--- /dev/null
+#Fri Nov 19 11:04:13 GMT 2010\r
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+org.eclipse.jdt.core.formatter.join_lines_in_comments=true\r
+org.eclipse.jdt.core.formatter.join_wrapped_lines=true\r
+org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line=false\r
+org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line=false\r
+org.eclipse.jdt.core.formatter.keep_imple_if_on_one_line=false\r
+org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line=false\r
+org.eclipse.jdt.core.formatter.lineSplit=80\r
+org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column=false\r
+org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column=false\r
+org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body=0\r
+org.eclipse.jdt.core.formatter.number_of_empty_lines_to_preserve=1\r
+org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line=false\r
+org.eclipse.jdt.core.formatter.tabulation.char=tab\r
+org.eclipse.jdt.core.formatter.tabulation.size=4\r
+org.eclipse.jdt.core.formatter.use_on_off_tags=false\r
+org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=false\r
+org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true\r
+org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested=true\r
--- /dev/null
+#Fri Nov 19 11:04:13 GMT 2010\r
+eclipse.preferences.version=1\r
+formatter_profile=org.eclipse.jdt.ui.default_profile\r
+formatter_settings_version=11\r
}\r
\r
/**\r
- * Reader for JRonn horizontal file format >Foobar M G D T T A G 0.48 0.42\r
- * 0.42 0.48 0.52 0.53 0.54 All values are tab delimited\r
+ * Reader for JRonn horizontal file format\r
+ * \r
+ * <pre>\r
+ * >Foobar M G D T T A G 0.48 0.42\r
+ * 0.42 0.48 0.52 0.53 0.54\r
+ * \r
+ * <pre>\r
+ * Where all values are tab delimited\r
* \r
* @param inStream\r
- * @return\r
+ * the InputStream connected to the JRonn output file\r
+ * @return List of {@link AnnotatedSequence} objects\r
* @throws IOException\r
+ * is thrown if the inStream has problems accessing the data\r
* @throws UnknownFileFormatException\r
+ * is thrown if the inStream represents an unknown source of\r
+ * data, i.e. not a JRonn output\r
*/\r
public static List<AnnotatedSequence> readJRonn(final InputStream inStream)\r
throws IOException, UnknownFileFormatException {\r
* @throws IOException\r
* @throws UnknownFileFormatException\r
*/\r
- public static List<MultiAnnotatedSequence<DisemblResultAnnot>> readDisembl(\r
+ static List<MultiAnnotatedSequence<DisemblResultAnnot>> readDisembl(\r
final InputStream input) throws IOException,\r
UnknownFileFormatException {\r
Scanner scan = new Scanner(input);\r
System.out.println("Pres: " + msaws.getPresets().getPresets());\r
String jobId = msaws.analize(fsl);\r
System.out.println("J: " + jobId);\r
- HashSet<Score> result = msaws.getConservation(jobId);\r
+ HashSet<Score> result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 1);\r
assertEquals(result.iterator().next().getMethod(), Method.SHENKIN);\r
PresetManager<AACon> presets = msaws.getPresets();\r
jobId = msaws.presetAnalize(fsl,\r
presets.getPresetByName("Quick conservation"));\r
- result = msaws.getConservation(jobId);\r
+ result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 13);\r
\r
jobId = msaws.presetAnalize(fsl,\r
presets.getPresetByName("Slow conservation"));\r
- result = msaws.getConservation(jobId);\r
+ result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 5);\r
\r
jobId = msaws.presetAnalize(fsl,\r
presets.getPresetByName("Complete conservation"));\r
- result = msaws.getConservation(jobId);\r
+ result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 18);\r
\r
PresetManager<AACon> presets = msaws.getPresets();\r
String jobId = msaws.presetAnalize(fsl,\r
presets.getPresetByName("Quick conservation"));\r
- HashSet<Score> result = msaws.getConservation(jobId);\r
+ HashSet<Score> result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 13);\r
\r
jobId = msaws.presetAnalize(fsl,\r
presets.getPresetByName("Slow conservation"));\r
- result = msaws.getConservation(jobId);\r
+ result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 5);\r
\r
jobId = msaws.presetAnalize(fsl,\r
presets.getPresetByName("Complete conservation"));\r
- result = msaws.getConservation(jobId);\r
+ result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 18);\r
\r
try {\r
options.getArgument("Calculation method").setDefaultValue("SMERFS");\r
String jobId = msaws.customAnalize(fsl, options.getArguments());\r
- HashSet<Score> result = msaws.getConservation(jobId);\r
+ HashSet<Score> result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 1);\r
assertEquals(\r
options.removeArgument("Normalize");\r
System.out.println(options);\r
jobId = msaws.customAnalize(fsl, options.getArguments());\r
- result = msaws.getConservation(jobId);\r
+ result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 1);\r
assertEquals(\r
/**\r
* Interface for tools that results to one or more annotation to sequence(s)\r
* \r
- * @author pvtroshin\r
- * \r
- * Date November 2010\r
+ * @author Peter Troshin\r
* \r
* @param <T>\r
* executable type / web service type\r
+ * \r
+ * @version 1.0 November 2010\r
*/\r
@WebService(targetNamespace = "http://msa.data.compbio/01/12/2010/")\r
public interface Annotation<T> extends JABAService, JManagement, Metadata<T> {\r
\r
/**\r
* \r
+ * Analyse the sequences. The actual analysis algorithm is defined by the\r
+ * type T.\r
+ * \r
* Any dataset containing a greater number of sequences or the average\r
* length of the sequences are greater then defined in the default Limit\r
* will not be accepted for an alignment operation and\r
* thrown if input list of fasta sequence is null or empty\r
* @throws UnsupportedRuntimeException\r
* thrown if server OS does not support native executables for a\r
- * given web service, e.g. JWS2 is deployed on Windows and Mafft\r
- * service is called\r
+ * given web service, e.g. JABAWS is deployed on Windows and\r
+ * Mafft service is called\r
* @throws LimitExceededException\r
* is throw if the input sequences number or average length\r
* exceeds what is defined by the limit\r
JobSubmissionException;\r
\r
/**\r
- * \r
- * @see Option\r
- * \r
- * Default Limit is used to decide whether the calculation will be\r
- * permitted or denied\r
+ * Analyse the sequences according to custom settings defined in options\r
+ * list. The actual analysis algorithm is defined by the type T. Default\r
+ * Limit is used to decide whether the calculation will be permitted or\r
+ * denied\r
* \r
* @param sequences\r
* List of FastaSequence objects. The programme does not perform\r
* @param options\r
* A list of Options\r
* @return jobId - unique identifier for the job\r
- * @throws JobSubmissionException. This\r
- * exception is thrown when the job could not be submitted due\r
- * to the following reasons: 1) The number of sequences in the\r
+ * @throws JobSubmissionException\r
+ * is thrown when the job could not be submitted due to the\r
+ * following reasons: 1) The number of sequences in the\r
* submission or their average length is greater then defined by\r
* the default Limit. 2) Any problems on the server side e.g. it\r
* is misconfigured or malfunction, is reported via this\r
* thrown if input list of fasta sequence is null or empty\r
* @throws UnsupportedRuntimeException\r
* thrown if server OS does not support native executables for a\r
- * given web service, e.g. JWS2 is deployed on Windows and Mafft\r
- * service is called\r
+ * given web service, e.g. JABAWS is deployed on Windows and\r
+ * Mafft service is called\r
* @throws LimitExceededException\r
* is throw if the input sequences number or average length\r
* exceeds what is defined by the limit\r
+ * @see Option\r
*/\r
@WebMethod\r
String customAnalize(\r
JobSubmissionException, WrongParameterException;\r
\r
/**\r
- * \r
+ * Analyse the sequences according to the preset settings. The actual\r
+ * analysis algorithm is defined by the type T.\r
* \r
* Limit for a presetName is used whether the calculation will be permitted\r
* or denied. If no Limit was defined for a presetName, than default limit\r
* @param preset\r
* A list of Options\r
* @return String - jobId - unique identifier for the job\r
- * @throws JobSubmissionException. This\r
- * exception is thrown when the job could not be submitted due\r
- * to the following reasons: 1) The number of sequences in the\r
+ * @throws JobSubmissionException\r
+ * is thrown when the job could not be submitted due to the\r
+ * following reasons: 1) The number of sequences in the\r
* submission or their average length is greater then defined by\r
* the default Limit. 2) Any problems on the server side e.g. it\r
* is misconfigured or malfunction, is reported via this\r
* thrown if input list of fasta sequence is null or empty\r
* @throws UnsupportedRuntimeException\r
* thrown if server OS does not support native executables for a\r
- * given web service, e.g. JWS2 is deployed on Windows and Mafft\r
- * service is called\r
+ * given web service, e.g. JABAWS is deployed on Windows and\r
+ * Mafft service is called\r
* @throws LimitExceededException\r
* is throw if the input sequences number or average length\r
* exceeds what is defined by the limit\r
* \r
* @param jobId\r
* a unique job identifier\r
- * @return\r
+ * @return the HashSet of Score objects\r
* @throws ResultNotAvailableException\r
* this exception is throw if the job execution was not\r
* successful or the result of the execution could not be found.\r
* invalid format\r
*/\r
@WebMethod\r
- HashSet<Score> getConservation(@WebParam(name = "jobId") String jobId)\r
+ HashSet<Score> getAnnotation(@WebParam(name = "jobId") String jobId)\r
throws ResultNotAvailableException;\r
\r
}\r
/**\r
* Connects to a web service by the host and the service name\r
* \r
- * @param <T>\r
+ * @param T\r
* web service type\r
* @param host\r
* @param service\r
}\r
\r
@Override\r
- public HashSet<Score> getConservation(String jobId)\r
+ public HashSet<Score> getAnnotation(String jobId)\r
throws ResultNotAvailableException {\r
WSUtil.validateJobId(jobId);\r
AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+All Classes\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">\r
+\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white">\r
+<FONT size="+1" CLASS="FrameHeadingFont">\r
+<B>All Classes</B></FONT>\r
+<BR>\r
+\r
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
+<TR>\r
+<TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence" target="classFrame">Alignment</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence" target="classFrame">AlignmentMetadata</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence" target="classFrame">AnnotatedSequence</A>\r
+<BR>\r
+<A HREF="compbio/data/msa/Annotation.html" title="interface in compbio.data.msa" target="classFrame"><I>Annotation</I></A>\r
+<BR>\r
+<A HREF="compbio/metadata/Argument.html" title="interface in compbio.metadata" target="classFrame"><I>Argument</I></A>\r
+<BR>\r
+<A HREF="compbio/metadata/ChunkHolder.html" title="class in compbio.metadata" target="classFrame">ChunkHolder</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence" target="classFrame">ClustalAlignmentUtil</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence" target="classFrame">DisemblResultAnnot</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence" target="classFrame">FastaSequence</A>\r
+<BR>\r
+<A HREF="compbio/ws/client/IOHelper.html" title="class in compbio.ws.client" target="classFrame">IOHelper</A>\r
+<BR>\r
+<A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa" target="classFrame"><I>JABAService</I></A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence" target="classFrame">JalviewAnnotation</A>\r
+<BR>\r
+<A HREF="compbio/data/msa/JManagement.html" title="interface in compbio.data.msa" target="classFrame"><I>JManagement</I></A>\r
+<BR>\r
+<A HREF="compbio/metadata/JobExecutionException.html" title="class in compbio.metadata" target="classFrame">JobExecutionException</A>\r
+<BR>\r
+<A HREF="compbio/metadata/JobStatus.html" title="enum in compbio.metadata" target="classFrame">JobStatus</A>\r
+<BR>\r
+<A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata" target="classFrame">JobSubmissionException</A>\r
+<BR>\r
+<A HREF="compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client" target="classFrame">Jws2Client</A>\r
+<BR>\r
+<A HREF="compbio/metadata/Limit.html" title="class in compbio.metadata" target="classFrame">Limit</A>\r
+<BR>\r
+<A HREF="compbio/metadata/LimitExceededException.html" title="class in compbio.metadata" target="classFrame">LimitExceededException</A>\r
+<BR>\r
+<A HREF="compbio/metadata/LimitsManager.html" title="class in compbio.metadata" target="classFrame">LimitsManager</A>\r
+<BR>\r
+<A HREF="compbio/data/msa/Metadata.html" title="interface in compbio.data.msa" target="classFrame"><I>Metadata</I></A>\r
+<BR>\r
+<A HREF="compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client" target="classFrame">MetadataHelper</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/Method.html" title="enum in compbio.data.sequence" target="classFrame">Method</A>\r
+<BR>\r
+<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa" target="classFrame"><I>MsaWS</I></A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence" target="classFrame">MultiAnnotatedSequence</A>\r
+<BR>\r
+<A HREF="compbio/metadata/Option.html" title="class in compbio.metadata" target="classFrame">Option</A>\r
+<BR>\r
+<A HREF="compbio/metadata/Parameter.html" title="class in compbio.metadata" target="classFrame">Parameter</A>\r
+<BR>\r
+<A HREF="compbio/metadata/Preset.html" title="class in compbio.metadata" target="classFrame">Preset</A>\r
+<BR>\r
+<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata" target="classFrame">PresetManager</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/Program.html" title="enum in compbio.data.sequence" target="classFrame">Program</A>\r
+<BR>\r
+<A HREF="compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata" target="classFrame">ResultNotAvailableException</A>\r
+<BR>\r
+<A HREF="compbio/metadata/RunnerConfig.html" title="class in compbio.metadata" target="classFrame">RunnerConfig</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/Score.html" title="class in compbio.data.sequence" target="classFrame">Score</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence" target="classFrame">SequenceUtil</A>\r
+<BR>\r
+<A HREF="compbio/ws/client/Services.html" title="enum in compbio.ws.client" target="classFrame">Services</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence" target="classFrame">UnknownFileFormatException</A>\r
+<BR>\r
+<A HREF="compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata" target="classFrame">UnsupportedRuntimeException</A>\r
+<BR>\r
+<A HREF="compbio/metadata/ValueConstrain.html" title="class in compbio.metadata" target="classFrame">ValueConstrain</A>\r
+<BR>\r
+<A HREF="compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata" target="classFrame">ValueConstrain.Type</A>\r
+<BR>\r
+<A HREF="compbio/metadata/WrongParameterException.html" title="class in compbio.metadata" target="classFrame">WrongParameterException</A>\r
+<BR>\r
+<A HREF="compbio/ws/client/WSTester.html" title="class in compbio.ws.client" target="classFrame">WSTester</A>\r
+<BR>\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+All Classes\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">\r
+\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white">\r
+<FONT size="+1" CLASS="FrameHeadingFont">\r
+<B>All Classes</B></FONT>\r
+<BR>\r
+\r
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
+<TR>\r
+<TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>\r
+<BR>\r
+<A HREF="compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><I>Annotation</I></A>\r
+<BR>\r
+<A HREF="compbio/metadata/Argument.html" title="interface in compbio.metadata"><I>Argument</I></A>\r
+<BR>\r
+<A HREF="compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
+<BR>\r
+<A HREF="compbio/ws/client/IOHelper.html" title="class in compbio.ws.client">IOHelper</A>\r
+<BR>\r
+<A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><I>JABAService</I></A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence">JalviewAnnotation</A>\r
+<BR>\r
+<A HREF="compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><I>JManagement</I></A>\r
+<BR>\r
+<A HREF="compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
+<BR>\r
+<A HREF="compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>\r
+<BR>\r
+<A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
+<BR>\r
+<A HREF="compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
+<BR>\r
+<A HREF="compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
+<BR>\r
+<A HREF="compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
+<BR>\r
+<A HREF="compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
+<BR>\r
+<A HREF="compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><I>Metadata</I></A>\r
+<BR>\r
+<A HREF="compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A>\r
+<BR>\r
+<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><I>MsaWS</I></A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence">MultiAnnotatedSequence</A>\r
+<BR>\r
+<A HREF="compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<BR>\r
+<A HREF="compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<BR>\r
+<A HREF="compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
+<BR>\r
+<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>\r
+<BR>\r
+<A HREF="compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
+<BR>\r
+<A HREF="compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<BR>\r
+<A HREF="compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
+<BR>\r
+<A HREF="compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>\r
+<BR>\r
+<A HREF="compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>\r
+<BR>\r
+<A HREF="compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
+<BR>\r
+<A HREF="compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>\r
+<BR>\r
+<A HREF="compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
+<BR>\r
+<A HREF="compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
+<BR>\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+Annotation\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Annotation";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="navbar_top_firstrow"><!-- --></A>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Annotation.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV CLASS \r
+ <A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/Annotation.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Annotation.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
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+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.msa</FONT>\r
+<BR>\r
+Interface Annotation<T></H2>\r
+<DL>\r
+<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type / web service type</DL>\r
+<DL>\r
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, <A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>, <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public interface <B>Annotation<T></B><DT>extends <A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, <A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>, <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T></DL>\r
+</PRE>\r
+\r
+<P>\r
+Interface for tools that results to one or more annotation to sequence(s)\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 November 2010</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>Peter Troshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/Annotation.html#analize(java.util.List)">analize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/Annotation.html#customAnalize(java.util.List, java.util.List)">customAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>>> options)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences according to custom settings defined in options
+ list.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashSet.html?is-external=true" title="class or interface in java.util">HashSet</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/Annotation.html#getAnnotation(java.lang.String)">getAnnotation</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</CODE>\r
+\r
+<BR>\r
+ Return the result of the job.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/Annotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>> preset)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences according to the preset settings.</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_compbio.data.msa.JManagement"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="../../../compbio/data/msa/JManagement.html#cancelJob(java.lang.String)">cancelJob</A>, <A HREF="../../../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)">getJobStatus</A>, <A HREF="../../../compbio/data/msa/JManagement.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_compbio.data.msa.Metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="../../../compbio/data/msa/Metadata.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/data/msa/Metadata.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/data/msa/Metadata.html#getPresets()">getPresets</A>, <A HREF="../../../compbio/data/msa/Metadata.html#getRunnerOptions()">getRunnerOptions</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="analize(java.util.List)"><!-- --></A><H3>\r
+analize</H3>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>analize</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)\r
+ throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
+ <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
+ <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
+<DL>\r
+<DD>Analyse the sequences. The actual analysis algorithm is defined by the
+ type T.
+
+ Any dataset containing a greater number of sequences or the average
+ length of the sequences are greater then defined in the default Limit
+ will not be accepted for an alignment operation and
+ JobSubmissionException will be thrown.\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
+ any sequence validity checks. Nor does it checks whether the
+ sequences names are unique. It is responsibility of the caller
+ to validate this information\r
+<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - is thrown when the job could not be submitted due to the
+ following reasons: 1) The number of sequences in the
+ submission or their average length is greater then defined by
+ the default Limit. 2) Any problems on the server side e.g. it
+ is misconfigured or malfunction, is reported via this
+ exception. In the first case the information on the limit
+ could be obtained from an exception.\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE> - thrown if input list of fasta sequence is null or empty\r
+<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
+ given web service, e.g. JABAWS is deployed on Windows and
+ Mafft service is called\r
+<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
+ exceeds what is defined by the limit</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="customAnalize(java.util.List, java.util.List)"><!-- --></A><H3>\r
+customAnalize</H3>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>customAnalize</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>>> options)\r
+ throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
+ <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
+ <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
+ <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
+<DL>\r
+<DD>Analyse the sequences according to custom settings defined in options
+ list. The actual analysis algorithm is defined by the type T. Default
+ Limit is used to decide whether the calculation will be permitted or
+ denied\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
+ any sequence validity checks. Nor does it checks whether the
+ sequences names are unique. It is responsibility of the caller
+ to validate this information<DD><CODE>options</CODE> - A list of Options\r
+<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - is thrown when the job could not be submitted due to the
+ following reasons: 1) The number of sequences in the
+ submission or their average length is greater then defined by
+ the default Limit. 2) Any problems on the server side e.g. it
+ is misconfigured or malfunction, is reported via this
+ exception. In the first case the information on the limit
+ could be obtained from an exception.\r
+<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
+ supported, 2) The value of the option is defined outside the
+ boundaries. In both cases exception object contain the
+ information on the violating Option.\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE> - thrown if input list of fasta sequence is null or empty\r
+<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
+ given web service, e.g. JABAWS is deployed on Windows and
+ Mafft service is called\r
+<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
+ exceeds what is defined by the limit<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="presetAnalize(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
+presetAnalize</H3>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>presetAnalize</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>> preset)\r
+ throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
+ <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
+ <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
+ <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
+<DL>\r
+<DD>Analyse the sequences according to the preset settings. The actual
+ analysis algorithm is defined by the type T.
