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package jalview.io; |
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import jalview.analysis.SequenceIdMatcher; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.Annotation; |
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import jalview.datamodel.SequenceI; |
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import java.awt.Color; |
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import java.io.IOException; |
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import java.util.ArrayList; |
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import java.util.HashMap; |
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import java.util.LinkedHashMap; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.regex.Matcher; |
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import java.util.regex.Pattern; |
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@author |
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| 49% |
Uncovered Elements: 131 (257) |
Complexity: 70 |
Complexity Density: 0.44 |
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public class TCoffeeScoreFile extends AlignFile |
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{ |
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static final Color[] colors = { new Color(102, 102, 255), |
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new Color(0, 255, 0), |
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new Color(102, 255, 0), |
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new Color(204, 255, 0), |
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new Color(255, 255, 0), |
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new Color(255, 204, 0), |
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new Color(255, 153, 0), |
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new Color(255, 102, 0), |
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new Color(255, 51, 0), |
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new Color(255, 34, 0) |
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}; |
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public final static String TCOFFEE_SCORE = "TCoffeeScore"; |
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static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern |
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.compile("^\\d+\\s([^\\s]+)\\s+\\d+$"); |
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@link |
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Header header; |
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LinkedHashMap<String, StringBuilder> scores; |
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Integer fWidth; |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public TCoffeeScoreFile(Object inFile, DataSourceType fileSourceType)... |
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throws IOException |
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{ |
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super(inFile, fileSourceType); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public TCoffeeScoreFile(FileParse source) throws IOException... |
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{ |
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super(source); |
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} |
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@param |
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@return |
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| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 3 |
Complexity Density: 3 |
|
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2 |
public int getHeight()... |
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{ |
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return scores != null && scores.size() > 0 ? scores.size() - 1 : 0; |
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} |
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@return |
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| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
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2 |
public int getWidth()... |
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{ |
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return fWidth != null ? fWidth : 0; |
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} |
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@param |
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@return |
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| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 3 |
Complexity Density: 3 |
|
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public String getScoresFor(String id)... |
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{ |
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return scores != null && scores.containsKey(id) |
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? scores.get(id).toString() |
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: ""; |
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} |
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@return@link |
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| 75% |
Uncovered Elements: 2 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
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public List<String> getScoresList()... |
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{ |
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if (scores == null) |
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{ |
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return null; |
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} |
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List<String> result = new ArrayList<String>(scores.size()); |
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for (Map.Entry<String, StringBuilder> it : scores.entrySet()) |
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{ |
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result.add(it.getValue().toString()); |
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} |
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return result; |
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} |
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@return |
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| 88.9% |
Uncovered Elements: 2 (18) |
Complexity: 5 |
Complexity Density: 0.42 |
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1 |
public byte[][] getScoresArray()... |
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{ |
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if (scores == null) |
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{ |
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return null; |
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} |
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byte[][] result = new byte[scores.size()][]; |
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int rowCount = 0; |
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for (Map.Entry<String, StringBuilder> it : scores.entrySet()) |
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{ |
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String line = it.getValue().toString(); |
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byte[] seqValues = new byte[line.length()]; |
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for (int j = 0, c = line.length(); j < c; j++) |
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{ |
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byte val = (byte) (line.charAt(j) - '0'); |
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seqValues[j] = (val >= 0 && val <= 9) ? val : -1; |
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} |
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result[rowCount++] = seqValues; |
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} |
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return result; |
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} |
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| 70.6% |
Uncovered Elements: 10 (34) |
Complexity: 6 |
Complexity Density: 0.25 |
|
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@Override... |
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public void parse() throws IOException |
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{ |
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header = readHeader(this); |
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if (header == null) |
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{ |
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error = true; |
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return; |
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} |
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scores = new LinkedHashMap<String, StringBuilder>(); |
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for (Map.Entry<String, Integer> entry : header.scores.entrySet()) |
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{ |
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scores.put(entry.getKey(), new StringBuilder()); |
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} |
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Block block; |
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while ((block = readBlock(this, header.scores.size())) != null) |
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{ |
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for (Map.Entry<String, String> entry : block.items.entrySet()) |
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{ |
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StringBuilder scoreStringBuilder = scores.get(entry.getKey()); |
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if (scoreStringBuilder == null) |
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{ |
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error = true; |
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errormessage = String.format( |
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"Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section", |
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entry.getKey()); |
282 |
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return; |
283 |
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} |
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scoreStringBuilder.append(entry.getValue()); |
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} |
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} |
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292 |
6 |
for (StringBuilder str : scores.values()) |
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{ |
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51 |
if (fWidth == null) |
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{ |
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fWidth = str.length(); |
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} |
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else if (fWidth != str.length()) |
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{ |
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error = true; |
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errormessage = "Invalid T-Coffee score file: All the score sequences must have the same length"; |
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return; |
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} |
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} |
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306 |
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return; |
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} |
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| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 0.67 |
|
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57 |
static int parseInt(String str)... |
310 |
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{ |
311 |
57 |
try |
312 |
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{ |
313 |
57 |
return Integer.parseInt(str); |
314 |
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} catch (NumberFormatException e) |
315 |
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{ |
316 |
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317 |
0 |
return 0; |
318 |
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} |
319 |
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} |
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324 |
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@param |
325 |
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326 |
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@return@link |
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@throws |
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329 |
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| 59.3% |
Uncovered Elements: 22 (54) |
Complexity: 15 |
Complexity Density: 0.44 |
|
330 |
7 |
static Header readHeader(FileParse reader) throws IOException... |
331 |
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{ |
332 |
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333 |
7 |
Header result = null; |
334 |
7 |
try |
335 |
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{ |
336 |
7 |
result = new Header(); |
337 |
7 |
result.head = reader.nextLine(); |
338 |
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339 |
7 |
String line; |
340 |
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341 |
