API Specification Errors
Errors in Class: org.biojava.bio.structure.align.pairwise.AlternativeAlignment

Category 2: Member Error

logger

Field missing comment.

/**  */

getRmsd()

Method missing comment, but reasonably self-evident.

/**
 * Returns the rmsd value.
 */

setScore(float)

Method missing comment, but reasonably self-evident.

/**
 * Specifies the score value.
 */

getPercId()

Method missing comment, but reasonably self-evident.

/**
 * Returns the perc id value.
 */

setPercId(int)

Method missing comment, but reasonably self-evident.

/**
 * Specifies the perc id value.
 */

setAltAligNumber(int)

Method missing comment, but reasonably self-evident.

/**
 * Specifies the alt alig number value.
 */

finish(StrucAligParameters, Atom[], Atom[])

Method missing comment.

/**
 *
 */

getDistanceMatrix(Atom[], Atom[])

Method missing comment, but reasonably self-evident.

/**
 * Returns the distance matrix value.
 */

getPDBresnum1()

Method missing comment, but reasonably self-evident.

/**
 * Returns the PDBresnum 1 value.
 */

setPDBresnum1(String[])

Method missing comment, but reasonably self-evident.

/**
 * Specifies the PDBresnum 1 value.
 */

getPDBresnum2()

Method missing comment, but reasonably self-evident.

/**
 * Returns the PDBresnum 2 value.
 */

setPDBresnum2(String[])

Method missing comment, but reasonably self-evident.

/**
 * Specifies the PDBresnum 2 value.
 */

calculateSuperpositionByIdx(Atom[], Atom[])

Method missing comment.

/**
 *
 */

Category 3: Tag Error

setRms(double)

Invalid tag.

 ?
 ? @param rms   --MISSING TEXT

apairs_from_seed(int, int, int)

Invalid tag.

 ?
 ? @param l   --MISSING TEXT
 ? @param i   --MISSING TEXT
 ? @param j   --MISSING TEXT

toPDB(Structure, Structure)

Invalid tag.

 ?
 ? @param s1   --MISSING TEXT
 ? @param s2   --MISSING TEXT

setDistanceMatrix(Matrix)

Invalid tag.

 ?
 ? @param distanceMatrix   --MISSING TEXT

Category 4: Text/Link Error

toString()

Html Error in First Sentence
--Missing a period

print the idx positions of this alignment

 * Overrides Object.toString.

getCluster()

Missing @see tag.
Html Error in First Sentence
--Missing a period

get the number of the cluster this alignment belongs to

 *
 * @see #setCluster

setCluster(int)

Missing @see tag.

 *
 * @see #getCluster

setRms(double)

Html Error in First Sentence
--Missing a period

the rms in the structurally equivalent regions

getScore()

Missing @see tag.
Html Error in First Sentence
--Missing a period

the alignment score

 *
 * @see #setScore

getGaps()

Html Error in First Sentence
--Missing a period

return the number of gaps in this alignment

getEqr()

Html Error in First Sentence
--Missing a period

returns the number of euqivalent residues in this alignment

getIdx1()

Html Error in First Sentence
--Missing a period

the positions of the structure equivalent positions in atom set 1

getIdx2()

Html Error in First Sentence
--Missing a period

the positions of the structure equivalent atoms in atom set 2

getAltAligNumber()

Missing @see tag.
Html Error in First Sentence
--Missing a period

returns the sequential number of this alternative alignment

 *
 * @see #setAltAligNumber

getRotationMatrix()

Html Error in First Sentence
--Missing a period

returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1

getShift()

Html Error in First Sentence
--Missing a period

returns the shift vector that has to be applied on structure to to shift on structure one

calcScores(Atom[], Atom[])

Html Error in First Sentence
--Missing a period

calculates scores for this alignment ( %id )

getDistanceMatrix()

Missing @see tag.
Html Error in First Sentence
--Missing a period

The distance matrix this alignment is based on

 *
 * @see #setDistanceMatrix