File Mapping.java

Branches:

Statements:

109

Methods:

Classes:

LOC:

314

NCLOC:

242

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	0.275362327.5%

Class Mapping

Class Mapping	Line # 42	Total Statements 109	Complexity 18	TOTAL Coverage 0.275362327.5%
setUpJvOptionPane() : void setUpJvOptionPane() : void	4545	2.02	1.01	1.0 1.0100%
pdbEntryPositionMap() : void pdbEntryPositionMap() : void	5959	39.039	2.02	0.0 0.00%
testPDBentryMapping() : void testPDBentryMapping() : void	140140	39.039	10.010	0.0 0.00%
mapFer1From3W5V() : void mapFer1From3W5V() : void	244244	6.06	2.02	0.75 0.7575%
compareTransferredToRefPDBAnnot() : void compareTransferredToRefPDBAnnot() : void	266266	23.023	3.03	1.0 1.0100%

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 = StructureSelectionManager

.getStructureSelectionManager(null);

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

{

101

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

102

}

103

System.out.println("");

104

for (AlignmentAnnotation ss : uprot

105

.getAnnotation("Secondary Structure"))

106

{

107

ss.adjustForAlignment();

108

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

109

assertTrue(ss.hasIcons);

110

char expected = 'H';

111

for (int p : helices)

112

{

113

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

114

- 1)];

115

assertTrue("Expected a helix at position " + p

116

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

117

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

118

a.secondaryStructure, expected);

}

expected = 'E';

for (int p : sheets)

{

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

124

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

125

a != null);

126

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

127

a.secondaryStructure, expected);

}

expected = ' ';

for (int p : coils)

{

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

133

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

134

+ a.secondaryStructure, a == null);

}

}

}

}

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

141

public void testPDBentryMapping() throws Exception

142

{

143

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

144

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

145

"EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");

146

Sequence sq1 = new Sequence(sq);

147

String inFile;

148

StructureSelectionManager ssm = StructureSelectionManager

149

.getStructureSelectionManager(null);

150

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

151

// source

152

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

153

new String[]

154

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

155

null, null);

156

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

157

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

158

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

159

int nsecStr = 0, nsTemp = 0;

160

// test for presence of transferred annotation on sequence

161

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.",

174

1, nsecStr);

175

assertEquals(

176

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

177

2, nsTemp);

178

// Now test the transfer function and compare annotated positions

179

for (StructureMapping origMap : mp)

180

{

181

if (origMap.getSequence() == sq)

182

{

183

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

184

(origMap.getPDBResNum(sq.getEnd())

185

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

186

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

187

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

188

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

189

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

190

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

191

// annotation on the associated sequence

192

for (AlignmentAnnotation alan : firstChain.getAnnotation())

193

{

194

AlignmentAnnotation transfer = origMap.transfer(alan);

195

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

196

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

197

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

198

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

199

200

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

201

{

202

// walk along the pdb chain's jalview sequence

203

int rseqpos;

204

int fpos = origMap

205

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

206

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

// mapping

if (fpos < 1)

{

continue;

}

// p is index into PDB residue entries

213

// rseqpos is pdb sequence position for position p

214

// fpos is sequence position for associated position for rseqpos

215

// tanpos is the column for the mapped sequence position

216

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

217

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

218

{

219

// gone beyond mapping to the sequence

break;

}

Annotation a = transfer.annotations[tanpos],

224

b = alan.annotations[p];

225

assertEquals(

226

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

227

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

228

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

229

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

230

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

231

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

}

}

}

}

}

/**

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

* transform

@Test(groups = { "Functional" })

245

public void mapFer1From3W5V() throws Exception

246

{

247

AlignFrame seqf = new FileLoader(false).LoadFileWaitTillLoaded(

248

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

249

DataSourceType.PASTE, FileFormat.Fasta);

250

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

251

StructureSelectionManager ssm = StructureSelectionManager

252

.getStructureSelectionManager(null);

253

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

254

new String[]