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Seekerandreasprlic
Seeker
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andreasprlic
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/* I've noticed some misprints in BioJavaX Documentation and in the source code. */
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‎wiki/User_talk:Seeker.md‎

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@@ -22,8 +22,10 @@ instead of **getNCBITaxon()** method.
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------------------------------------------------------------------------
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Iwas working with sequence file in GenBank format. This file contained
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the following text fragment:
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I was working with the sequence file in GenBank format when I notised
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one irrational thing.
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That file contained the following text fragment:
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`
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...
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The output was as follows:
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<code>
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`Function:`
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`initation of replication cycle and DNA`
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`elongation`
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`Note:`
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`decatenates newly replicated chromosomal DNA and`
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`relaxes positive and negative DNA supercoiling`
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`Translation:`
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`MEQQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHEKMGRPAVEVIMT               `
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\<\\code\>
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`
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Function:
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initation of replication cycle and DNA
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elongation
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Note:
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decatenates newly replicated chromosomal DNA and
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relaxes positive and negative DNA supercoiling
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Translation:
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MEQQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHEKMGRPAVEVIMT
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`
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As one can see from the output the **getValue()** method of the
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**SimpleNote** class returns String objects that contain *new line
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symbols* when its object represents **function** & **note** terms. I
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symbols* when its object represents **function** & **note** notes. I
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consider this rather irrational. One can also see that there are no *new
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line symbols* in the case of **translation** term. This is well.
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line symbols* in the case of **translation** note. This is well.

‎wiki/User_talk:Seeker.mediawiki‎

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If I clearly understand, the '''RichSequence''' object is ment by ''sequence''. But there is no '''getNCBITaxon()''' method in the '''RichSequence''' class. There is '''getTaxon()''' method in the '''RichSequence''' class. Thus, exectly this method should be used here instead of '''getNCBITaxon()''' method.
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Iwas working with sequence file in GenBank format. This file contained the following text fragment:
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I was working with the sequence file in GenBank format when I notised one irrational thing.
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That file contained the following text fragment:
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<code>
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relaxes positive and negative DNA supercoiling
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Translation:
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MEQQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHEKMGRPAVEVIMT
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<\code>
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</code>
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As one can see from the output the '''getValue()''' method of the '''SimpleNote''' class returns String objects that contain ''new line symbols'' when its object represents '''function''' & '''note''' terms.
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I consider this rather irrational. One can also see that there are no ''new line symbols'' in the case of '''translation''' term. This is well.
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As one can see from the output the '''getValue()''' method of the '''SimpleNote''' class returns String objects that contain ''new line symbols'' when its object represents '''function''' & '''note''' notes.
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I consider this rather irrational. One can also see that there are no ''new line symbols'' in the case of '''translation''' note. This is well.

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