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java.lang.Objectorg.biojava.bio.structure.align.xml.AFPChainXMLParser
public class AFPChainXMLParser
Constructor Summary | |
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AFPChainXMLParser()
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Method Summary | |
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static String |
flipAlignment(String xml)
Takes an XML representation of the alignment and flips the positions of name1 and name2 |
static AFPChain |
fromXML(String xml,
Atom[] ca1,
Atom[] ca2)
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static AFPChain |
fromXML(String xml,
String name1,
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(String xml)
returns true if the alignment XML contains an error message |
static AFPChain[] |
parseMultiXML(String xml)
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static void |
rebuildAFPChain(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
replace the PDB res nums with atom positions: |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public AFPChainXMLParser()
Method Detail |
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public static AFPChain fromXML(String xml, String name1, String name2, Atom[] ca1, Atom[] ca2) throws StructureException
xml
- name1
- name1
- ca1
- ca2
-
StructureException
public static AFPChain fromXML(String xml, Atom[] ca1, Atom[] ca2)
public static boolean isErrorXML(String xml)
xml
-
public static String flipAlignment(String xml) throws IOException, StructureException
xml
- String representing the alignment
IOException
StructureException
public static void rebuildAFPChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
afpChain
- ca1
- ca2
- public static AFPChain[] parseMultiXML(String xml)
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