File Mapping.java

Branches:

Statements:

109

Methods:

Classes:

LOC:

310

NCLOC:

238

Total complexity:

Complexity density:

0.17

Statements/Method:

21.8

Methods/Class:

Average method complexity:

3.6

Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Mapping	42	109	18	0.00%

Class Mapping

Class Mapping	Line # 42	Total Statements 109	Complexity 18	TOTAL Coverage 0.00%
setUpJvOptionPane() : void setUpJvOptionPane() : void	4545	2.02	1.01	0.0 0.00%
pdbEntryPositionMap() : void pdbEntryPositionMap() : void	5959	39.039	2.02	0.0 0.00%
testPDBentryMapping() : void testPDBentryMapping() : void	139139	39.039	10.010	0.0 0.00%
mapFer1From3W5V() : void mapFer1From3W5V() : void	242242	6.06	2.02	0.0 0.00%
compareTransferredToRefPDBAnnot() : void compareTransferredToRefPDBAnnot() : void	263263	23.023	3.03	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.structure;

import static org.testng.AssertJUnit.assertEquals;

import static org.testng.AssertJUnit.assertTrue;

import org.testng.Assert;

import org.testng.AssertJUnit;

import org.testng.annotations.BeforeClass;

import org.testng.annotations.Test;

import jalview.datamodel.AlignmentAnnotation;

import jalview.datamodel.Annotation;

import jalview.datamodel.Sequence;

import jalview.datamodel.SequenceI;

import jalview.gui.AlignFrame;

import jalview.gui.JvOptionPane;

import jalview.io.DataSourceType;

import jalview.io.FileFormat;

import jalview.io.FileLoader;

import jalview.io.StructureFile;

public class Mapping

{

@BeforeClass(alwaysRun = true)

public void setUpJvOptionPane()

{

JvOptionPane.setInteractiveMode(false);

JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);

}

* more test data

* 1QCF|A/101-121 SFQKGDQMVVLEESGEWWKAR Ser 114 jumps to Gly 116 at position

* 115 in PDB Res Numbering secondary structure numbers in jmol seem to be in

* msd numbering, not pdb res numbering.

@Test(groups = { "Functional" }, enabled = false)

public void pdbEntryPositionMap() throws Exception

{

Assert.fail("This test intentionally left to fail");

for (int offset = 0; offset < 20; offset += 6)

{

// check we put the secondary structure in the right position

Sequence uprot = new Sequence("TheProtSeq",

"DAWEIPRESLKLEKKLGAGQFGEVWMATYNKHTKVAVKTMKPGSMSVEAFLAEANVMKTL");

uprot.setStart(offset + 258); // make it harder - create a fake

// relocation problem for jalview to

// deal with

uprot.setEnd(uprot.getStart() + uprot.getLength() - 1);

// original numbers taken from

// http://www.ebi.ac.uk/pdbe-srv/view/entry/1qcf/secondary.html

// these are in numbering relative to the subsequence above

int coils[] = { 266, 275, 278, 287, 289, 298, 302, 316 },

helices[] = new int[]

{ 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 };

StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();

StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },

new String[]

{ "A" }, "test/jalview/ext/jmol/1QCF.pdb",

DataSourceType.FILE, null, null);

assertTrue(pmap != null);

SequenceI protseq = pmap.getSeqsAsArray()[0];

AlignmentAnnotation pstra = protseq

.getAnnotation("Secondary Structure")[0];

int pinds, pinde;

pstra.restrict((pinds = protseq.findIndex(258) - 1),

pinde = (protseq.findIndex(317) - 1));

int op;

System.out.println("PDB Annot");

for (char c : protseq.getSubSequence(pinds, pinde).getSequence())

{

System.out.print(c + ", ");

}

System.out.println("\n" + pstra + "\n\nsubsequence\n");

for (char c : uprot.getSequence())

{

100

System.out.print(c + ", ");

101

}

102

System.out.println("");

103

for (AlignmentAnnotation ss : uprot

104

.getAnnotation("Secondary Structure"))

105

{

106

ss.adjustForAlignment();

107

System.out.println("Uniprot Annot\n" + ss);

108

assertTrue(ss.hasIcons);

109

char expected = 'H';

110

for (int p : helices)

111

{

112

Annotation a = ss.annotations[op = (uprot.findIndex(offset + p)

113

- 1)];

114

assertTrue("Expected a helix at position " + p

115

+ uprot.getCharAt(op) + " but got coil", a != null);

116

assertEquals("Expected a helix at position " + p,

117

a.secondaryStructure, expected);

}

expected = 'E';

for (int p : sheets)

{

Annotation a = ss.annotations[uprot.findIndex(offset + p) - 1];

