charite.christo
Class Hyperrefs

java.lang.Object
  charite.christo.Hyperrefs

public class Hyperrefs
extends java.lang.Object

Selections of Residues (sors) can refere to URLs or database entries. Database IDs are translated into URLs.

Field Summary

static java.lang.String	PAIR_ALIGNMENT
static int	PLAIN_TEXT
static int	PROTEIN_FILE
static int	WEB_LINK

Method Summary

static java.lang.String[]	collectWordsAfter(java.lang.String prefix, java.lang.CharSequence haystack)
static java.lang.String	ensemblOrganism(java.lang.String ensID)
static java.lang.String	ensemblUrl(java.lang.String id, int mode)
static java.lang.String[][]	getDatabases(int id)
static java.lang.String[]	getKeysToHighlight()
static java.lang.String[]	getKeysWithBrace()
static java.lang.CharSequence	getProteinReferencesInHtmlFile(BA ba)
static boolean	hasNumericID(java.lang.String w)
static int	idxAW(java.lang.String haystack, java.lang.String... needles)
static char	isHtmlOrXml(BA ba)
static boolean	isHyperref(byte[] T, int pos, int end0)
static int	modificationCount()
static void	setPubmedOption(java.lang.String s)
static java.lang.String	toDbColonID(java.lang.String mayBeUrl)
static void	toSeqvista(java.io.File[] ff)
static java.lang.String	toUrlString(java.lang.String url_or_DBreference, int mode)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

WEB_LINK

public static final int WEB_LINK

See Also:

Constant Field Values

PLAIN_TEXT

public static final int PLAIN_TEXT

See Also:

Constant Field Values

PROTEIN_FILE

public static final int PROTEIN_FILE

See Also:

Constant Field Values

PAIR_ALIGNMENT

public static final java.lang.String PAIR_ALIGNMENT

See Also:

Constant Field Values

Method Detail

setPubmedOption

public static void setPubmedOption(java.lang.String s)

hasNumericID

public static boolean hasNumericID(java.lang.String w)

modificationCount

public static int modificationCount()

getKeysWithBrace

public static java.lang.String[] getKeysWithBrace()

getKeysToHighlight

public static java.lang.String[] getKeysToHighlight()

getDatabases

public static java.lang.String[][] getDatabases(int id)

isHyperref

public static boolean isHyperref(byte[] T,
                                 int pos,
                                 int end0)

toUrlString

public static java.lang.String toUrlString(java.lang.String url_or_DBreference,
                                           int mode)

ensemblOrganism

public static java.lang.String ensemblOrganism(java.lang.String ensID)

ensemblUrl

public static java.lang.String ensemblUrl(java.lang.String id,
                                          int mode)

idxAW

public static final int idxAW(java.lang.String haystack,
                              java.lang.String... needles)

toDbColonID

public static java.lang.String toDbColonID(java.lang.String mayBeUrl)

isHtmlOrXml

public static char isHtmlOrXml(BA ba)

getProteinReferencesInHtmlFile

public static java.lang.CharSequence getProteinReferencesInHtmlFile(BA ba)

collectWordsAfter

public static final java.lang.String[] collectWordsAfter(java.lang.String prefix,
                                                         java.lang.CharSequence haystack)

toSeqvista

public static void toSeqvista(java.io.File[] ff)