<p>It's a programming error that should look like this:</p>

<pre><code>StringBuffer sb = (...)
(...)
String s = (String)sb;
</code></pre>

<p>while it should be</p>

<pre><code>StringBuffer sb = (...)
(...)
String s = sb.toString();
</code></pre>

<p>( see also <a href="https://www.biostars.org/p/177992/" rel="nofollow noreferrer">https://www.biostars.org/p/177992/</a> ) . You cannot do anything about it but asking the authors of the software.</p>

CC BY-SA 4.0
2018-07-11T11:15:28.097Z
Sent an email to Cathy Riemer asking for help.
Biomagician
CC BY-SA 4.0
2018-07-11T09:50:52.997Z
2018-07-11T09:50:52.997Z
Pierre
<p>I have installed <a href="http://globin.bx.psu.edu/dist/gmaj/gmaj_install.html" rel="nofollow noreferrer">GMAJ</a> using:</p>

<pre><code>wget http://globin.bx.psu.edu/dist/gmaj/gmaj.zip  -O output/software/gmaj.zip
unzip -u output/software/gmaj.zip -d output/software/gmaj/
rm output/software/gmaj.zip
</code></pre>

<p>I ran <a href="http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html" rel="nofollow noreferrer">lastz</a> on two chromosomes from two different assemblies of <em>C. elegans</em>:</p>

<p><code>lastz c_elegans.PRJNA13758.WS263.genomicI.fa I.fa --format=maf &gt; MAF.maf</code></p>

<p>and got a MAF file.</p>

<p>Then, I tried to visualise the file using:</p>

<p><code>java -jar output/software/gmaj/gmaj.jar MAF.maf</code></p>

<p>but I got the following error:</p>

<pre><code>Exception in thread "main" java.lang.ClassCastException: java.lang.StringBuffer cannot be cast to java.lang.String
    at edu.psu.bx.gmaj.MajGui.setDefaults(MajGui.java:272)
    at edu.psu.bx.gmaj.Maj.&lt;init&gt;(Maj.java:53)
    at edu.psu.bx.gmaj.MajMain.main(MajMain.java:86)
</code></pre>

<p>Can someone help me resolve this error or suggest an alternative way to visualise my alignment?</p>

<p>I work on Mac OS X.</p>

<p>Cheers.</p>

<phylogenetics><visualization><software-installation><maf>
GMAJ error: Exception in thread "main" java.lang.ClassCastException: java.lang.StringBuffer cannot be cast to java.lang.String
# GMAJ error: Exception in thread "main" java.lang.ClassCastException: java.lang.StringBuffer cannot be cast to java.lang.String

(Asked by: username_0 on 2018-07-10)

I have installed GMAJ using:
wget http://globin.bx.psu.edu/dist/gmaj/gmaj.zip  -O output/software/gmaj.zip
unzip -u output/software/gmaj.zip -d output/software/gmaj/
rm output/software/gmaj.zip

I ran lastz on two chromosomes from two different assemblies of C. elegans:
lastz c_elegans.PRJNA13758.WS263.genomicI.fa I.fa --format=maf > MAF.maf
and got a MAF file.
Then, I tried to visualise the file using:
java -jar output/software/gmaj/gmaj.jar MAF.maf
but I got the following error:
Exception in thread "main" java.lang.ClassCastException: java.lang.StringBuffer cannot be cast to java.lang.String
    at edu.psu.bx.gmaj.MajGui.setDefaults(MajGui.java:272)
    at edu.psu.bx.gmaj.Maj.(Maj.java:53)
    at edu.psu.bx.gmaj.MajMain.main(MajMain.java:86)

Can someone help me resolve this error or suggest an alternative way to visualise my alignment?
I work on Mac OS X.
Cheers.

**Tags:** phylogenetics, visualization, software-installation, maf

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## 1 answers

### Answer by username_1 on 2018-07-11. Score: 1

It's a programming error that should look like this:
StringBuffer sb = (...)
(...)
String s = (String)sb;

while it should be
StringBuffer sb = (...)
(...)
String s = sb.toString();

( see also https://www.biostars.org/p/177992/ ) . You cannot do anything about it but asking the authors of the software.

> **Comments:**
> **username_0**: Sent an email to Cathy Riemer asking for help.  

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