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josemduartejosemduarte
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Javadoc fix: many errors in struct align package
1 parent d2053f3 commit 435ebe9

8 files changed

Lines changed: 46 additions & 44 deletions

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‎biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java‎

Lines changed: 30 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,7 @@ public interface Atom extends Cloneable, PDBRecord {
4848
* @param s a trimmed String specifying the name value
4949
* @see #getName
5050
*/
51-
public void setName(String s);
51+
void setName(String s);
5252

5353
/**
5454
* Get atom name, e.g. "CA".
@@ -57,50 +57,50 @@ public interface Atom extends Cloneable, PDBRecord {
5757
* @return a trimmed String representing the name value
5858
* @see #setName
5959
*/
60-
public String getName();
60+
String getName();
6161

6262
/**
6363
* Set element of the atom name, e.g. {@link Element#Fe}
6464
* @param e an Element enumeration
6565
* @see #getElement
6666
*/
67-
public void setElement(Element e);
67+
void setElement(Element e);
6868

6969
/**
7070
* Get element of the atom, e.g. {@link Element#Ca}
7171
* @return an Element enumeration
7272
* @see #setElement
7373
*/
74-
public Element getElement();
74+
Element getElement();
7575

7676
/**
7777
* Set PDB atom number.
7878
* @param i an int specifying the PDBserial value
7979
* @see #getPDBserial
8080
*/
81-
public void setPDBserial(int i) ;
81+
void setPDBserial(int i) ;
8282

8383
/**
8484
* Get PDB atom number.
8585
* @return an int representing the PDBserial value
8686
* @see #setPDBserial
8787
*/
88-
public int getPDBserial() ;
88+
int getPDBserial() ;
8989

9090
/**
9191
* Set the coordinates.
9292
* @param c an array of doubles specifying the coords value
9393
* @see #getCoords
9494
*/
95-
public void setCoords(double[] c);
95+
void setCoords(double[] c);
9696

9797
/**
9898
* Get the coordinates.
9999
* @return a new array of doubles representing the coords value
100100
* @see #setCoords
101101
* @see #getCoordsAsPoint3d()
102102
*/
103-
public double[] getCoords() ;
103+
double[] getCoords() ;
104104

105105
/**
106106
* Get the coordinates.
@@ -110,155 +110,153 @@ public interface Atom extends Cloneable, PDBRecord {
110110
* @return a reference to the Point3d coordinates
111111
* @see #getCoords()
112112
*/
113-
public Point3d getCoordsAsPoint3d();
113+
Point3d getCoordsAsPoint3d();
114114

115115
/**
116116
* Set the X coordinate.
117117
* @param x a double
118118
* @see #getX()
119119
*/
120-
public void setX(double x);
120+
void setX(double x);
121121

122122
/**
123123
* Set the Y coordinate.
124124
* @param y a double
125125
* @see #getY()
126126
*/
127-
public void setY(double y);
127+
void setY(double y);
128128

129129
/**
130130
* Set the Z coordinate.
131131
* @param z a double
132132
* @see #getZ()
133133
*/
134-
public void setZ(double z);
134+
void setZ(double z);
135135

136136
/**
137137
* Get coordinate X.
138138
* @return a double
139139
* @see #setX(double)
140140
*/
141-
public double getX() ;
141+
double getX() ;
142142

143143
/**
144144
* Get coordinate Y.
145145
* @return a double
146146
* @see #setY(double)
147147
*/
148-
public double getY() ;
148+
double getY() ;
149149

150150
/**
151151
* Get coordinate Z.
152152
* @return a double
153153
* @see #setZ(double)
154154
*/
155-
public double getZ() ;
155+
double getZ() ;
156156

157157
/**
158158
* Set alternate Location.
159159
* @param c a Character object specifying the alt loc value
160160
* @see #getAltLoc
161161
*/
162-
public void setAltLoc(Character c);
162+
void setAltLoc(Character c);
163163

164164
/**
165165
* Get alternate Location.
166166
* @return a Character object representing the alt loc value. Default altLoc ('.' in mmCIF files)
167167
* is represented by ' ' (space character, ascii 32).
168168
* @see #setAltLoc
169169
*/
170-
public Character getAltLoc();
170+
Character getAltLoc();
171171

172172
/**
173173
* Set occupancy.
174174
* @param occupancy a float specifying the occupancy value
175175
* @see #getOccupancy
176176
*/
177-
public void setOccupancy(float occupancy) ;
177+
void setOccupancy(float occupancy) ;
178178

179179
/**
180180
* Get occupancy.
181181
* @return a float representing the occupancy value
182182
* @see #setOccupancy
183183
*/
184-
public float getOccupancy();
184+
float getOccupancy();
185185

186186
/**
187187
* Set temp factor .
188188
* @param temp a float specifying the temp factor value
189189
* @see #getTempFactor
190190
*/
191-
public void setTempFactor(float temp) ;
191+
void setTempFactor(float temp) ;
192192

193193
/**
194194
* Get temp factor.
195195
* @return a float representing the temp factor value
196196
* @see #setTempFactor
197197
*/
198-
public float getTempFactor() ;
198+
float getTempFactor() ;
199199

200200
/**
201201
* Return an identical copy of this object .
202202
* @return an identical copy of this object
203203
*/
204-
public Object clone();
204+
Object clone();
205205

206206
/**
207207
* Set the back-reference to its parent Group.
208208
* @param parent the parent Group
209209
* @see #getGroup()
210210
*/
211211

212-
public void setGroup(Group parent);
212+
void setGroup(Group parent);
213213

214214
/**
215215
* Return the parent Group of the Atom.
216216
* returns null if the referenced object is not Group
217217
* @return Group the parent Group of the Atom, or null
218218
* @see #setGroup(Group)
219219
*/
220-
public Group getGroup();
220+
Group getGroup();
221221

222222
/**
223223
* Add a bond
224224
* @param bond to be added
225225
* @see #getBonds()
226226
*/
227-
public void addBond(Bond bond);
227+
void addBond(Bond bond);
228228

229229
/**
230230
* Get all {@link Bond}s this atom is part of.
231231
*
232232
* @return a list of {@link Bond}s or null if no bonds exist for this Atom
233233
*/
234-
public List<Bond> getBonds();
234+
List<Bond> getBonds();
235235

236236
/**
237237
* Sets the bonds
238238
* @param bonds
239239
*/
240-
public void setBonds(List<Bond> bonds);
241-
240+
void setBonds(List<Bond> bonds);
242241

243242
/**
244243
* Test if another atom has a bond to this atom
245244
*
246245
* @param other
247246
* @return
248247
*/
249-
public boolean hasBond(Atom other);
248+
boolean hasBond(Atom other);
250249

251250
/**
252251
* Get the charge of this atom
253252
*
254253
* @return a the integer charge.
255254
*/
256-
public short getCharge();
255+
short getCharge();
257256

258257
/**
259258
* Set the charge of this atom
260259
*
261-
* @return void.
262260
*/
263-
public void setCharge(short charge);
261+
void setCharge(short charge);
264262
}

‎biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -346,15 +346,15 @@ public interface Group extends Serializable {
346346
* The main group (this group) will contain the first altloc (be it the default '.' or 'A' or a mix of '.' and 'A').
347347
* <p>
348348
* This method will return the altloc groups that are not the main group, e.g.:
349-
*
349+
* <ul>
350350
* <li> if '.' (default), 'A' and 'B' altlocs are present in file, the main group will contain
351351
* the default '.' and this method will return 2 altloc groups
352352
* </li>
353353
*
354354
* <li> if 'A' and 'B' are present in file without a default '.' group, then the main group will contain the 'A'
355355
* location whilst this method will return only 1 altloc group with the 'B' location
356356
* </li>
357-
*
357+
* </ul>
358358
* <p>
359359
* Note that atoms with the default altloc (.) are included in all groups. Atoms with other altlocs (typically A, B, etc)
360360
* will be sorted into groups by altloc.

