public class AFPChainXMLParser
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
DEFAULT_ALGORITHM_NAME |
Constructor and Description |
---|
AFPChainXMLParser() |
Modifier and Type | Method and Description |
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static java.lang.String |
flipAlignment(java.lang.String xml)
Takes an XML representation of the alignment and flips the positions of name1 and name2
|
static AFPChain |
fromXML(java.lang.String xml,
Atom[] ca1,
Atom[] ca2) |
static AFPChain |
fromXML(java.lang.String xml,
java.lang.String name1,
java.lang.String name2,
Atom[] ca1,
Atom[] ca2)
new utility method that checks that the order of the pair in the XML alignment is correct and flips the direction if needed
|
static boolean |
isErrorXML(java.lang.String xml)
returns true if the alignment XML contains an error message
|
static AFPChain[] |
parseMultiXML(java.lang.String xml) |
static void |
rebuildAFPChain(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
replace the PDB res nums with atom positions:
|
public static final java.lang.String DEFAULT_ALGORITHM_NAME
public static AFPChain fromXML(java.lang.String xml, java.lang.String name1, java.lang.String name2, Atom[] ca1, Atom[] ca2) throws java.io.IOException, StructureException
xml
- name1
- name1
- ca1
- ca2
- java.io.IOException
StructureException
public static AFPChain fromXML(java.lang.String xml, Atom[] ca1, Atom[] ca2) throws java.io.IOException
java.io.IOException
public static boolean isErrorXML(java.lang.String xml)
xml
- public static java.lang.String flipAlignment(java.lang.String xml) throws java.io.IOException, StructureException
xml
- String representing the alignmentjava.io.IOException
StructureException
public static void rebuildAFPChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
afpChain
- ca1
- ca2
- public static AFPChain[] parseMultiXML(java.lang.String xml) throws java.io.IOException
java.io.IOException