+
+ Limit for a presetName is used whether the calculation will be permitted
+ or denied. If no Limit was defined for a presetName, than default limit
+ is used.\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
+ any sequence validity checks. Nor does it checks whether the
+ sequences names are unique. It is responsibility of the caller
+ to validate this information<DD><CODE>preset</CODE> - A list of Options\r
+<DT><B>Returns:</B><DD>String - jobId - unique identifier for the job\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - is thrown when the job could not be submitted due to the
+ following reasons: 1) The number of sequences in the
+ submission or their average length is greater then defined by
+ the default Limit. 2) Any problems on the server side e.g. it
+ is misconfigured or malfunction, is reported via this
+ exception. In the first case the information on the limit
+ could be obtained from an exception.\r
+<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
+ supported, 2) The value of the option is defined outside the
+ boundaries. In both cases exception object contain the
+ information on the violating Option.\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE> - thrown if input list of fasta sequence is null or empty\r
+<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
+ given web service, e.g. JABAWS is deployed on Windows and
+ Mafft service is called\r
+<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
+ exceeds what is defined by the limit</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getAnnotation(java.lang.String)"><!-- --></A><H3>\r
+getAnnotation</H3>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashSet.html?is-external=true" title="class or interface in java.util">HashSet</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> <B>getAnnotation</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)\r
+ throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
+<DL>\r
+<DD>Return the result of the job.\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier\r
+<DT><B>Returns:</B><DD>the HashSet of Score objects\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE> - this exception is throw if the job execution was not
+ successful or the result of the execution could not be found.
+ (e.g. removed). Exception could also be thrown is dues to the
+ lower level problems on the server i.e. IOException,
+ FileNotFoundException problems as well as
+ UnknownFileFormatException.\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE> - thrown if jobId is empty or cannot be recognised e.g. in
+ invalid format</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Annotation.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV CLASS \r
+ <A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/Annotation.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Annotation.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+JABAService\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="JABAService";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/JABAService.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/JABAService.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JABAService.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.msa</FONT>\r
+<BR>\r
+Interface JABAService</H2>\r
+<DL>\r
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa">Annotation</A><T>, <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><T></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public interface <B>JABAService</B></DL>\r
+</PRE>\r
+\r
+<P>\r
+This is a marker interface, contains no methods\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<P>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/JABAService.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/JABAService.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JABAService.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+JManagement\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="JManagement";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/JManagement.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/JManagement.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JManagement.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.msa</FONT>\r
+<BR>\r
+Interface JManagement</H2>\r
+<DL>\r
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa">Annotation</A><T>, <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><T></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public interface <B>JManagement</B></DL>\r
+</PRE>\r
+\r
+<P>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/JManagement.html#cancelJob(java.lang.String)">cancelJob</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</CODE>\r
+\r
+<BR>\r
+ Stop running the job <code>jobId</code> but leave its output untouched</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</CODE>\r
+\r
+<BR>\r
+ Return the status of the job.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/JManagement.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId,\r
+ long position)</CODE>\r
+\r
+<BR>\r
+ Reads 1kb chunk from the statistics file which is specific to a given web
+ service from the <code>position</code>.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
+cancelJob</H3>\r
+<PRE>\r
+boolean <B>cancelJob</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</PRE>\r
+<DL>\r
+<DD>Stop running the job <code>jobId</code> but leave its output untouched\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE> - is thrown if jobId is empty or cannot be recognised e.g. in
+ invalid format</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
+getJobStatus</H3>\r
+<PRE>\r
+<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</PRE>\r
+<DL>\r
+<DD>Return the status of the job.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier\r
+<DT><B>Returns:</B><DD>JobStatus - status of the job\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE> - is thrown if jobId is empty or cannot be recognised e.g. in
+ invalid format<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><CODE>JobStatus</CODE></A></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>\r
+pullExecStatistics</H3>\r
+<PRE>\r
+<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullExecStatistics</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId,\r
+ long position)</PRE>\r
+<DL>\r
+<DD>Reads 1kb chunk from the statistics file which is specific to a given web
+ service from the <code>position</code>. If in time of a request less then
+ 1kb data is available from the position to the end of the file, then it
+ returns all the data available from the position to the end of the file.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier<DD><CODE>position</CODE> - - next position within the file to read\r
+<DT><B>Returns:</B><DD>ChunkHolder - which contains a chunk of data and a next position
+ within the file from which no data has been read\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE> - thrown if jobId is empty or cannot be recognised e.g. in
+ invalid format and also if the position value is negative<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><CODE>ChunkHolder</CODE></A></DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/JManagement.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/JManagement.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JManagement.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Metadata\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Metadata";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Metadata.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/Metadata.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Metadata.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.msa</FONT>\r
+<BR>\r
+Interface Metadata<T></H2>\r
+<DL>\r
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa">Annotation</A><T>, <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><T></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public interface <B>Metadata<T></B></DL>\r
+</PRE>\r
+\r
+<P>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/Metadata.html#getLimit(java.lang.String)">getLimit</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> presetName)</CODE>\r
+\r
+<BR>\r
+ Get a Limit for a preset.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/Metadata.html#getLimits()">getLimits</A></B>()</CODE>\r
+\r
+<BR>\r
+ List Limits supported by a web service.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/Metadata.html#getPresets()">getPresets</A></B>()</CODE>\r
+\r
+<BR>\r
+ Get presets supported by a web service</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/Metadata.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
+\r
+<BR>\r
+ Get options supported by a web service</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="getRunnerOptions()"><!-- --></A><H3>\r
+getRunnerOptions</H3>\r
+<PRE>\r
+<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>> <B>getRunnerOptions</B>()</PRE>\r
+<DL>\r
+<DD>Get options supported by a web service\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>RunnerConfig the list of options and parameters supported by a
+ web service.</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getPresets()"><!-- --></A><H3>\r
+getPresets</H3>\r
+<PRE>\r
+<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>> <B>getPresets</B>()</PRE>\r
+<DL>\r
+<DD>Get presets supported by a web service\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>PresetManager the object contains information about presets
+ supported by a web service</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
+getLimit</H3>\r
+<PRE>\r
+<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>> <B>getLimit</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> presetName)</PRE>\r
+<DL>\r
+<DD>Get a Limit for a preset.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the
+ default preset is returned. If no limit for a particular
+ preset is defined then the default preset is returned\r
+<DT><B>Returns:</B><DD>Limit</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getLimits()"><!-- --></A><H3>\r
+getLimits</H3>\r
+<PRE>\r
+<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>> <B>getLimits</B>()</PRE>\r
+<DL>\r
+<DD>List Limits supported by a web service.\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>LimitManager</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Metadata.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/Metadata.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Metadata.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+MsaWS\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="MsaWS";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MsaWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><B>PREV CLASS</B></A> \r
+ NEXT CLASS</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/MsaWS.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="MsaWS.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.msa</FONT>\r
+<BR>\r
+Interface MsaWS<T></H2>\r
+<DL>\r
+<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type / web service type</DL>\r
+<DL>\r
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, <A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>, <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public interface <B>MsaWS<T></B><DT>extends <A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, <A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>, <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T></DL>\r
+</PRE>\r
+\r
+<P>\r
+Multiple Sequence Alignment (MSA) Web Services Interface\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin
+
+ Date November 2010</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with default settings.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>>> options)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with options.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</CODE>\r
+\r
+<BR>\r
+ Return the result of the job.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> preset)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with preset.</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_compbio.data.msa.JManagement"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="../../../compbio/data/msa/JManagement.html#cancelJob(java.lang.String)">cancelJob</A>, <A HREF="../../../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)">getJobStatus</A>, <A HREF="../../../compbio/data/msa/JManagement.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_compbio.data.msa.Metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="../../../compbio/data/msa/Metadata.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/data/msa/Metadata.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/data/msa/Metadata.html#getPresets()">getPresets</A>, <A HREF="../../../compbio/data/msa/Metadata.html#getRunnerOptions()">getRunnerOptions</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="align(java.util.List)"><!-- --></A><H3>\r
+align</H3>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>align</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)\r
+ throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
+ <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
+ <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
+<DL>\r
+<DD>Align a list of sequences with default settings.
