X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Frunner%2Fmsa%2Fclass-use%2FTcoffee.html;fp=website%2Ffull_javadoc%2Fcompbio%2Frunner%2Fmsa%2Fclass-use%2FTcoffee.html;h=d54f3b8b436ebf9cc3888865d6a53f5aa9de39de;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html b/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html new file mode 100644 index 0000000..d54f3b8 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html @@ -0,0 +1,283 @@ + + + + + + +Uses of Class compbio.runner.msa.Tcoffee + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.runner.msa.Tcoffee

+
+ + + + + + + + + + + + + +
+Packages that use Tcoffee
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
compbio.ws.server  
+  +

+ + + + + +
+Uses of Tcoffee in compbio.runner.msa
+  +

+ + + + + + + + + +
Methods in compbio.runner.msa that return Tcoffee
+ TcoffeeTcoffee.setInput(String inFile) + +
+           
+  +

+ + + + + + + + + + + + + +
Methods in compbio.runner.msa that return types with arguments of type Tcoffee
+ CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) + +
+           
+ Class<Tcoffee>Tcoffee.getType() + +
+           
+  +

+ + + + + +
+Uses of Tcoffee in compbio.ws.server
+  +

+ + + + + + + + + + + + + + + + + + + + + +
Methods in compbio.ws.server that return types with arguments of type Tcoffee
+ Limit<Tcoffee>TcoffeeWS.getLimit(String presetName) + +
+           
+ LimitsManager<Tcoffee>TcoffeeWS.getLimits() + +
+           
+ PresetManager<Tcoffee>TcoffeeWS.getPresets() + +
+           
+ RunnerConfig<Tcoffee>TcoffeeWS.getRunnerOptions() + +
+           
+  +

+ + + + + + + + + + + + + +
Method parameters in compbio.ws.server with type arguments of type Tcoffee
+ StringTcoffeeWS.customAlign(List<FastaSequence> sequences, + List<Option<Tcoffee>> options) + +
+           
+ StringTcoffeeWS.presetAlign(List<FastaSequence> sequences, + Preset<Tcoffee> preset) + +
+           
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + +