martinrschiller / bwt Goto Github PK
View Code? Open in Web Editor NEWBurrows Wheeler Transforms
Burrows Wheeler Transforms
CURRENT QUESTIONS FOR JAY************************************************************** 1) Why are their two different packages under main 2) you put a dependencies in several classes. Shouldn't this be in the pom file. Should I move them 3) Should I switch output to similar format as DNA input provider 4) when I run the program it says Failed to load Main-Class manifest attribute from bwt-1.0-SNAPSHOT.jar. I added manifest to main class - please check 5) BWT class why do we nee inputSeq line 47 and seq this line? 6) we never call BWTApplicationUsageExample? 7) why does the TestDNAInputProvision class not have an expected output to test. 8) DNAInputProviderSIMPLE seems like it should be a unittes not an input type 9) confused about intention of WEB dna input provided vs. refseq. 10) Why do you not use @override and extends in DNAInputProviderWEB THING FOR MRS TO DO************************************************************** Write unit tests for reading from website. Post on stack overflow Look up reflection look up override look up abstract class lookup class extends other class read about java collections lists arraylists, vectors, hashmaps, BWT PROGRAM************************************************************** Command to run program. >java -jar myjar.jar org.biotoolkit.algorithms.bwtx.DNAInputProviderINTERACTIVE Other DNAInputProvider classes could also be used to launch: DNAInputProviderWEB.java DNAInputProviderSIMPLE.java DNAInputProviderINTERACTIVE.java BWT PACKAGES, CLASSES AND FUNCTIONS************************************************************** org.biotoolkit.algorithms package Main package containing program. BWTApplication.java - main class BWTApplicaitonUsageExample.java - example of how to call the application org.biotoolkit.algorithmsbwtx package RefSeqInputProvider.java package-info.java DNAInputProviderWEB.java DNAInputProviderSIMPLE.java -overides the input for the DNAInputProvider class providing a dna sequence. DNAInputProviderINTERACTIVE.java DNAInputProvider.java - class that validates the the input is a correct DNA string. Called by other classes BWTCompressor.java - package compresses a bwt into a compressed string and returns to bwt.java src/java/test package - Contains Junit tests for each class TestDNAInputProvisioning.java - Contains Junit tests for DNAInput types TestBWTCompression.java - Contains Junit tests for BWT compression TestBWT.java - Contains Junit tests for BWT AppTest.java - Contains Junit tests that an app will run PLANS************************************************************** Hook up to database Read from a website Generate a simple UI MAVEN************************************************************** This is a mavenized version of the BWT project. To run unit tests: mvn test To package a jar: mvn package To add dependencies: Edit the pom file. To set up eclipse: 1) Run "mvn test" - this ensures that the code "works" 2) Run "mvn eclipse:eclipse" - this creates eclipse project 3) Import the project into eclipse. GIT************************************************************** Local path************************************************************** /Users/martinschiller/Desktop/SchillerDrive/Computer/Gitprojects/BWT
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