123

assertTrue("Expected a strand at position " + p + " but got coil",

124

a != null);

125

assertEquals("Expected a strand at position " + p,

126

a.secondaryStructure, expected);

}

expected = ' ';

for (int p : coils)

{

Annotation a = ss.annotations[uprot.findIndex(offset + p) - 1];

132

assertTrue("Expected coil at position " + p + " but got "

133

+ a.secondaryStructure, a == null);

}

}

}

}

@Test(groups = { "Functional" }, enabled = false)

140

public void testPDBentryMapping() throws Exception

141

{

142

Assert.fail("This test intentionally left to fail");

143

Sequence sq = new Sequence("1GAQ A subseq 126 to 219",

144

"EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");

145

Sequence sq1 = new Sequence(sq);

146

String inFile;

147

StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();

148

// Associate the 1GAQ pdb file with the subsequence 'imported' from another

149

// source

150

StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },

151

new String[]

152

{ "A" }, inFile = "examples/1gaq.txt", DataSourceType.FILE,

153

null, null);

154

assertTrue("PDB File couldn't be found", pde != null);

155

StructureMapping[] mp = ssm.getMapping(inFile);

156

assertTrue("No mappings made.", mp != null && mp.length > 0);

157

int nsecStr = 0, nsTemp = 0;

158

// test for presence of transferred annotation on sequence

159

for (AlignmentAnnotation alan : sq.getAnnotation())

{

if (alan.hasIcons)

{

nsecStr++;

}

if (alan.graph == alan.LINE_GRAPH)

{

nsTemp++;

}

}

assertEquals(

"Only one secondary structure should be transferred to associated sequence.",

172

1, nsecStr);

173

assertEquals(

174

"Only two line graphs should be transferred to associated sequence.",

175

2, nsTemp);

176

// Now test the transfer function and compare annotated positions

177

for (StructureMapping origMap : mp)

178

{

179

if (origMap.getSequence() == sq)

180

{

181

assertEquals("Mapping was incomplete.", sq.getLength() - 1,

182

(origMap.getPDBResNum(sq.getEnd())

183

- origMap.getPDBResNum(sq.getStart())));

184

// sanity check - if this fails, mapping from first position in sequence

185

// we want to transfer to is not where we expect

186

assertEquals(1, origMap.getSeqPos(126));

187

SequenceI firstChain = pde.getSeqs().get(0);

188

// Compare the annotated positions on the PDB chain sequence with the

189

// annotation on the associated sequence

190

for (AlignmentAnnotation alan : firstChain.getAnnotation())

191

{

192

AlignmentAnnotation transfer = origMap.transfer(alan);

193

System.out.println("pdb:" + firstChain.getSequenceAsString());

194

System.out.println("ann:" + alan.toString());

195

System.out.println("pdb:" + sq.getSequenceAsString());

196

System.out.println("ann:" + transfer.toString());

197

198

for (int p = 0, pSize = firstChain.getLength(); p < pSize; p++)

199

{

200

// walk along the pdb chain's jalview sequence

201

int rseqpos;

202

int fpos = origMap

203

.getSeqPos(rseqpos = firstChain.findPosition(p));

204

// only look at positions where there is a corresponding position in

// mapping

if (fpos < 1)

{

continue;

}

// p is index into PDB residue entries

211

// rseqpos is pdb sequence position for position p

212

// fpos is sequence position for associated position for rseqpos

213

// tanpos is the column for the mapped sequence position

214

int tanpos = sq.findIndex(fpos) - 1;

215

if (tanpos < 0 || transfer.annotations.length <= tanpos)

216

{

217

// gone beyond mapping to the sequence

break;

}

Annotation a = transfer.annotations[tanpos],

222

b = alan.annotations[p];

223

assertEquals(

224

"Non-equivalent annotation element at " + p + "("

225

+ rseqpos + ")" + " expected at " + fpos

226

+ " (alIndex " + tanpos + ")",

227

a == null ? a : a.toString(),

228

b == null ? b : b.toString());

229

System.out.print("(" + a + "|" + b + ")");

}

}

}

}

}

/**

* corner case for pdb mapping - revealed a problem with the AlignSeq->Mapping

* transform

@Test(groups = { "Functional" })

243

public void mapFer1From3W5V() throws Exception

244

{

245

AlignFrame seqf = new FileLoader(false).LoadFileWaitTillLoaded(

246

">FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor\nMATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGEVELQVPD\nDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKE\nEELTGA",

247

DataSourceType.PASTE, FileFormat.Fasta);

248

SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0);

249

StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();

250

StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },

251

new String[]

252

{ null }, "examples/3W5V.pdb", DataSourceType.FILE, null, null);