+
+ Any dataset containing a greater number of sequences or when the average
+ length of the sequences are greater then defined in the default Limit,
+ will not be accepted for an alignment operation and
+ JobSubmissionException will be thrown.\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
+ any sequence validity checks. Nor does it checks whether the
+ sequences names are unique. It is responsibility of the caller
+ to make sure of this\r
+<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - is thrown when the job could not be submitted due to the
+ following reasons: 1) The number of sequences in the
+ submission or their average length is greater then defined by
+ the default Limit. 2) Any problems on the server side e.g. it
+ is misconfigured or malfunction, is reported via this
+ exception. In the first case the information on the limit
+ could be obtained from an exception.\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE> - thrown if input list of FASTA sequences is null or empty\r
+<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
+ given web service, e.g. JABAWS is deployed on Windows and
+ Mafft service is called\r
+<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or their average
+ length exceeds what is defined by the limit</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>\r
+customAlign</H3>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>customAlign</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>>> options)\r
+ throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
+ <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
+ <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
+ <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
+<DL>\r
+<DD>Align a list of sequences with options.\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
+ any sequence validity checks. Nor does it checks whether the
+ sequences names are unique. It is responsibility of the caller
+ to validate this information<DD><CODE>options</CODE> - A list of Options\r
+<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - is thrown when the job could not be submitted due to the
+ following reasons: 1) The number of sequences in the
+ submission or their average length is greater then defined by
+ the default Limit. 2) Any problems on the server side e.g. it
+ is misconfigured or malfunction, is reported via this
+ exception. In the first case the information on the limit
+ could be obtained from an exception.\r
+<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
+ supported, 2) The value of the option is defined outside the
+ boundaries. In both cases exception object contain the
+ information on the violating Option.\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE> - thrown if input list of FASTA sequence is null or empty\r
+<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
+ given web service, e.g. JABAWS is deployed on Windows and
+ Mafft service is called\r
+<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or their average
+ length exceeds what is defined by the limit<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Default Limit is used to decide whether the calculation will be
+ permitted or denied</CODE></A></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
+presetAlign</H3>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>presetAlign</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> preset)\r
+ throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
+ <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
+ <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
+ <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
+<DL>\r
+<DD>Align a list of sequences with preset.
+
+ Limit for a presetName is used whether the calculation will be permitted
+ or denied. If no Limit was defined for a presetName, than default limit
+ is used.\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
+ any sequence validity checks. Nor does it checks whether the
+ sequences names are unique. It is responsibility of the caller
+ to validate this information<DD><CODE>preset</CODE> - A list of Options\r
+<DT><B>Returns:</B><DD>String - jobId - unique identifier for the job\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - is thrown when the job could not be submitted due to the
+ following reasons: 1) The number of sequences in the
+ submission or their average length is greater then defined by
+ the default Limit. 2) Any problems on the server side e.g. it
+ is misconfigured or malfunction, is reported via this
+ exception. In the first case the information on the limit
+ could be obtained from an exception.\r
+<DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
+ supported, 2) The value of the option is defined outside the
+ boundaries. In both cases exception object contain the
+ information on the violating Option.\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE> - thrown if input list of FASTA sequence is null or empty\r
+<DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
+ given web service, e.g. JABAWS is deployed on Windows and
+ Mafft service is called\r
+<DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
+ exceeds what is defined by the limit<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getResult(java.lang.String)"><!-- --></A><H3>\r
+getResult</H3>\r
+<PRE>\r
+<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResult</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)\r
+ throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
+<DL>\r
+<DD>Return the result of the job. This method waits for the job
+ <code>jobId</code> to complete before return.\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier\r
+<DT><B>Returns:</B><DD>Alignment\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE> - this exception is throw if the job execution was not
+ successful or the result of the execution could not be found.
+ (e.g. removed). Exception could also be thrown due to the
+ lower level problems on the server i.e. IOException,
+ FileNotFoundException problems as well as
+ UnknownFileFormatException.\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE> - thrown if jobId is empty or is not recognised e.g. in invalid
+ format</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MsaWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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+</TABLE>\r
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+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><B>PREV CLASS</B></A> \r
+ NEXT CLASS</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/MsaWS.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="MsaWS.html" target="_top"><B>NO FRAMES</B></A> \r
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+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
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+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Interface compbio.data.msa.Annotation\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
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+<!-- ========= START OF TOP NAVBAR ======= -->\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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+</TD>\r
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+ PREV \r
+ NEXT</FONT></TD>\r
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+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Interface<br>compbio.data.msa.Annotation</B></H2>\r
+</CENTER>\r
+No usage of compbio.data.msa.Annotation\r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/msa/\class-useAnnotation.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Annotation.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Interface compbio.data.msa.JABAService\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Interface compbio.data.msa.JABAService";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/msa/\class-useJABAService.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JABAService.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Interface<br>compbio.data.msa.JABAService</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.ws.client"><B>compbio.ws.client</B></A></TD>\r
+<TD>A command line client and web services testing client for
+ JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Subinterfaces of <A HREF="../../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> interface</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa">Annotation<T></A></B></CODE>\r
+\r
+<BR>\r
+ Interface for tools that results to one or more annotation to sequence(s)</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> interface</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS<T></A></B></CODE>\r
+\r
+<BR>\r
+ Multiple Sequence Alignment (MSA) Web Services Interface</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.ws.client"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A> in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A> that return <A HREF="../../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></CODE></FONT></TD>\r
+<TD><CODE><B>Jws2Client.</B><B><A HREF="../../../../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Services)">connect</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> host,\r
+ <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service)</CODE>\r
+\r
+<BR>\r
+ Connects to a web service by the host and the service name</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/msa/\class-useJABAService.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JABAService.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Interface compbio.data.msa.JManagement\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Interface compbio.data.msa.JManagement";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/msa/\class-useJManagement.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JManagement.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Interface<br>compbio.data.msa.JManagement</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Subinterfaces of <A HREF="../../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> interface</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa">Annotation<T></A></B></CODE>\r
