org.strbio.util
Class HTML

java.lang.Object
  org.strbio.util.HTML

public class HTML
extends java.lang.Object

Useful functions for manipulating HTML

  Version 1.0, 5/18/07
  

Version:

1.0, 5/18/07

Author:

JMC

Constructor Summary

HTML()

Method Summary

static java.lang.String	classifyFasta(java.lang.String fasta, java.lang.String cssClass, int start, int length) This function adds markup around a given section of a FASTA sequence stored as a String.
static java.lang.String	classifyMSF(java.lang.String msf, java.lang.String cssClass, int start, int length) This function adds markup around a given section of a Profile stored in a MSF-formatted String.
static java.lang.String	classifyMSF(java.lang.String msf, java.lang.String cssClass, int start, int length, int seqNum) This function is just like the classifyMSF function that marks up an entire profile, but this one can mark up only a single sequence in a profile if you prefer.
static java.lang.String	stripHTML(java.lang.String a) Strip all HTML in a string, returning a new String.

Methods inherited from class java.lang.Object

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

Constructor Detail

HTML

public HTML()

Method Detail

stripHTML

public static final java.lang.String stripHTML(java.lang.String a)

Strip all HTML in a string, returning a new String. HTML is considered anything between '<' and '>' characters.

classifyFasta

public static final java.lang.String classifyFasta(java.lang.String fasta,
                                                   java.lang.String cssClass,
                                                   int start,
                                                   int length)
                                            throws java.io.IOException

This function adds markup around a given section of a FASTA sequence stored as a String. The result can then be displayed on a web page between

       elements.  This is useful for colorizing (or otherwise changing
       the style) of a section of FASTA sequence.
       

       Use Polymer.writeFasta() with a PrintfWriter in front of a
       StringWriter to write your Polymer to a String, then use this
       function to mark it up.
       

       The start monomer is 0-indexed, and a string may be marked
       up multiple times (HTML elements are autodetected and ignored
       when counting monomers).  If the region to be marked up
       is partly outside the boundaries of the string, the portion of the
       sequence inside the boundaries will be marked.
       

       The input String can be legal FASTA format (starting with a header)
       or raw sequence without the header.  If there is a header, it's
       left unmodified.  Within the sequence, whitespace is left unchanged
       and not counted towards the number of monomers.  Anything in
       the sequence between angle brackets is assumed to be HTML, and also
       left unchanged and not counted towards the number of monomers.
       All other non-whitespace characters in the sequence are assumed
       to be monomers; there's no check as to whether they're valid.
       There's also no check as to whether the added markup is nested
       properly; that's up to you.
       

       Multiple FASTA sequences in one string are not supported, and
       the header (if present) must be the first line of the string
       and begin with '>'.



Throws:
java.io.IOException

classifyMSF

public static final java.lang.String classifyMSF(java.lang.String msf,
                                                 java.lang.String cssClass,
                                                 int start,
                                                 int length)
                                          throws java.io.IOException

This function adds markup around a given section of a Profile stored in a MSF-formatted String. The result can then be displayed on a web page between

       elements.  This is useful for colorizing (or otherwise changing
       the style) of a section of the profile.
       

       Use Profile.writeMSF() with a PrintfWriter in front of a
       StringWriter to write your Profile to a String, then use this
       function to mark it up.
       

       The start monomer is 0-indexed, and a string may be marked
       up multiple times (HTML elements are autodetected and ignored
       when counting monomers).  If the region to be marked up
       is partly outside the boundaries of the string, the portion of the
       sequence inside the boundaries will be marked.
       

       The input String must be a MSF formatted using Profile.writeMSF--
       it's too complicated to support arbitrary legal MSF.  If you
       have another format, try reading it to a Profile and re-writing it.
       

       There's no check as to whether the added markup is nested
       properly; that's up to you.



Throws:
java.io.IOException

classifyMSF

public static final java.lang.String classifyMSF(java.lang.String msf,
                                                 java.lang.String cssClass,
                                                 int start,
                                                 int length,
                                                 int seqNum)
                                          throws java.io.IOException

This function is just like the classifyMSF function that marks up an entire profile, but this one can mark up only a single sequence in a profile if you prefer.

If seqNum is -1, all sequences are marked up. Otherwise, only the Nth sequence (starting at 0) is marked up. Sequence detection is done very loosely, ignoring sequence names. It is assumed that the sequences will be in the same order within each group.

Throws:

java.io.IOException