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Coverage Report

  1. Project Clover database Wed Nov 13 2024 16:21:17 GMT
  2. Package mc_view

File PDBChain.java

 

Coverage histogram

../img/srcFileCovDistChart8.png
20% of files have more coverage

Code metrics

116
232
16
1
751
529
95
0.41
14.5
16
5.94

Classes

Class Line # Actions
PDBChain 44 232 95
0.7362637573.6%
 

Contributing tests

This file is covered by 67 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package mc_view;
22   
23    import java.awt.Color;
24    import java.util.List;
25    import java.util.Locale;
26    import java.util.Vector;
27   
28    import jalview.analysis.AlignSeq;
29    import jalview.datamodel.AlignmentAnnotation;
30    import jalview.datamodel.Annotation;
31    import jalview.datamodel.ContactMatrixI;
32    import jalview.datamodel.Mapping;
33    import jalview.datamodel.Sequence;
34    import jalview.datamodel.SequenceFeature;
35    import jalview.datamodel.SequenceI;
36    import jalview.datamodel.annotations.AnnotationRowBuilder;
37    import jalview.schemes.ColourSchemeI;
38    import jalview.schemes.ResidueProperties;
39    import jalview.structure.StructureImportSettings;
40    import jalview.structure.StructureMapping;
41    import jalview.util.Comparison;
42    import jalview.ws.datamodel.MappableContactMatrixI;
43   
 
44    public class PDBChain
45    {
46    public static final String RESNUM_FEATURE = "RESNUM";
47   
48    private static final String IEASTATUS = "IEA:jalview";
49   
50    public String id;
51   
52    public Vector<Bond> bonds = new Vector<>();
53   
54    public Vector<Atom> atoms = new Vector<>();
55   
56    public Vector<Residue> residues = new Vector<>();
57   
58    public int offset;
59   
60    /**
61    * sequence is the sequence extracted by the chain parsing code
62    */
63    public SequenceI sequence;
64   
65    /**
66    * shadow is the sequence created by any other parsing processes (e.g. Jmol,
67    * RNAview)
68    */
69    public SequenceI shadow = null;
70   
71    public boolean isNa = false;
72   
73    public boolean isVisible = true;
74   
75    public int pdbstart = 0;
76   
77    public int pdbend = 0;
78   
79    public int seqstart = 0;
80   
81    public int seqend = 0;
82   
83    public String pdbid = "";
84   
85    AnnotationRowBuilder tfacTemplate = new AnnotationRowBuilder(
86    "Temperature Factor");
87   
 
88  267 toggle public PDBChain(String thePdbid, String theId,
89    AnnotationRowBuilder template)
90    {
91  267 this(thePdbid, theId);
92  267 if (template != null)
93    {
94  34 tfacTemplate = template;
95    }
96    }
97   
98    /**
99    * import chain data assuming Temperature Factor is in the Temperature Factor
100    * column
101    *
102    * @param thePdbid
103    * @param theId
104    */
 
105  314 toggle public PDBChain(String thePdbid, String theId)
106    {
107  314 this.pdbid = thePdbid == null ? thePdbid
108    : thePdbid.toLowerCase(Locale.ROOT);
109  314 this.id = theId;
110    }
111   
112    /**
113    * character used to write newlines
114    */
115    protected String newline = System.getProperty("line.separator");
116   
117    public Mapping shadowMap;
118   
 
119  1 toggle public void setNewlineString(String nl)
120    {
121  1 newline = nl;
122    }
123   
 
124  2 toggle public String getNewlineString()
125    {
126  2 return newline;
127    }
128   
 
129  1 toggle public String print()
130    {
131  1 StringBuilder tmp = new StringBuilder(256);
132   
133  1 for (Bond b : bonds)
134    {
135  3 tmp.append(b.at1.resName).append(" ").append(b.at1.resNumber)
136    .append(" ").append(offset).append(newline);
137    }
138   
139  1 return tmp.toString();
140    }
141   
142    /**
143    * Annotate the residues with their corresponding positions in s1 using the
144    * alignment in as NOTE: This clears all atom.alignmentMapping values on the
145    * structure.
146    *
147    * @param as
148    * @param s1
149    */
 