+\r
+<BR>\r
+ Interface for tools that results to one or more annotation to sequence(s)</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> interface</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS<T></A></B></CODE>\r
+\r
+<BR>\r
+ Multiple Sequence Alignment (MSA) Web Services Interface</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/msa/\class-useJManagement.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JManagement.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Interface compbio.data.msa.Metadata\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Interface compbio.data.msa.Metadata";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/msa/\class-useMetadata.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Metadata.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Interface<br>compbio.data.msa.Metadata</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Subinterfaces of <A HREF="../../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> interface</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa">Annotation<T></A></B></CODE>\r
+\r
+<BR>\r
+ Interface for tools that results to one or more annotation to sequence(s)</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> interface</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS<T></A></B></CODE>\r
+\r
+<BR>\r
+ Multiple Sequence Alignment (MSA) Web Services Interface</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/msa/\class-useMetadata.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Metadata.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Interface compbio.data.msa.MsaWS\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Interface compbio.data.msa.MsaWS";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/msa/\class-useMsaWS.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="MsaWS.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Interface<br>compbio.data.msa.MsaWS</B></H2>\r
+</CENTER>\r
+No usage of compbio.data.msa.MsaWS\r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/msa/\class-useMsaWS.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="MsaWS.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+compbio.data.msa\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white">\r
+<FONT size="+1" CLASS="FrameTitleFont">\r
+<A HREF="../../../compbio/data/msa/package-summary.html" target="classFrame">compbio.data.msa</A></FONT>\r
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
+<TR>\r
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
+Interfaces</FONT> \r
+<FONT CLASS="FrameItemFont">\r
+<BR>\r
+<A HREF="Annotation.html" title="interface in compbio.data.msa" target="classFrame"><I>Annotation</I></A>\r
+<BR>\r
+<A HREF="JABAService.html" title="interface in compbio.data.msa" target="classFrame"><I>JABAService</I></A>\r
+<BR>\r
+<A HREF="JManagement.html" title="interface in compbio.data.msa" target="classFrame"><I>JManagement</I></A>\r
+<BR>\r
+<A HREF="Metadata.html" title="interface in compbio.data.msa" target="classFrame"><I>Metadata</I></A>\r
+<BR>\r
+<A HREF="MsaWS.html" title="interface in compbio.data.msa" target="classFrame"><I>MsaWS</I></A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+compbio.data.msa\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="compbio.data.msa";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV PACKAGE \r
+ <A HREF="../../../compbio/data/sequence/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/package-summary.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<H2>\r
+Package compbio.data.msa\r
+</H2>\r
+Web Service interfaces for JAva Bioinformatics Analysis Web Services.\r
+<P>\r
+<B>See:</B>\r
+<BR>\r
+ <A HREF="#package_description"><B>Description</B></A>\r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Interface Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa">Annotation<T></A></B></TD>\r
+<TD>Interface for tools that results to one or more annotation to sequence(s)</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></B></TD>\r
+<TD>This is a marker interface, contains no methods</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata<T></A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS<T></A></B></TD>\r
+<TD>Multiple Sequence Alignment (MSA) Web Services Interface</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+\r
+<P>\r
+<A NAME="package_description"><!-- --></A><H2>\r
+Package compbio.data.msa Description\r
+</H2>\r
+\r
+<P>\r
+Web Service interfaces for JAva Bioinformatics Analysis Web Services.\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 April 2010</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>Peter Troshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV PACKAGE \r
+ <A HREF="../../../compbio/data/sequence/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/package-summary.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+compbio.data.msa Class Hierarchy\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="compbio.data.msa Class Hierarchy";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ <A HREF="../../../compbio/data/sequence/package-tree.html"><B>NEXT</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/package-tree.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+Hierarchy For Package compbio.data.msa\r
+</H2>\r
+</CENTER>\r
+<DL>\r
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../overview-tree.html">All Packages</A></DL>\r
+<HR>\r
+<H2>\r
+Interface Hierarchy\r
+</H2>\r
+<UL>\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><B>JABAService</B></A><UL>\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="../../../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><B>Annotation</B></A><T> (also extends compbio.data.msa.<A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>, compbio.data.msa.<A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T>)\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A><T> (also extends compbio.data.msa.<A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>, compbio.data.msa.<A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T>)\r
+</UL>\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><B>JManagement</B></A><UL>\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="../../../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><B>Annotation</B></A><T> (also extends compbio.data.msa.<A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, compbio.data.msa.<A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T>)\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A><T> (also extends compbio.data.msa.<A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, compbio.data.msa.<A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T>)\r
+</UL>\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><B>Metadata</B></A><T><UL>\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="../../../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><B>Annotation</B></A><T> (also extends compbio.data.msa.<A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, compbio.data.msa.<A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>)\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A><T> (also extends compbio.data.msa.<A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, compbio.data.msa.<A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>)\r
+</UL>\r
+</UL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ <A HREF="../../../compbio/data/sequence/package-tree.html"><B>NEXT</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/package-tree.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Package compbio.data.msa\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Package compbio.data.msa";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/package-use.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Package<br>compbio.data.msa</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.ws.client"><B>compbio.ws.client</B></A></TD>\r
+<TD>A command line client and web services testing client for
+ JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Classes in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> used by <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/msa/class-use/JABAService.html#compbio.data.msa"><B>JABAService</B></A></B>\r
+\r
+<BR>\r
+ This is a marker interface, contains no methods</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/msa/class-use/JManagement.html#compbio.data.msa"><B>JManagement</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/msa/class-use/Metadata.html#compbio.data.msa"><B>Metadata</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.ws.client"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Classes in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> used by <A HREF="../../../compbio/ws/client/package-summary.html">compbio.ws.client</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/msa/class-use/JABAService.html#compbio.ws.client"><B>JABAService</B></A></B>\r
+\r
+<BR>\r
+ This is a marker interface, contains no methods</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+Alignment\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Alignment";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Alignment.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV CLASS \r
+ <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/Alignment.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Alignment.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
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+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.sequence</FONT>\r
+<BR>\r
+Class Alignment</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.Alignment</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE><FONT SIZE="-1">@Immutable\r
+</FONT>public final class <B>Alignment</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+Multiple sequence alignment.
