How To Remove NewLine Characters from Strings?

[sjohri214]

Hi all,

The question I have is, How do I remove newLine characters from Long Strings such as the following:


>gi|23821530|dbj||SEG_D10989S Bos taurus gene for endothelin receptor
GGGATCCCGAGCAAACTGCGGAGGCCACACTGTCAGGCATTCCCTCGGCGTTTCGTCAGAGCCAGACCCT
CCCGCTGCTGAAGGGAGGCGCGCTCTGCTCCCGGGCTGCCGGGAACCCAGCCGCGCGCCGGGGAAGGAGG
TCCCTGCCTGGTGCGTCCGGACCAAGAGGTAACCGTTCTGCTTGGTGTTTAATTCAAATCTGTGATTGAA
CCTTATCCTGGGGCTTCAGTTTGGATTACTTCTTAGGTTTGTTTTTGTTTGTTTGTTTGTTTTTTAACCT
GTAGCTACAGCAGATTAAAATGGGATTGGAGTGAAGGAGAGGGCTTGAGTGTCTGAAGTCACTCGAAGGG
GATAGAAACTTCCGAGTTAATCCAGATAGAGACTCTTCCAAATAGACCAAGTGGAGATGTCCGGGAGATT
TTCCGAGTCAGCCGGCTCAGTCCTGGGGTGTGTGTATGGGGGGTGGGGGCGGTGCCGAAGAGCGGAAGGA
AGGGGTCTGAAAGTCCAGACATGCGGCATCCGGGGTTGCTGTGGAGTCGAAAGCAGAGACTGGCGATGCC
CTTGATCTCTAACCTGCCTTGATTTGCCCCGTCCCCGCGCGCCCTTGGCCAGAACGAATACTGCTCCCTC
TGCGCACACCAGGAGCTCAAAGCTTTGCTTTGGACACCCGTCCTCTCCTCCCCGTCACACCCCTTCCAGG
ATACCCCGCCCCACTGCGAGTCATTTACCCCTCAGGGGACGCAGGGGAGGAAAAACCAGCGAAAGCTGGC
TCTGGAGGGACGGTCTAGGGGCGCAAGCGAGTCCCACGCGCCAGAGTTCCCCACTCCCGCGCCAGCTCGA
CTTATTAATACTTTTGCGCACTGAGAGTGCGGGCGCTGCTGCGCTTGAGGATAGCGGCTTGCAGGGGCGT
GGCTGGGGACGCTGACCCGGGTGTCCTGTCTTCCTTCCCTTGCTGGTCTCTAGACTCGGAAAGCGGAGGA
GCGGCCACCCGACTCCCTCTGGAGCAGGCAGCAGCATGCAGCCGCTGCCCAGCTTGTGCGGACGCGCCCT
GGTGGCGCTGATCCTTGCCTGCGGCGTGGCGGGGATCCAAGCAGAAGAGAGGGAATTCCCGCCAGCCGGG
GCCACTCAGCCACTTCCGGGGACCGGAGAGATGATGGAGACCCCGACTGAGACCTCCTGGCCCGGGAGGT
CCAACGCCAGCGACCCGCGATCGTCCGCAACACCGCAGATTCCTAGAGGGGGAAGGATGGCGGGAATCCC
ACCGCGCACCCCACCCCCGTGCGATGGACCCATAGAGATCAAGGAGACTTTCAAGTACATCAACACGGTG
GTGTCCTGCCTAGTGTTCGTGCTGGGCATCATCGGAAACTCCACGCTACTGAGAATCATTTACAAGAACA
AGTGCATGCGAAACGGTCCAAATATCTTGATAGCCAGCCTGGCTCTCGGAGACCTGCTGCACATTATCAT
TGATATCCCCATCAATACCTACAAGGTAAGGGGTGCCCTGCCACTAAGTATACATACAGGTTCAAGAGCA
CCCTGTGAACATCTCCCTAACAGAGCTCTGTGTCTCCTCAATGCAGCTGCTTGCCAAGGACTGGCCCTTT
GGGGTTGAGATGTGTAAGCTGGTGCCTTTCATTCAGAAGGCCTCCGTGGGCATCACTGTGCTGAGTCTAT
GTGCTCTAAGTATTGACAGGTAAGAGCAAGTATCTAAGCGACATATATCCTGACCACGATCCTAGTGCTT
GCTACGTTACTTAGAAAGTAAACTGTAATTCAATAAAAACCAGGCTCTGCCAGCTTGGCAATTGATTCTG
TTTTGTTCTTCAGATATCGAGCTGTTGCTTCTTGGAGTCGGATTAAAGGAATCGGGGTTCCAAAATGGAC
AGCAGTAGAAATTGTTTTAATTTGGGTGGTCTCCGTGGTTCTGGCTGTCCCTGAGGCTGTGGGTTTTGAT
ATAATTACCAGTGATCACATAGGAAATAAACTGAGAATCTGCTTGCTCCATCCCACTCAGAAAACAGCAT
TTATGCAGGTAAATTTTACTTTTTTTTTCCCTTCCCCCATAGTTTTACAAGACAGCTAAAGACTGGTGGC
TATTTAGTTTCTATTTCTGCCTGCCGCTGGCCATCACTGCATTGTTTTATACCCTGATGACTTGTGAAAT
GTTGAGAAAGAAGAGTGGTATGCAAATTGCCTTAAATGATCACTTAAAACAGGTAAGGTTTATTTCAGAG
ACGGGAAGTGGCCAAAACAGTATTTTGCCTGGTCCTTGTCTTTGCTCTGTGTTGGCTTCCTCTTCATCTT
AGCAGGATTTTGAAGCTCACTCTTTATGATCAGCATGATCCCCGTAGATGTGAATTTTTAAGGTAAGTAT
AAATAAATTTTCATATTATTTTTGCAGCTTTTTGTTGGTATTGGACTACATTGGCATCAACATGGCCTCC
CTGAATTCCTGTATTAACCCAATAGCTCTGTATTTGGTGAGCAAAAGATTCAAAAACTGCTTTAAGGTAA
GACAGTATCGAAAATCAAAATGGTGAGCAAGGAGGGTTGTGATAGTGTAACTTGATGTAAACTTATAACG
AAGTTACTTTGCTTTGTGCAGTCATGTTTATGCTGCTGGTGCCAATCATTTGAAGAAAAACAGTCCTTGG
AGGAAAAGCAGTCGTGCTTAAAGTTCAAAGCTAACGATCACGGATATGACAACTTCCGTTCCAGTAATAA
ATACAGCTCATCTTGAAAGAAGGATTATTCATTTTCTTTATTTTGGACAGAAATCATTCAAACAAAGAGG
TATCTGTCAAAGTAAAACAAAACAACGTGTGTGTTTGCACAAAACAATGTACAAATGTAAGAGTGATTAT
TTTCTTCACACTCAAGAGTTCCACATGACGTTTGATGAGCTGTTTCCAGCATGAGAAGACAAGCAGTGAG
AATTAAGAAAGCCTTATTGTGAAAGCACTTAATTCTTTTACAGTTAGCACTTCACTATATTATAGCTCTT
CAGAACTTCGGTCTATTCATACACCACTTACATTTAACTTGAGTTCACTCA


I need to be able to get rid of the Newline characters since the presence of these characters results in exceptions when i post the data to a web server.

I would be very grateful for any assistance

Thanks for any help

sjohri214

 

[jfryer]

If the strings are only ever going to contain G,C,A,T you could convert the string into a Char array, loop thru the string and if the char if a C G A or T copy it to a new char array, else ignore it.

eg

for(int i=0,l=CGATArray.length; i<l; i++)
{
   if ((CGATArray[i] == 'A') ||
       (CGATArray[i] == 'G') ||
       (CGATArray[i] == 'C') ||
       (CGATArray[i] == 'T'))
   {
      NewCGATArray[i] == CGATArray[i];
   }
}

Not overly neat, but it should do what you want.

Another option may be to use the

replaceAll

method in the

String

class, replacing \n with an empty string "".

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There are no onions, only magic
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[sjohri214]

Hi,

The Data is being pasted into a jTextArea from a .txt file.. the I'm having is that I'm trying to Post this data to a web browser "

http://www.ncbi.nlm.nih.gov/blast",

but because of the presence of newline characters I get an exception stating that my query string i.e. java.net.MalformedURLException: Illegal character in URL. This is resolved when I simply post a single line to the web server. For the time being I'm trying to process individual genes to the Blast server and then retreive the results within a given e-value threshold.

Thanks for the Help