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java.lang.Objectorg.biojava.bio.structure.align.model.AfpChainWriter
public class AfpChainWriter
A class to convert the data in an AfpChain object to various String outputs.
Field Summary | |
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static String |
newline
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Constructor Summary | |
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AfpChainWriter()
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Method Summary | |
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static String |
toAlignedPairs(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
Prints the alignment in the simplest form: a list of aligned residues. |
static String |
toCE(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
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static String |
toDBSearchResult(AFPChain afpChain)
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static String |
toFatCat(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
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static String |
toFatCatCore(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2,
boolean printLegend,
boolean longHeader,
boolean showHTML,
boolean showAlignmentBlock)
Output in FatCatCore format |
static String |
toRotMat(AFPChain afpChain)
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static String |
toScoresList(AFPChain afpChain)
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static String |
toWebSiteDisplay(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition. |
static String |
toWebSiteDisplay(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2,
boolean showAlignmentBlock)
Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition. |
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 String newline
Constructor Detail |
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public AfpChainWriter()
Method Detail |
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public static String toFatCat(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
public static String toScoresList(AFPChain afpChain)
public static String toFatCatCore(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean printLegend, boolean longHeader, boolean showHTML, boolean showAlignmentBlock)
Note that if a circular permutation has occured the residue numbers may be innaccurate.
afpChain
- ca1
- ca2
- printLegend
- longHeader
- showHTML
- showAlignmentBlock
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public static String toWebSiteDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
afpChain
- ca1
- ca2
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public static String toWebSiteDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showAlignmentBlock)
afpChain
- ca1
- ca2
-
public static String toAlignedPairs(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
152 A ALA 161S A VAL
Note that this format loses information about blocks.
afpChain
- ca1
- ca2
-
public static String toDBSearchResult(AFPChain afpChain)
public static String toRotMat(AFPChain afpChain)
public static String toCE(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
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