);

110

111

for (int i = 0; i < height; i++)

112

{

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SequencePoint sp = new SequencePoint(seqs[i], scores[i]);

points.add(sp);

}

}

public void updateRc(RotatableCanvasI rc)

119

{

120

rc.setPoints(points, pasimap.getHeight());

121

}

122

123

public boolean isNucleotide()

{

return nucleotide;

}

public void setNucleotide(boolean nucleotide)

129

{

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this.nucleotide = nucleotide;

}

/**

* Answers the index of the principal dimension of the PaSiMap

* @return

public int getTop()

{

return top;

}

public void setTop(int t)

{

top = t;

}

/**

* Updates the 3D coordinates for the list of points to the given dimensions.

150

* Principal dimension is getTop(). Next greatest eigenvector is getTop()-1.

151

* Note - pasimap.getComponents starts counting the spectrum from rank-2 to

152

* zero, rather than rank-1, so getComponents(dimN ...) == updateRcView(dimN+1

* ..)

* @param dim1

* @param dim2

* @param dim3

public void updateRcView(int dim1, int dim2, int dim3)

160

{

161

// note: actual indices for components are dim1-1, etc (patch for JAL-1123)

162

Point[] scores = pasimap.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 1);

163

164

for (int i = 0; i < pasimap.getHeight(); i++)

165

{

166

points.get(i).coord = scores[i];

}

}

public String getDetails()

171

{

172

return pasimap.getDetails();

173

}

174

175

public String getAlignmentOutput()

176

{

177

return pasimap.getAlignmentOutput();

178

}

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public AlignmentViewport getInputData()

{

return inputData;

}

public void setInputData(AlignmentViewport data)

{

inputData = data;

}

public String getPointsasCsv(boolean transformed, int xdim, int ydim,

191

int zdim)

192

{

193

StringBuffer csv = new StringBuffer();

194

csv.append("\"Sequence\"");

if (transformed)

{

csv.append(",");

csv.append(xdim);

csv.append(",");

csv.append(ydim);

csv.append(",");

csv.append(zdim);

}

else

{

for (int d = 1, dmax = (int) pasimap.getDim(); d <= dmax; d++)

{

csv.append("," + d);

}

}

csv.append("\n");

for (int s = 0; s < seqs.length; s++)

213

{

214

csv.append("\"" + seqs[s].getName() + "\"");

215

if (!transformed)

216

{

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double[] fl = pasimap.component(s);

218

for (int d = fl.length - 1; d >= 0; d--)

{

csv.append(",");

csv.append(fl[d]);

}

}

else

{

Point p = points.get(s).coord;

227

csv.append(",").append(p.x);

228

csv.append(",").append(p.y);

229

csv.append(",").append(p.z);

}

csv.append("\n");

}

return csv.toString();

234

}

235

236

public String getScoreModelName()

237

{

238

return scoreModel == null ? "" : scoreModel.getName();

239

}

240

241

public void setScoreModel(ScoreModelI sm)

242

{

243

this.scoreModel = sm;

244

}

245

246

public List<SequencePoint> getSequencePoints()

{

return points;

}

public void setSequencePoints(List<SequencePoint> sp)

{

points = sp;

}

/**

* Answers the object holding the values of the computed PaSiMap

* @return

public PaSiMap getPasimapData()

{

return pasimap;

}

public void setPaSiMap(PaSiMap data)

{

pasimap = data;

}

public boolean isCancelled()

272

{

273

if (pasimap==null || pasimap.isCancelled())

{

return true;

}

return false;

}

public void cancel()

{

pasimap.cancel();

}

public boolean canCancel()

286

{

287

return (!isCancelled() && pasimap.isCancellable());

288

}

289

}

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File PaSiMapModel.java

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Class PaSiMapModel

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