+
+ Does not give any guarantees on the content of individual FastaSequece
+ records. It does not guarantee neither the uniqueness of the names of
+ sequences nor it guarantees the uniqueness of the sequences.\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 September 2009</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+<DT><B>See Also:</B><DD><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><CODE>FastaSequence</CODE></A>, \r
+<A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><CODE>AlignmentMetadata</CODE></A></DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> metadata)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,\r
+ char gapchar)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
+\r
+<BR>\r
+ Please note that this implementation does not take the order of sequences
+ into account!</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getMetadata()">getMetadata</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getSequences()">getSequences</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getSize()">getSize</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#hashCode()">hashCode</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#toString()">toString</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="Alignment(java.util.List, compbio.data.sequence.Program, char)"><!-- --></A><H3>\r
+Alignment</H3>\r
+<PRE>\r
+public <B>Alignment</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,\r
+ char gapchar)</PRE>\r
+<DL>\r
+<DL>\r
+<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - <DD><CODE>program</CODE> - <DD><CODE>gapchar</CODE> - </DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)"><!-- --></A><H3>\r
+Alignment</H3>\r
+<PRE>\r
+public <B>Alignment</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> metadata)</PRE>\r
+<DL>\r
+<DL>\r
+<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - <DD><CODE>metadata</CODE> - </DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="getSequences()"><!-- --></A><H3>\r
+getSequences</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> <B>getSequences</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>list of FastaSequence records</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getSize()"><!-- --></A><H3>\r
+getSize</H3>\r
+<PRE>\r
+public int <B>getSize</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>a number of sequence in the alignment</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getMetadata()"><!-- --></A><H3>\r
+getMetadata</H3>\r
+<PRE>\r
+public <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> <B>getMetadata</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>AlignmentMetadata object</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toString()"><!-- --></A><H3>\r
+toString</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="hashCode()"><!-- --></A><H3>\r
+hashCode</H3>\r
+<PRE>\r
+public int <B>hashCode</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
+equals</H3>\r
+<PRE>\r
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
+<DL>\r
+<DD>Please note that this implementation does not take the order of sequences
+ into account!\r
+<P>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Alignment.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV CLASS \r
+ <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/Alignment.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Alignment.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+AlignmentMetadata\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="AlignmentMetadata";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/AlignmentMetadata.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/AlignmentMetadata.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="AlignmentMetadata.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.sequence</FONT>\r
+<BR>\r
+Class AlignmentMetadata</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.AlignmentMetadata</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE><FONT SIZE="-1">@Immutable\r
+</FONT>public class <B>AlignmentMetadata</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+Alignment metadata e.g. method/program being used to generate the alignment
+ and its parameters\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 September 2009</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html#AlignmentMetadata(compbio.data.sequence.Program, char)">AlignmentMetadata</A></B>(<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,\r
+ char gapchar)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> char</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html#getGapchar()">getGapchar</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html#getProgram()">getProgram</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html#hashCode()">hashCode</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="AlignmentMetadata(compbio.data.sequence.Program, char)"><!-- --></A><H3>\r
+AlignmentMetadata</H3>\r
+<PRE>\r
+public <B>AlignmentMetadata</B>(<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,\r
+ char gapchar)</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="getProgram()"><!-- --></A><H3>\r
+getProgram</H3>\r
+<PRE>\r
+public <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>getProgram</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getGapchar()"><!-- --></A><H3>\r
+getGapchar</H3>\r
+<PRE>\r
+public char <B>getGapchar</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
+equals</H3>\r
+<PRE>\r
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="hashCode()"><!-- --></A><H3>\r
+hashCode</H3>\r
+<PRE>\r
+public int <B>hashCode</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/AlignmentMetadata.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/AlignmentMetadata.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="AlignmentMetadata.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
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+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
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+</FONT></TD>\r
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+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+AnnotatedSequence\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="AnnotatedSequence";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/AnnotatedSequence.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+ <A HREF="AnnotatedSequence.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
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+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.sequence</FONT>\r
+<BR>\r
+Class AnnotatedSequence</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">compbio.data.sequence.FastaSequence</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.AnnotatedSequence</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>AnnotatedSequence</B><DT>extends <A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html#AnnotatedSequence(compbio.data.sequence.FastaSequence, float[])">AnnotatedSequence</A></B>(<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> fsequence,\r
+ float[] annotation)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html#AnnotatedSequence(java.lang.String, java.lang.String, float[])">AnnotatedSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> id,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence,\r
+ float[] annotation)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> float[]</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html#getAnnotation()">getAnnotation</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html#hashCode()">hashCode</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html#toString()">toString</A></B>()</CODE>\r
+\r
+<BR>\r
+ Same as oneLineFasta</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_compbio.data.sequence.FastaSequence"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class compbio.data.sequence.<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)">countMatchesInSequence</A>, <A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)">getFormatedSequence</A>, <A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormattedFasta()">getFormattedFasta</A>, <A HREF="../../../compbio/data/sequence/FastaSequence.html#getId()">getId</A>, <A HREF="../../../compbio/data/sequence/FastaSequence.html#getLength()">getLength</A>, <A HREF="../../../compbio/data/sequence/FastaSequence.html#getOnelineFasta()">getOnelineFasta</A>, <A HREF="../../../compbio/data/sequence/FastaSequence.html#getSequence()">getSequence</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="AnnotatedSequence(java.lang.String, java.lang.String, float[])"><!-- --></A><H3>\r
+AnnotatedSequence</H3>\r
+<PRE>\r
+public <B>AnnotatedSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> id,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence,\r
+ float[] annotation)</PRE>\r
+<DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="AnnotatedSequence(compbio.data.sequence.FastaSequence, float[])"><!-- --></A><H3>\r
+AnnotatedSequence</H3>\r
+<PRE>\r
+public <B>AnnotatedSequence</B>(<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> fsequence,\r
+ float[] annotation)</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="getAnnotation()"><!-- --></A><H3>\r
+getAnnotation</H3>\r
+<PRE>\r
+public float[] <B>getAnnotation</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="hashCode()"><!-- --></A><H3>\r
+hashCode</H3>\r
+<PRE>\r
+public int <B>hashCode</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html#hashCode()">hashCode</A></CODE> in class <CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
+equals</H3>\r
+<PRE>\r
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)">equals</A></CODE> in class <CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toString()"><!-- --></A><H3>\r
+toString</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
+<DL>\r
+<DD><B>Description copied from class: <CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html#toString()">FastaSequence</A></CODE></B></DD>\r
+<DD>Same as oneLineFasta\r
+<P>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html#toString()">toString</A></CODE> in class <CODE><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/AnnotatedSequence.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/AnnotatedSequence.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="AnnotatedSequence.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
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+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+ClustalAlignmentUtil\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="ClustalAlignmentUtil";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClustalAlignmentUtil.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/ClustalAlignmentUtil.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ClustalAlignmentUtil.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
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+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.sequence</FONT>\r
+<BR>\r
+Class ClustalAlignmentUtil</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.ClustalAlignmentUtil</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public final class <B>ClustalAlignmentUtil</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+Tools to read and write clustal formated files\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 September 2009</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>Petr Troshin based on jimp class</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+<!-- =========== FIELD SUMMARY =========== -->\r
+\r
+<A NAME="field_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Field Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static char</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</A></B></CODE>\r
+\r
+<BR>\r
+ Dash char to be used as gap char in the alignments</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#ClustalAlignmentUtil()">ClustalAlignmentUtil</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)">isValidClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> input)</CODE>\r
+\r