150  194 toggle public void makeExactMapping(AlignSeq as, SequenceI s1)
151    {
152  194 int pdbpos = as.getSeq2Start() - 2;
153  194 int alignpos = s1.getStart() + as.getSeq1Start() - 3;
154    // first clear out any old alignmentMapping values:
155  194 for (Atom atom : atoms)
156    {
157  21216 atom.alignmentMapping = -1;
158    }
159    // and now trace the alignment onto the atom set.
160  21403 for (int i = 0; i < as.astr1.length(); i++)
161    {
162  21209 if (as.astr1.charAt(i) != '-')
163    {
164  21209 alignpos++;
165    }
166   
167  21209 if (as.astr2.charAt(i) != '-')
168    {
169  21209 pdbpos++;
170    }
171   
172  21209 boolean sameResidue = Comparison.isSameResidue(as.astr1.charAt(i),
173    as.astr2.charAt(i), false);
174  21209 if (sameResidue)
175    {
176  21164 if (pdbpos >= residues.size())
177    {
178  0 continue;
179    }
180  21164 Residue res = residues.elementAt(pdbpos);
181  21164 for (Atom atom : res.atoms)
182    {
183  21167 atom.alignmentMapping = alignpos;
184    }
185    }
186    }
187    }
188   
189    /**
190    * Annotate the residues with their corresponding positions in s1 using the
191    * alignment in as NOTE: This clears all atom.alignmentMapping values on the
192    * structure.
193    *
194    * @param as
195    * @param s1
196    */
 
197  0 toggle public void makeExactMapping(StructureMapping mapping, SequenceI s1)
198    {
199    // first clear out any old alignmentMapping values:
200  0 for (Atom atom : atoms)
201    {
202  0 atom.alignmentMapping = -1;
203    }
204  0 SequenceI ds = s1;
205  0 while (ds.getDatasetSequence() != null)
206    {
207  0 ds = ds.getDatasetSequence();
208    }
209  0 int pdboffset = 0;
210  0 for (Residue res : residues)
211    {
212    // res.number isn't set correctly for discontinuous/mismapped residues
213  0 int seqpos = mapping.getSeqPos(res.atoms.get(0).resNumber);
214  0 char strchar = sequence.getCharAt(pdboffset++);
215  0 if (seqpos == StructureMapping.UNASSIGNED_VALUE)
216    {
217  0 continue;
218    }
219  0 char seqchar = ds.getCharAt(seqpos - ds.getStart());
220   
221  0 boolean sameResidue = Comparison.isSameResidue(seqchar, strchar,
222    false);
223  0 if (sameResidue)
224    {
225  0 for (Atom atom : res.atoms)
226    {
227  0 atom.alignmentMapping = seqpos - 1;
228    }
229    }
230    }
231    }
232   
233    /**
234    * Copies over the RESNUM seqfeatures from the internal chain sequence to the
235    * mapped sequence
236    *
237    * @param seq
238    * @param status
239    * The Status of the transferred annotation
240    *
241    * @param altPDBID
242    * the group id for the features on the destination sequence (e.g.
243    * the official accession ID)
244    */
 
