## org.biojava.bio.structure.align.pairwise
Class FragmentJoiner

    java.lang.Object
      org.biojava.bio.structure.align.pairwise.FragmentJoiner

    public class FragmentJoiner

extends java.lang.Object

Joins the initial Fragments together to larger Fragments

Since:
  1.5
Version:
  %I% %G%
Author:
  Andreas Prlic, Peter Lackner

Field Summary
`static java.util.logging.Logger` `logger`

Constructor Summary
`FragmentJoiner()`

Method Summary
`JointFragments[]` `approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] fraglst, StrucAligParameters params)`
`JointFragments[]` `frag_pairwise_compat(FragmentPair[] fraglst, int angleDiff, float fragCompatDist, int maxRefine)` Calculate the pairwise compatibility of fpairs.
`static double` `getRMS(Atom[] ca1, Atom[] ca2, JointFragments frag)`
`static boolean` `reduceFragments(java.util.List fragments, FragmentPair f, Matrix rmsmat)` In helices often many similar fragments can be found.
`static java.lang.Object` `resizeArray(java.lang.Object oldArray, int newSize)` Reallocates an array with a new size, and copies the contents of the old array to the new array.

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Field Detail

### logger

    public static java.util.logging.Logger logger

Constructor Detail

### FragmentJoiner

    public FragmentJoiner()

Method Detail

### resizeArray

    public static java.lang.Object resizeArray(java.lang.Object oldArray,
                                               int newSize)

  Reallocates an array with a new size, and copies the contents of the old array to the new array.

  Parameters:
    `oldArray` - the old array, to be reallocated.
    `newSize` - the new array size.
  Returns:
    A new array with the same contents.

### reduceFragments

    public static boolean reduceFragments(java.util.List fragments,
                                          FragmentPair f,
                                          Matrix rmsmat)

  In helices often many similar fragments can be found. To reduce these to a few representative ones this check can be used. It does a distance check between all known Fragments and a new one. If this one is on a similar diagonal and it has a lower rms, this one is a better representation. Note: shifts of one are not allowed.

  Parameters:
    `fragments` -
    `f` -
    `rmsmat` -
  Returns:
    true - if this is a better representant for a group of locala fragments.

### approach_ap3

    public JointFragments[] approach_ap3(Atom[] ca1,
                                         Atom[] ca2,
                                         FragmentPair[] fraglst,
                                         StrucAligParameters params)

### getRMS

    public static double getRMS(Atom[] ca1,
                                Atom[] ca2,
                                JointFragments frag)

### frag_pairwise_compat

    public JointFragments[] frag_pairwise_compat(FragmentPair[] fraglst,
                                                 int angleDiff,
                                                 float fragCompatDist,
                                                 int maxRefine)

  Calculate the pairwise compatibility of fpairs. Iterates through a list of fpairs and joins them if they have compatible rotation and translation parameters.

  Parameters:
    `fraglst` - FragmentPair[] array
    `angleDiff` - angle cutoff
    `fragCompatDist` - distance cutoff
    `maxRefine` - max number of solutions to keep
  Returns:
    JointFragments[]