? |
while ((line = reader.nextLine()) != null) |
342 |
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{ |
343 |
41 |
if (line.startsWith("SCORE=")) |
344 |
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{ |
345 |
6 |
result.score = parseInt(line.substring(6).trim()); |
346 |
6 |
break; |
347 |
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} |
348 |
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} |
349 |
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|
350 |
? |
if ((line = reader.nextLine()) == null || !"*".equals(line.trim())) |
351 |
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{ |
352 |
1 |
error(reader, |
353 |
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"Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)"); |
354 |
1 |
return null; |
355 |
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} |
356 |
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if ((line = reader.nextLine()) == null |
357 |
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|| !"BAD AVG GOOD".equals(line.trim())) |
358 |
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{ |
359 |
0 |
error(reader, |
360 |
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"Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)"); |
361 |
0 |
return null; |
362 |
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} |
363 |
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if ((line = reader.nextLine()) == null || !"*".equals(line.trim())) |
364 |
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{ |
365 |
0 |
error(reader, |
366 |
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"Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)"); |
367 |
0 |
return null; |
368 |
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} |
369 |
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370 |
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371 |
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372 |
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373 |
? |
while ((line = reader.nextLine()) != null) |
374 |
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{ |
375 |
57 |
if ("".equals(line)) |
376 |
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{ |
377 |
6 |
break; |
378 |
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} |
379 |
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|
380 |
51 |
int p = line.indexOf(":"); |
381 |
51 |
if (p == -1) |
382 |
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{ |
383 |
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|
384 |
0 |
continue; |
385 |
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} |
386 |
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|
387 |
51 |
String id = line.substring(0, p).trim(); |
388 |
51 |
int val = parseInt(line.substring(p + 1).trim()); |
389 |
51 |
if ("".equals(id)) |
390 |
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{ |
391 |
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|
392 |
0 |
continue; |
393 |
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} |
394 |
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|
395 |
51 |
result.scores.put(id, val); |
396 |
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} |
397 |
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|
398 |
6 |
if (result == null) |
399 |
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{ |
400 |
0 |
error(reader, "T-COFFEE score file had no per-sequence scores"); |
401 |
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} |
402 |
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|
403 |
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} catch (IOException e) |
404 |
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{ |
405 |
0 |
error(reader, "Unexpected problem parsing T-Coffee score ascii file"); |
406 |
0 |
throw e; |
407 |
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} |
408 |
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|
409 |
6 |
return result; |
410 |
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} |
411 |
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| 66.7% |
Uncovered Elements: 2 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
412 |
1 |
private static void error(FileParse reader, String errm)... |
413 |
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{ |
414 |
1 |
reader.error = true; |
415 |
1 |
if (reader.errormessage == null) |
416 |
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{ |
417 |
0 |
reader.errormessage = errm; |
418 |
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} |
419 |
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else |
420 |
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{ |
421 |
1 |
reader.errormessage += "\n" + errm; |
422 |
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} |
423 |
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} |
424 |
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425 |
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426 |
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427 |
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428 |
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@param |
429 |
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|
430 |
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@param |
431 |
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|
432 |
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@return@link |
433 |
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|
434 |
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@throws |
435 |
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|
436 |
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|
|
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| 68.6% |
Uncovered Elements: 11 (35) |
Complexity: 9 |
Complexity Density: 0.43 |
|
437 |
19 |
static Block readBlock(FileParse reader, int size) throws IOException... |
438 |
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{ |
439 |
19 |
Block result = new Block(size); |
440 |
19 |
String line; |
441 |
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442 |
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443 |
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444 |
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445 |
? |
while ((line = reader.nextLine()) != null && "".equals(line.trim())) |
446 |
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{ |
447 |
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|
448 |
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} |
449 |
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|
450 |
19 |
if (line == null) |
451 |
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{ |
452 |
6 |
return null; |
453 |
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} |
454 |
