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Viewing changes to src/org/usadellab/trimmomatic/trim/TrimmerFactory.java

  • Committer: Package Import Robot
  • Author(s): Andreas Tille, Olivier Sallou
  • Date: 2013-08-07 12:14:33 UTC
  • mfrom: (1.1.1)
  • Revision ID: package-import@ubuntu.com-20130807121433-qxchmfrrodridtvz
Tags: 0.30+dfsg-1
http://bugs.debian.org/718850
* New upstream version
* debian/copyright:
   - DEP5
   - Add Files-Excluded to document what was removed from original source
* debian/watch: handle +dfsg suffix
* debian/get-orig-source: use new uscan if available
* debian/control:
   - cme fix dpkg-control
   - debhelper 9
   - use anonscm in Vcs fields
   - Build-Depends: default-jdk | ...
     Closes: #718850
[ Olivier Sallou]
    * Manage java libs with javahelper
    * Provide upstream missing MANIFEST.MF

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src/org/usadellab/trimmomatic/trim/TrimmerFactory.java
 
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package org.usadellab.trimmomatic.trim;
 
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import java.io.IOException;
 
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public class TrimmerFactory
 
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{
 
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        public TrimmerFactory()
 
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        {
 
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        }
 
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        public Trimmer makeTrimmer(String desc) throws IOException
 
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        {
 
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                String trimmerName=desc;
 
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                String args="";
 
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                int idx=desc.indexOf(':');
 
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                if(idx>0)
 
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                        {
 
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                        trimmerName=desc.substring(0,idx);
 
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                        if(idx<desc.length()-1)
 
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                                args=desc.substring(idx+1);
 
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                        }
 
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                if(trimmerName.equals("ILLUMINACLIP"))
 
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                        return IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(args);
 
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                if(trimmerName.equals("LEADING"))
 
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                        return new LeadingTrimmer(args);
 
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                if(trimmerName.equals("TRAILING"))
 
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                        return new TrailingTrimmer(args);
 
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                if(trimmerName.equals("HEADCROP"))
 
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                        return new HeadCropTrimmer(args);
 
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                if(trimmerName.equals("CROP"))
 
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                        return new CropTrimmer(args);
 
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                if(trimmerName.equals("SLIDINGWINDOW"))
 
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                        return new SlidingWindowTrimmer(args);
 
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                if(trimmerName.equals("MAXINFO"))
 
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                        return new MaximumInformationTrimmer(args);
 
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                if(trimmerName.equals("MINLEN"))
 
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                        return new MinLenTrimmer(args);
 
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                if(trimmerName.equals("AVGQUAL"))
 
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                        return new AvgQualTrimmer(args);
 
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                if(trimmerName.equals("TOPHRED33"))
 
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                        return new ToPhred33Trimmer(args);
 
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                if(trimmerName.equals("TOPHRED64"))
 
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                        return new ToPhred64Trimmer(args);
 
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                throw new RuntimeException("Unknown trimmer: "+trimmerName);
 
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        }
 
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}