245  193 toggle public void transferRESNUMFeatures(SequenceI seq, String status,
246    String altPDBID)
247    {
248  193 if (altPDBID == null)
249    {
250  0 altPDBID = pdbid;
251    }
252  193 SequenceI sq = seq;
253  384 while (sq != null && sq.getDatasetSequence() != null)
254    {
255  191 sq = sq.getDatasetSequence();
256  191 if (sq == sequence)
257    {
258  0 return;
259    }
260    }
261   
262    /*
263    * Remove any existing features for this chain if they exist ?
264    * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
265    * totfeat=seqsfeatures.length; // Remove any features for this exact chain
266    * ? for (int i=0; i<seqsfeatures.length; i++) { }
267    */
268  193 if (status == null)
269    {
270  193 status = PDBChain.IEASTATUS;
271    }
272   
273  193 List<SequenceFeature> features = sequence.getSequenceFeatures();
274  193 for (SequenceFeature feature : features)
275    {
276  21210 if (feature.getFeatureGroup() != null
277    && feature.getFeatureGroup().equals(pdbid))
278    {
279  21210 int newBegin = 1
280    + residues.elementAt(feature.getBegin() - offset).atoms
281    .elementAt(0).alignmentMapping;
282  21210 int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
283    .elementAt(0).alignmentMapping;
284  21210 SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
285    altPDBID, feature.getScore());
286  21210 tx.setStatus(status
287  21210 + ((tx.getStatus() == null || tx.getStatus().length() == 0)
288    ? ""
289    : ":" + tx.getStatus()));
290  21210 if (tx.begin != 0 && tx.end != 0)
291    {
292  21161 sq.addSequenceFeature(tx);
293    }
294    }
295    }
296    }
297   
298    /**
299    * Traverses the list of residues and constructs bonds where CA-to-CA atoms or
300    * P-to-P atoms are found. Also sets the 'isNa' flag if more than 99% of
301    * residues contain a P not a CA.
302    */
 
303  304 toggle public void makeCaBondList()
304    {
305  304 boolean na = false;
306  304 int numNa = 0;
307  48051 for (int i = 0; i < (residues.size() - 1); i++)
308    {
309  47747 Residue tmpres = residues.elementAt(i);
310  47747 Residue tmpres2 = residues.elementAt(i + 1);
311  47747 Atom at1 = tmpres.findAtom("CA");
312  47747 Atom at2 = tmpres2.findAtom("CA");
313  47747 na = false;
314  47747 if ((at1 == null) && (at2 == null))
315    {
316  2 na = true;
317  2 at1 = tmpres.findAtom("P");
318  2 at2 = tmpres2.findAtom("P");
319    }
320  47747 if ((at1 != null) && (at2 != null))
321    {
322  47747 if (at1.chain.equals(at2.chain))
323    {
324  47747 if (na)
325    {
326  2 numNa++;
327    }
328  47747 makeBond(at1, at2);
329    }
330    }
331    else
332    {
333  0 System.out.println("not found " + i);
334    }
335    }
336   
337    /*
338    * If > 99% 'P', flag as nucleotide; note the count doesn't include the last
339    * residue
340    */
341  304 if (residues.size() > 1 && (numNa / (residues.size() - 1) > 0.99))
342    {
343  1 isNa = true;
344    }
345    }
346   
347    /**
348    * Construct a bond from atom1 to atom2 and add it to the list of bonds for
349    * this chain
350    *
351    * @param at1
352    * @param at2
353    */
 
354  47757 toggle public void makeBond(Atom at1, Atom at2)
355    {
356  47757 bonds.addElement(new Bond(at1, at2));
357    }
358   
359    /**
360    * Traverses the list of atoms and
361    * <ul>
362    * <li>constructs a list of Residues, each containing all the atoms that share
363    * the same residue number</li>
364    * <li>adds a RESNUM sequence feature for each position</li>
365    * <li>creates the sequence string</li>
366    * <li>determines if nucleotide</li>
367    * <li>saves the residue number of the first atom as 'offset'</li>
368    * <li>adds temp factor annotation if the flag is set to do so</li>
369    * </ul>
370    *
371    * @param visibleChainAnnotation
372    */
 
