-Mafft -

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Frunner%2Fmsa%2FMafft.html;fp=website%2Ffull_javadoc%2Fcompbio%2Frunner%2Fmsa%2FMafft.html;h=0000000000000000000000000000000000000000;hb=0bbebf27d045b1345bc042bdf24ef2e6808df251;hp=45b6b8d05ad7ddb6278d64d116507d3a071ffb40;hpb=5be600c3985aa7bcb8d8b51d77d773c76e6802bb;p=jabaws.git diff --git a/website/full_javadoc/compbio/runner/msa/Mafft.html b/website/full_javadoc/compbio/runner/msa/Mafft.html deleted file mode 100644 index 45b6b8d..0000000 --- a/website/full_javadoc/compbio/runner/msa/Mafft.html +++ /dev/null @@ -1,418 +0,0 @@ - - - - - - -Mafft - - - - - - - - - - - - -

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- -compbio.runner.msa -
-Class Mafft

-java.lang.Object
-  compbio.engine.client.SkeletalExecutable<Mafft>
-      compbio.runner.msa.Mafft
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All Implemented Interfaces:: Executable<Mafft>, PipedExecutable<Mafft>

public class Mafft
extends SkeletalExecutable<Mafft>
implements PipedExecutable<Mafft>
extends SkeletalExecutable<Mafft>
implements PipedExecutable<Mafft>

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Author:: pvtroshin

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-Nested Class Summary
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Nested classes/interfaces inherited from interface compbio.engine.client.Executable
Executable.ExecProvider
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-Field Summary
-static String KEY_VALUE_SEPARATOR - -
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Fields inherited from class compbio.engine.client.SkeletalExecutable
ERROR, INPUT, OUTPUT
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-Constructor Summary
Mafft() - -
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-Method Summary
- Mafft addParameters(List<String> parameters) - -
-          Mafft input must always be the last parameter!
- Alignment getResults(String workDirectory) - -
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- Class<Mafft> getType() - -
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- Mafft setInput(String inFile) - -
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Methods inherited from class compbio.engine.client.SkeletalExecutable
equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString
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Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
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Methods inherited from interface compbio.engine.client.Executable
getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, loadRunConfiguration
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Nested classes/interfaces inherited from interface compbio.engine.client.Executable
`Executable.ExecProvider`

-Field Summary
-`static String`	`KEY_VALUE_SEPARATOR` - - -

Fields inherited from class compbio.engine.client.SkeletalExecutable
`ERROR, INPUT, OUTPUT`

-Constructor Summary
`Mafft()` - - -

-Method Summary
- `Mafft`	`addParameters(List<String> parameters)` - - - Mafft input must always be the last parameter!
- `Alignment`	`getResults(String workDirectory)` - - -
- `Class<Mafft>`	`getType()` - - -
- `Mafft`	`setInput(String inFile)` - - -

Methods inherited from class compbio.engine.client.SkeletalExecutable
`equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString`

Methods inherited from class java.lang.Object
`getClass, notify, notifyAll, wait, wait, wait`

Methods inherited from interface compbio.engine.client.Executable
`getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, loadRunConfiguration`

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-Field Detail
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-KEY_VALUE_SEPARATOR

-public static final String KEY_VALUE_SEPARATOR

See Also:: Constant Field Values

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-Constructor Detail

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-Mafft

-public Mafft()