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455 |
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|
456 |
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|
457 |
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|
458 |
13 |
do |
459 |
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{ |
460 |
119 |
if ("".equals(line.trim())) |
461 |
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{ |
462 |
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|
463 |
8 |
break; |
464 |
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} |
465 |
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466 |
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|
467 |
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|
468 |
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|
469 |
111 |
int p = line.indexOf(" "); |
470 |
111 |
if (p == -1) |
471 |
|
{ |
472 |
0 |
if (reader.warningMessage == null) |
473 |
|
{ |
474 |
0 |
reader.warningMessage = ""; |
475 |
|
} |
476 |
0 |
reader.warningMessage += "Possible parsing error - expected to find a space in line: '" |
477 |
|
+ line + "'\n"; |
478 |
0 |
continue; |
479 |
|
} |
480 |
|
|
481 |
111 |
String id = line.substring(0, p).trim(); |
482 |
111 |
String val = line.substring(p + 1).trim(); |
483 |
|
|
484 |
111 |
Matcher m = SCORES_WITH_RESIDUE_NUMS.matcher(val); |
485 |
111 |
if (m.matches()) |
486 |
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{ |
487 |
12 |
val = m.group(1); |
488 |
|
} |
489 |
|
|
490 |
111 |
result.items.put(id, val); |
491 |
|
|
492 |
? |
} while ((line = reader.nextLine()) != null); |
493 |
|
|
494 |
13 |
return result; |
495 |
|
} |
496 |
|
|
497 |
|
|
498 |
|
|
499 |
|
|
|
|
| 50% |
Uncovered Elements: 3 (6) |
Complexity: 3 |
Complexity Density: 1.5 |
|
500 |
|
static class Header |
501 |
|
{ |
502 |
|
String head; |
503 |
|
|
504 |
|
int score; |
505 |
|
|
506 |
|
LinkedHashMap<String, Integer> scores = new LinkedHashMap<String, Integer>(); |
507 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
508 |
0 |
public int getScoreAvg()... |
509 |
|
{ |
510 |
0 |
return score; |
511 |
|
} |
512 |
|
|
|
|
| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
513 |
9 |
public int getScoreFor(String ID)... |
514 |
|
{ |
515 |
|
|
516 |
9 |
return scores.containsKey(ID) ? scores.get(ID) : -1; |
517 |
|
|
518 |
|
} |
519 |
|
} |
520 |
|
|
521 |
|
|
522 |
|
|
523 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 3 |
Complexity Density: 0.75 |
|
524 |
|
static class Block |
525 |
|
{ |
526 |
|
int size; |
527 |
|
|
528 |
|
Map<String, String> items; |
529 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
530 |
19 |
public Block(int size)... |
531 |
|
{ |
532 |
19 |
this.size = size; |
533 |
19 |
this.items = new HashMap<String, String>(size); |
534 |
|
} |
535 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
536 |
8 |
String getScoresFor(String id)... |
537 |
|
{ |
538 |
8 |
return items.get(id); |
539 |
|
} |
540 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
541 |
1 |
String getConsensus()... |
542 |
|
{ |
543 |
1 |
return items.get("cons"); |
544 |
|
} |
545 |
|
} |
546 |
|
|
547 |
|
|
548 |
|
|
549 |
|
|
550 |
|
@param |
551 |
|
|
552 |
|
@param |
553 |
|
|
554 |
|
@return |
555 |
|
|
|
|
| 0% |
Uncovered Elements: 73 (73) |
Complexity: 18 |
Complexity Density: 0.37 |
|
556 |
0 |
public boolean annotateAlignment(AlignmentI al, boolean matchids)... |
557 |
|
{ |
558 |
0 |
if (al.getHeight() != getHeight() || al.getWidth() != getWidth()) |
559 |
|
{ |
560 |
0 |
String info = String.format( |
561 |
|
"align w: %s, h: %s; score: w: %s; h: %s ", al.getWidth(), |
562 |
|
al.getHeight(), getWidth(), getHeight()); |
563 |
0 |
warningMessage = "Alignment shape does not match T-Coffee score file shape -- " |
564 |
|
+ info; |
565 |
0 |
return false; |
566 |
|
} |
567 |
0 |
boolean added = false; |
568 |
0 |
int i = 0; |
569 |
0 |
SequenceIdMatcher sidmatcher = new SequenceIdMatcher( |
570 |
|
al.getSequencesArray()); |
571 |
0 |
byte[][] scoreMatrix = getScoresArray(); |
572 |
|
|
573 |
|
|
574 |
0 |
for (Map.Entry<String, StringBuilder> id : scores.entrySet()) |
575 |
|
{ |
576 |
0 |
byte[] srow = scoreMatrix[i]; |
577 |
0 |
SequenceI s; |
578 |
0 |
if (matchids) |
579 |
|
{ |
580 |
0 |
s = sidmatcher.findIdMatch(id.getKey()); |
581 |
|
} |
582 |
|
else |
583 |
|
{ |
584 |
0 |
s = al.getSequenceAt(i); |
585 |
|
} |
586 |
0 |
i++; |
587 |
0 |
if (s == null && i != scores.size() && !id.getKey().equals("cons")) |
588 |
|
{ |
589 |
0 |
System.err |
590 |
0 |
.println("No " + (matchids ? "match " : " sequences left ") |
591 |
|
+ " for TCoffee score set : " + id.getKey()); |
592 |
0 |
continue; |
593 |
|
} |
594 |
0 |
int jSize = al.getWidth() < srow.length ? al.getWidth() : srow.length; |
595 |
0 |
Annotation[] annotations = new Annotation[al.getWidth()]; |
596 |
0 |
for (int j = 0; j < jSize; j++) |
597 |
|
{ |
598 |
0 |
byte val = srow[j]; |
599 |
0 |
if (s != null && jalview.util.Comparison.isGap(s.getCharAt(j))) |
600 |
|
{ |
601 |
0 |
annotations[j] = null; |
602 |
0 |
if (val > 0) |
603 |
|
{ |
604 |
0 |
jalview.bin.Console.errPrintln( |
605 |
|
"Warning: non-zero value for positional T-COFFEE score for gap at " |
606 |
|
+ j + " in sequence " + s.getName()); |
607 |
|
} |
608 |
|
} |
609 |
|
else |
610 |
|
{ |
611 |
0 |
annotations[j] = new Annotation(s == null ? "" + val : null, |
612 |
0 |
s == null ? "" + val : null, '\0', val * 1f, |
613 |
0 |
val >= 0 && val < colors.length ? colors[val] |
614 |
|
: Color.white); |
615 |
|
} |
616 |
|
} |
617 |
|
|
618 |
0 |
AlignmentAnnotation aa = al.findOrCreateAnnotation(TCOFFEE_SCORE, |
619 |
|
TCOFFEE_SCORE, false, s, null); |
620 |
0 |
if (s != null) |
621 |
|
{ |
622 |
0 |
aa.label = "T-COFFEE"; |
623 |
0 |
aa.description = "" + id.getKey(); |
624 |
0 |
aa.annotations = annotations; |
625 |
0 |
aa.visible = false; |
626 |
0 |
aa.belowAlignment = false; |
627 |
0 |
aa.setScore(header.getScoreFor(id.getKey())); |
628 |
0 |
aa.createSequenceMapping(s, s.getStart(), true); |
629 |
0 |
s.addAlignmentAnnotation(aa); |
630 |
0 |
aa.adjustForAlignment(); |
631 |
|
} |
632 |
|
else |
633 |
|
{ |
634 |
0 |
aa.graph = AlignmentAnnotation.NO_GRAPH; |
635 |
0 |
aa.label = "T-COFFEE"; |
636 |
0 |
aa.description = "TCoffee column reliability score"; |
637 |
0 |
aa.annotations = annotations; |
638 |
0 |
aa.belowAlignment = true; |
639 |
0 |
aa.visible = true; |
640 |
0 |
aa.setScore(header.getScoreAvg()); |
641 |
|
} |
642 |
0 |
aa.showAllColLabels = true; |
643 |
0 |
aa.validateRangeAndDisplay(); |
644 |
0 |
added = true; |
645 |
|
} |
646 |
|
|
647 |
0 |
return added; |
648 |
|
} |
649 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
650 |
0 |
@Override... |
651 |
|
public String print(SequenceI[] sqs, boolean jvsuffix) |
652 |
|
{ |
653 |
|
|
654 |
0 |
return "Not valid."; |
655 |
|
} |
656 |
|
} |