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java.lang.Objectorg.biojava.bio.structure.align.gui.DisplayAFP
public class DisplayAFP
A utility class for visualistion of structure alignments
Field Summary | |
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static boolean |
debug
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Constructor Summary | |
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DisplayAFP()
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Method Summary | |
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static Structure |
createArtificalStructure(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other. |
static StructureAlignmentJmol |
display(AFPChain afpChain,
Group[] twistedGroups,
Atom[] ca1,
Atom[] ca2,
List<Group> hetatms,
List<Group> nucleotides,
List<Group> hetatms2,
List<Group> nucleotides2)
Note: ca2, hetatoms2 and nucleotides2 should not be rotated. |
static Structure |
getAlignedStructure(Atom[] ca1,
Atom[] ca2)
Get an artifical Structure containing both chains. |
static Atom[] |
getAtomArray(Atom[] ca,
List<Group> hetatms,
List<Group> nucleotides)
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static Atom |
getAtomForAligPos(AFPChain afpChain,
int chainNr,
int aligPos,
Atom[] ca,
boolean getPrevious)
return the atom at alignment position aligPos. |
static int |
getBlockNrForAlignPos(AFPChain afpChain,
int aligPos)
Deprecated. use AFPAlignmentDisplay.getBlockNrForAlignPos instead... |
static List<Integer> |
getEQRAlignmentPos(AFPChain afpChain)
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static List<String> |
getPDBresnum(int aligPos,
AFPChain afpChain,
Atom[] ca)
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static void |
showAlignmentImage(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2,
StructureAlignmentJmol jmol)
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static void |
showAlignmentImage(AFPChain afpChain,
String result)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final boolean debug
Constructor Detail |
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public DisplayAFP()
Method Detail |
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public static final List<Integer> getEQRAlignmentPos(AFPChain afpChain)
public static final List<String> getPDBresnum(int aligPos, AFPChain afpChain, Atom[] ca)
public static int getBlockNrForAlignPos(AFPChain afpChain, int aligPos)
afpChain
- aligPos
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public static final Atom getAtomForAligPos(AFPChain afpChain, int chainNr, int aligPos, Atom[] ca, boolean getPrevious) throws StructureException
chainNr
- the number of the aligned pair. 0... first chain, 1... second chain.afpChain
- an afpChain objectaligPos
- position on the alignmentgetPrevious
- gives the previous position if false, gives the next posible atom
StructureException
public static final Structure getAlignedStructure(Atom[] ca1, Atom[] ca2) throws StructureException
ca1
- ca2
-
StructureException
public static final Atom[] getAtomArray(Atom[] ca, List<Group> hetatms, List<Group> nucleotides) throws StructureException
StructureException
public static final StructureAlignmentJmol display(AFPChain afpChain, Group[] twistedGroups, Atom[] ca1, Atom[] ca2, List<Group> hetatms, List<Group> nucleotides, List<Group> hetatms2, List<Group> nucleotides2) throws StructureException
StructureException
public static void showAlignmentImage(AFPChain afpChain, Atom[] ca1, Atom[] ca2, StructureAlignmentJmol jmol)
public static void showAlignmentImage(AFPChain afpChain, String result)
public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException
afpChain
- the container of the alignmentca1
- atoms for protein 1ca2
- atoms for protein 2
StructureException
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