373  307 toggle public void makeResidueList(boolean visibleChainAnnotation)
374    {
375  307 int count = 0;
376  307 Object symbol;
377  307 boolean deoxyn = false;
378  307 boolean nucleotide = false;
379  307 StringBuilder seq = new StringBuilder(256);
380  307 Vector<SequenceFeature> resFeatures = new Vector<>();
381  307 Vector<Annotation> resAnnotation = new Vector<>();
382  307 int iSize = atoms.size() - 1;
383  307 int resNumber = -1;
384  307 char insCode = ' ';
385   
386  48367 for (int i = 0; i <= iSize; i++)
387    {
388  48060 Atom tmp = atoms.elementAt(i);
389  48060 resNumber = tmp.resNumber;
390  48060 insCode = tmp.insCode;
391   
392  48060 int res = resNumber;
393  48060 char ins = insCode;
394   
395  48060 if (i == 0)
396    {
397  307 offset = resNumber;
398    }
399   
400  48060 Vector<Atom> resAtoms = new Vector<>();
401    // Add atoms to a vector while the residue number
402    // remains the same as the first atom's resNumber (res)
403  96141 while ((resNumber == res) && (ins == insCode) && (i < atoms.size()))
404    {
405  48081 resAtoms.add(atoms.elementAt(i));
406  48081 i++;
407   
408  48081 if (i < atoms.size())
409    {
410  47774 resNumber = atoms.elementAt(i).resNumber;
411  47774 insCode = atoms.elementAt(i).insCode;
412    }
413    else
414    {
415  307 resNumber++;
416    }
417    }
418   
419    // We need this to keep in step with the outer for i = loop
420  48060 i--;
421   
422    // Add inserted residues as features to the base residue
423  48060 Atom currAtom = resAtoms.get(0);
424  48060 if (currAtom.insCode != ' ' && !residues.isEmpty()
425    && residues.lastElement().atoms
426    .get(0).resNumber == currAtom.resNumber)
427    {
428  0 String desc = currAtom.resName + ":" + currAtom.resNumIns + " "
429    + pdbid + id;
430  0 SequenceFeature sf = new SequenceFeature("INSERTION", desc,
431    offset + count - 1, offset + count - 1, "PDB_INS");
432  0 resFeatures.addElement(sf);
433  0 residues.lastElement().atoms.addAll(resAtoms);
434    }
435    else
436    {
437    // Make a new Residue object with the new atoms vector
438  48060 residues.addElement(new Residue(resAtoms, resNumber - 1, count));
439   
440  48060 Residue tmpres = residues.lastElement();
441  48060 Atom tmpat = tmpres.atoms.get(0);
442    // Make A new SequenceFeature for the current residue numbering
443  48060 String desc = tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid
444    + id;
445  48060 SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc,
446    offset + count, offset + count, pdbid);
447  48060 resFeatures.addElement(sf);
448  48060 resAnnotation.addElement(new Annotation(tmpat.tfactor));
449    // Keep totting up the sequence
450   
451  ? if ((symbol = ResidueProperties.getAA3Hash()
452    .get(tmpat.resName)) == null)
453    {
454  7 String nucname = tmpat.resName.trim();
455    // use the aaIndex rather than call 'toLower' - which would take a bit
456    // more time.
457  7 deoxyn = nucname.length() == 2
458    && ResidueProperties.aaIndex[nucname
459    .charAt(0)] == ResidueProperties.aaIndex['D'];
460  7 if (tmpat.name.equalsIgnoreCase("CA")
461    || ResidueProperties.nucleotideIndex[nucname
462  3 .charAt((deoxyn ? 1 : 0))] == -1)
463    {
464  4 char r = ResidueProperties.getSingleCharacterCode(
465    ResidueProperties.getCanonicalAminoAcid(tmpat.resName));
466  4 seq.append(r == '0' ? 'X' : r);
467    // System.err.println("PDBReader:Null aa3Hash for " +
468    // tmpat.resName);
469    }
470    else
471    {
472    // nucleotide flag
473  3 nucleotide = true;
474  3 seq.append(nucname.charAt((deoxyn ? 1 : 0)));
475    }
476    }
477    else
478    {
479  48053 if (nucleotide)
480    {
481  0 System.err.println(
482    "Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
483    }
484  48053 seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
485    }
486  48060 count++;
487    }
488    }
489   
490  307 if (id.length() < 1)
491    {
492  0 id = " ";
493    }
494  307 isNa = nucleotide;
495  307 sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
496    // resNumber-offset
497    // ~=
498    // seq.size()
499    // Add normalised feature scores to RESNUM indicating start/end of sequence
500    // sf.setScore(offset+count);
501   
502    // System.out.println("PDB Sequence is :\nSequence = " + seq);
503    // System.out.println("No of residues = " + residues.size());
504   
505  307 if (StructureImportSettings.isShowSeqFeatures())
506    {
507  293 iSize = resFeatures.size();
508  45001 for (int i = 0; i < iSize; i++)
509    {
510  44708 sequence.addSequenceFeature(resFeatures.elementAt(i));
511  44708 resFeatures.setElementAt(null, i);
512    }
513    }
514  307 if (visibleChainAnnotation)
515    {
516  203 Annotation[] annots = new Annotation[resAnnotation.size()];
517  203 float max = 0f;
518  203 float min = 0f;
519  203 iSize = annots.length;
520  33539 for (int i = 0; i < iSize; i++)
521    {
522  33336 annots[i] = resAnnotation.elementAt(i);
523  33336 tfacTemplate.processAnnotation(annots[i]);
524  33336 max = Math.max(max, annots[i].value);
525  33336 min = Math.min(min, annots[i].value);
526  33336 resAnnotation.setElementAt(null, i);
527    }
528  203 if (tfacTemplate.isHasMinMax())
529    {
530  27 max = tfacTemplate.getMax();
531  27 min = tfacTemplate.getMin();
532    }
533   
534  203 AlignmentAnnotation tfactorann = new AlignmentAnnotation(
535    tfacTemplate.getName(),
536  203 (tfacTemplate.isHasDescription()
537    ? tfacTemplate.getDescription()
538    : tfacTemplate.getName()) + " for " + pdbid + id,
539    annots, min, max, AlignmentAnnotation.LINE_GRAPH);
540  203 tfactorann.setTFType(tfacTemplate.getTFType());
541  203 tfactorann.setCalcId(getClass().getName());
542   
543  203 tfactorann.setSequenceRef(sequence);
544  203 sequence.addAlignmentAnnotation(tfactorann);
545    }
546    }
547   
548    /**
549    * Colour start/end of bonds by charge
550    * <ul>
551    * <li>ASP and GLU red</li>
552    * <li>LYS and ARG blue</li>
553    * <li>CYS yellow</li>
554    * <li>others light gray</li>
555    * </ul>
556    */
 
557  1 toggle public void setChargeColours()
558    {
559  1 for (Bond b : bonds)
560    {
561  3 if (b.at1 != null && b.at2 != null)
562    {
563  3 b.startCol = getChargeColour(b.at1.resName);
564  3 b.endCol = getChargeColour(b.at2.resName);
565    }
566    else
567    {
568  0 b.startCol = Color.gray;
569  0 b.endCol = Color.gray;
570    }
571    }
572    }
573   
 
574  13 toggle public static Color getChargeColour(String resName)
575    {
576  13 Color result = Color.lightGray;
577  13 if ("ASP".equals(resName) || "GLU".equals(resName))
578    {
579  3 result = Color.red;
580    }
581  10 else if ("LYS".equals(resName) || "ARG".equals(resName))
582    {
583  4 result = Color.blue;
584    }
585  6 else if ("CYS".equals(resName))
586    {
587  3 result = Color.yellow;
588    }
589  13 return result;
590    }
591   
592    /**
593    * Sets the start/end colours of bonds to those of the start/end atoms
594    * according to the specified colour scheme. Note: currently only works for
595    * peptide residues.
596    *
597    * @param cs
598    */
 
599  1 toggle public void setChainColours(ColourSchemeI cs)
600    {
601  1 int index;
602  1 for (Bond b : bonds)
603    {
604  3 try
605    {
606  3 index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
607  3 b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
608    null, null, 0f);
609   
610  3 index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
611  2 b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
612    null, null, 0f);
613   
614    } catch (Exception e)
615    {
616  1 b.startCol = Color.gray;
617  1 b.endCol = Color.gray;
618    }
619    }
620    }
621   
 
622  1 toggle public void setChainColours(Color col)
623    {
624  1 for (Bond b : bonds)
625    {
626  2 b.startCol = col;
627  2 b.endCol = col;
628    }
629    }
630   
631    /**
632    * copy any sequence annotation onto the sequence mapped using the provided
633    * StructureMapping
634    *
635    * @param mapping
636    * - positional mapping between destination sequence and pdb resnum
637    * @param sqmpping
638    * - mapping between destination sequence and local chain
639    */
 
640  193 toggle public void transferResidueAnnotation(StructureMapping mapping,
641    jalview.datamodel.Mapping sqmpping)
642    {
643  193 SequenceI sq = mapping.getSequence();
644  193 SequenceI dsq = sq;
645  193 if (sqmpping == null)
646    {
647    // SIFTS mappings are recorded in the StructureMapping object...
648   
649  0 sqmpping = mapping.getSeqToPdbMapping();
650    }
651  193 if (sq != null)
652    {
653  384 while (dsq.getDatasetSequence() != null)
654    {
655  191 dsq = dsq.getDatasetSequence();
656    }
657    // any annotation will be transferred onto the dataset sequence
658   
659  193 if (shadow != null && shadow.getAnnotation() != null)
660    {
661   
662  0 for (AlignmentAnnotation ana : shadow.getAnnotation())
663    {
664    // match on calcId, label and description so annotations from
665    // different structures are preserved
666  0 List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
667    ana.getCalcId(), ana.label, ana.description);
668  0 if (transfer == null || transfer.size() == 0)
669    {
670  0 ContactMatrixI cm = shadow.getContactMatrixFor(ana);
671  0 ana = new AlignmentAnnotation(ana);
672    // TODO map contact matrix under mapping
673  0 ana.liftOver(sequence, shadowMap);
674  0 ana.liftOver(dsq, sqmpping);
675  0 dsq.addAlignmentAnnotation(ana);
676  0 if (cm != null)
677    {
678  0 dsq.addContactListFor(ana, cm);
679    }
680    }
681    else
682    {
683  0 continue;
684    }
685    }
686    }
687    else
688    {
689  193 if (sequence != null && sequence.getAnnotation() != null)
690    {
691  154 for (AlignmentAnnotation ana : sequence.getAnnotation())
692    {
693    // match on calcId, label and description so annotations from
694    // different structures are preserved
695  335 List<AlignmentAnnotation> transfer = dsq
696    .getAlignmentAnnotations(ana.getCalcId(), ana.label,
697    ana.description);
698  335 if (transfer == null || transfer.size() == 0)
699    {
700  177 ContactMatrixI cm = sequence.getContactMatrixFor(ana);
701  177 ana = new AlignmentAnnotation(ana);
702  177 ana.liftOver(dsq, sqmpping);
703  177 dsq.addAlignmentAnnotation(ana);
704  177 if (cm != null && cm instanceof MappableContactMatrixI)
705    {
706  36 dsq.addContactListFor(ana, ((MappableContactMatrixI) cm)
707    .liftOver(dsq, sqmpping));
708    }
709    }
710    else
711    {
712  158 continue;
713    }
714    }
715    }
716    }
717  193 if (false)
718    {
719    // Useful for debugging mappings - adds annotation for mapped position
720  0 float min = -1, max = 0;
721  0 Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
722  0 for (int i = sq.getStart(), j = sq
723  0 .getEnd(), k = 0; i <= j; i++, k++)
724    {
725  0 int prn = mapping.getPDBResNum(k + 1);
726   
727  0 an[k] = new Annotation(prn);
728  0 if (min == -1)
729    {
730  0 min = k;
731  0 max = k;
732    }
733    else
734    {
735  0 if (min > k)
736    {
737  0 min = k;
738    }
739  0 else if (max < k)
740    {
741  0 max = k;
742    }
743    }
744    }
745  0 sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
746    "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
747    an, min, max, AlignmentAnnotation.LINE_GRAPH));
748    }
749    }
750    }
751    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 13 2024 16:28:33 GMT using coverage data from Wed Nov 13 2024 16:28:18 GMT.
  • OpenClover is free and open-source software.