TestCasesEffectCollapse (Snp Effect 4.3t API)

java.lang.Object
- org.snpeff.snpEffect.testCases.unity.TestCasesBase
- - org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse

```
public class TestCasesEffectCollapse
extends TestCasesBase
```
Test Splice sites variants The sample transcript used is: Transcript:1:751-1139, strand: +, id:transcript_0, Protein Exons: 1:751-810 'exon_0_0', rank: 1, frame: ., sequence: cgattgacctacatagtaatgagttttgttggtccgtaagacttcgcccaaaaccgcgca 1:1013-1139 'exon_0_1', rank: 2, frame: ., sequence: cttcgactactcgggggtctaagcacgttttctgcagggaaagtaatatatgcttgtgcgcaaccatggtaacagggattcacggccccgttaatggtatgacctaagccccatacgagtcatccaa CDS : cgattgacctacatagtaatgagttttgttggtccgtaagacttcgcccaaaaccgcgcacttcgactactcgggggtctaagcacgttttctgcagggaaagtaatatatgcttgtgcgcaaccatggtaacagggattcacggccccgttaatggtatgacctaagccccatacgagtcatccaa Protein : RLTYIVMSFVGP*DFAQNRALRLLGGLSTFSAGKVIYACAQPW*QGFTAPLMV*PKPHTSHP?

Author:

pcingola

Field Summary
- Fields inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
  addUtrs, chromoBases, chromoSequence, chromosome, codonTable, config, debug, gene, genome, genomeName, maxExons, maxGeneLen, maxTranscripts, minExons, numGenes, onlyMinusStrand, onlyPlusStrand, rand, randSeed, shiftHgvs, snpEffectPredictor, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, transcript, verbose

Constructor Summary

Constructors
Constructor Description

TestCasesEffectCollapse()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`init()`
`void`	`test_01()`
`void`	`test_02()`
`void`	`test_03()`
`void`	`test_04()`
`void`	`test_05()`

Methods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
after, before, checkApply, checkApplyDel, checkApplyIns, checkApplyMixed, checkApplyMnp, checkApplySnp, checkEffect, checkEffect, formatVersion, hasEffect, initRand, initSnpEffPredictor, initSnpEffPredictor, prependSequenceToFirstExon, showTranscripts

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail
- TestCasesEffectCollapse
```
public TestCasesEffectCollapse()
```

Method Detail

init
```
protected void init()
```
Overrides:

init in class TestCasesBase

test_01
```
public void test_01()
```

test_02
```
public void test_02()
```

test_03
```
public void test_03()
```

test_04
```
public void test_04()
```

test_05
```
public void test_05()
```