‎biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -149,7 +149,7 @@ public static Structure getBiologicalAssembly(String pdbId, boolean multiModel)
149149
* using multiModel={@value AtomCache#DEFAULT_BIOASSEMBLY_STYLE}
150150
* <p>
151151
* For more documentation on quaternary structures see:
152-
* {@link http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies}
152+
* <a href="http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies">http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies</a>
153153
*
154154
*
155155
* @param pdbId
@@ -165,6 +165,7 @@ public static Structure getBiologicalAssembly(String pdbId) throws IOException,
165165
* Returns the biological assembly for the given PDB id and bioassembly identifier.
166166
* <p>
167167
* The output Structure will be different depending on the multiModel parameter:
168+
* <ul>
168169
* <li>
169170
* the symmetry-expanded chains are added as new models, one per transformId. All original models but
170171
* the first one are discarded.
@@ -173,6 +174,7 @@ public static Structure getBiologicalAssembly(String pdbId) throws IOException,
173174
* as original with symmetry-expanded chains added with renamed chain ids and names (in the form
174175
* originalAsymId_transformId and originalAuthId_transformId)
175176
* </li>
177+
* </ul>
176178
* @param pdbId
177179
* @param biolAssemblyNr - the ith biological assembly that is available for a PDB ID (we start counting at 1, 0 represents the asym unit).
178180
* @param multiModel if true the output Structure will be a multi-model one with one transformId per model,

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java‎

Lines changed: 4 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -300,7 +300,7 @@ private static Matrix permuteMatrix(Matrix mat, int cpRows, int cpCols) {
300300
/**
301301
* Modifies the {@link AFPChain#setOptAln(int[][][]) optAln} of an AFPChain
302302
* by permuting the second protein.
303-
*
303+
* <p>
304304
* Sets residue numbers in the second protein to <i>(i-cp)%len</i>
305305
*
306306
* @param afpChain
@@ -425,7 +425,7 @@ private static void assignOptAln(AFPChain afpChain, List<List<List<Integer>>> bl
425425
/**
426426
* Finds the optimal alignment between two proteins allowing for a circular
427427
* permutation (CP).
428-
*
428+
* <p>
429429
* The precise algorithm is controlled by the
430430
* {@link OptimalCECPParameters parameters}. If the parameter
431431
* {@link OptimalCECPParameters#isTryAllCPs() tryAllCPs} is true, all possible
@@ -456,10 +456,9 @@ public AFPChain align(Atom[] ca1, Atom[] ca2, Object param)
456456
/**
457457
* Finds the optimal alignment between two proteins allowing for a circular
458458
* permutation (CP).
459-
*
459+
* <p>
460460
* This algorithm performs a CE alignment for each possible CP site. This is
461-
* quite slow. Use {@link #alignHeuristic(Atom[], Atom[], Object)} for a
462-
* faster algorithm.
461+
* quite slow.
463462
*
464463
* @param ca1 CA atoms of the first protein
465464
* @param ca2 CA atoms of the second protein

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -973,6 +973,10 @@ public void setOptRmsd(double[] optRmsd)
973973
this.optRmsd = optRmsd;
974974
}
975975

976+
/**
977+
* The number of aligned residues in the final alignment.
978+
* @return
979+
*/
976980
public int getOptLength()
977981
{
978982
return optLength;
@@ -1023,7 +1027,7 @@ public void setAlnseq2(char[] alnseq2)
10231027

10241028
/**
10251029
* @return The total length of the alignment, including gaps
1026-
* @see #getOptLength(), the number of aligned residues in the final alignment.
1030+
* @see #getOptLength()
10271031
*/
10281032
public int getAlnLength()
10291033
{

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -306,7 +306,6 @@ public XMLWriter toXML(PrintWriter pw)
306306
* @param xw the XML writer to use
307307
* @return the writer again
308308
* @throws IOException
309-
* @see org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
310309
*/
311310

312311
public XMLWriter toXML(XMLWriter xw)

‎biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -501,7 +501,7 @@ public static Graph<Integer, DefaultEdge> buildSymmetryGraph(
501501
* @param symmetry
502502
* CeSymmResult
503503
* @throws StructureException
504-
* @result List of structures, by repeat index sequentially
504+
* @return List of structures, by repeat index sequentially
505505
*
506506
*/
507507
public static List<Structure> divideStructure(CeSymmResult symmetry)

‎biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -185,7 +185,7 @@ public static TreeMap<Integer,SpaceGroup> getAllSpaceGroups() {
185185
* A parser for the symop.lib file provided by CCP4. Note: this file is not getting re-distributed by BioJava.
186186
* It can be downloaded from:
187187
*
188-
* <a href="http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&view=markup">http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&view=markup</a>
188+
* <a href="http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&view=markup">http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&amp;view=markup</a>
189189
* <p>
190190
* Note: this file is not needed by BioJava. BioJava loads equivalent information from the file spacegroups.xml
191191
*

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