+<BR>\r
+ Please note this method closes the input stream provided as a parameter</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> file)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> instream)</CODE>\r
+\r
+<BR>\r
+ Read Clustal formatted alignment.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)">writeClustalAlignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outStream,\r
+ <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> alignment)</CODE>\r
+\r
+<BR>\r
+ Write Clustal formatted alignment Limitations: does not record the
+ consensus.</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ FIELD DETAIL =========== -->\r
+\r
+<A NAME="field_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Field Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="gapchar"><!-- --></A><H3>\r
+gapchar</H3>\r
+<PRE>\r
+public static final char <B>gapchar</B></PRE>\r
+<DL>\r
+<DD>Dash char to be used as gap char in the alignments\r
+<P>\r
+<DL>\r
+<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.data.sequence.ClustalAlignmentUtil.gapchar">Constant Field Values</A></DL>\r
+</DL>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="ClustalAlignmentUtil()"><!-- --></A><H3>\r
+ClustalAlignmentUtil</H3>\r
+<PRE>\r
+public <B>ClustalAlignmentUtil</B>()</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="readClustalFile(java.io.InputStream)"><!-- --></A><H3>\r
+readClustalFile</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> instream)\r
+ throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A>,\r
+ <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></PRE>\r
+<DL>\r
+<DD>Read Clustal formatted alignment. Limitations: Does not read consensus
+
+ Sequence names as well as the sequences are not guaranteed to be unique!\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE>{@link</CODE> - IOException}\r
+<DD><CODE>{@link</CODE> - UnknownFileFormatException}\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE>\r
+<DD><CODE><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="isValidClustalFile(java.io.InputStream)"><!-- --></A><H3>\r
+isValidClustalFile</H3>\r
+<PRE>\r
+public static boolean <B>isValidClustalFile</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> input)</PRE>\r
+<DL>\r
+<DD>Please note this method closes the input stream provided as a parameter\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>input</CODE> - \r
+<DT><B>Returns:</B><DD>true if the file is recognised as Clustal formatted alignment,
+ false otherwise</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)"><!-- --></A><H3>\r
+writeClustalAlignment</H3>\r
+<PRE>\r
+public static void <B>writeClustalAlignment</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outStream,\r
+ <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> alignment)\r
+ throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
+<DL>\r
+<DD>Write Clustal formatted alignment Limitations: does not record the
+ consensus. Potential bug - records 60 chars length alignment where
+ Clustal would have recorded 50 chars.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>outStream</CODE> - <DD><CODE>alignment</CODE> - \r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="readClustalFile(java.io.File)"><!-- --></A><H3>\r
+readClustalFile</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> file)\r
+ throws <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ClustalAlignmentUtil.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/ClustalAlignmentUtil.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ClustalAlignmentUtil.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+DisemblResultAnnot\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="DisemblResultAnnot";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/DisemblResultAnnot.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/DisemblResultAnnot.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="DisemblResultAnnot.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
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+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.sequence</FONT>\r
+<BR>\r
+Enum DisemblResultAnnot</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">java.lang.Enum</A><<A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A>>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.DisemblResultAnnot</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><<A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A>></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public enum <B>DisemblResultAnnot</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><<A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A>></DL>\r
+</PRE>\r
+\r
+<P>\r
+<HR>\r
+\r
+<P>\r
+<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
+\r
+<A NAME="enum_constant_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Enum Constant Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html#COILS">COILS</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html#HOTLOOPS">HOTLOOPS</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html#REM465">REM465</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html#valueOf(java.lang.String)">valueOf</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ Returns the enum constant of this type with the specified name.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A>[]</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html#values()">values</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns an array containing the constants of this enum type, in
+the order they are declared.</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#compareTo(E)" title="class or interface in java.lang">compareTo</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#getDeclaringClass()" title="class or interface in java.lang">getDeclaringClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#name()" title="class or interface in java.lang">name</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#ordinal()" title="class or interface in java.lang">ordinal</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#valueOf(java.lang.Class, java.lang.String)" title="class or interface in java.lang">valueOf</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
+\r
+<A NAME="enum_constant_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Enum Constant Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="COILS"><!-- --></A><H3>\r
+COILS</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A> <B>COILS</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="REM465"><!-- --></A><H3>\r
+REM465</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A> <B>REM465</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="HOTLOOPS"><!-- --></A><H3>\r
+HOTLOOPS</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A> <B>HOTLOOPS</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="values()"><!-- --></A><H3>\r
+values</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A>[] <B>values</B>()</PRE>\r
+<DL>\r
+<DD>Returns an array containing the constants of this enum type, in
+the order they are declared. This method may be used to iterate
+over the constants as follows:
+<pre>
+for (DisemblResultAnnot c : DisemblResultAnnot.values())
+ System.out.println(c);
+</pre>\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
+the order they are declared</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
+valueOf</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A> <B>valueOf</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</PRE>\r
+<DL>\r
+<DD>Returns the enum constant of this type with the specified name.
+The string must match <I>exactly</I> an identifier used to declare an
+enum constant in this type. (Extraneous whitespace characters are
+not permitted.)\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
+<DT><B>Returns:</B><DD>the enum constant with the specified name\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</A></CODE> - if this enum type has no constant
+with the specified name\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE> - if the argument is null</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/DisemblResultAnnot.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/DisemblResultAnnot.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="DisemblResultAnnot.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+FastaSequence\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="FastaSequence";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FastaSequence.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/FastaSequence.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="FastaSequence.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.sequence</FONT>\r
+<BR>\r
+Class FastaSequence</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.FastaSequence</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE><FONT SIZE="-1">@Immutable\r
+</FONT>public class <B>FastaSequence</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+A FASTA formatted sequence. Please note that this class does not make any
+ assumptions as to what sequence it stores e.g. it could be nucleotide,
+ protein or even gapped alignment sequence! The only guarantee it makes is
+ that the sequence does not contain white space characters e.g. spaces, new
+ lines etc\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 September 2009</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#FastaSequence(java.lang.String, java.lang.String)">FastaSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> id,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence)</CODE>\r
+\r
+<BR>\r
+ Upon construction the any whitespace characters are removed from the
+ sequence</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)">countMatchesInSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> theString,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> theRegExp)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)">getFormatedSequence</A></B>(int width)</CODE>\r
+\r
+<BR>\r
+ Format sequence per width letter in one string.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormattedFasta()">getFormattedFasta</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getId()">getId</A></B>()</CODE>\r
+\r
+<BR>\r
+ Gets the value of id</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getLength()">getLength</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getOnelineFasta()">getOnelineFasta</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getSequence()">getSequence</A></B>()</CODE>\r
+\r
+<BR>\r
+ Gets the value of sequence</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#hashCode()">hashCode</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#toString()">toString</A></B>()</CODE>\r
+\r
+<BR>\r
+ Same as oneLineFasta</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="FastaSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
+FastaSequence</H3>\r
+<PRE>\r
+public <B>FastaSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> id,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence)</PRE>\r
+<DL>\r
+<DD>Upon construction the any whitespace characters are removed from the
+ sequence\r
+<P>\r
+<DL>\r
+<DT><B>Parameters:</B><DD><CODE>id</CODE> - <DD><CODE>sequence</CODE> - </DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="getId()"><!-- --></A><H3>\r
+getId</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getId</B>()</PRE>\r
+<DL>\r
+<DD>Gets the value of id\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>the value of id</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getSequence()"><!-- --></A><H3>\r
+getSequence</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getSequence</B>()</PRE>\r
+<DL>\r
+<DD>Gets the value of sequence\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>the value of sequence</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="countMatchesInSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
+countMatchesInSequence</H3>\r
+<PRE>\r
+public static int <B>countMatchesInSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> theString,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> theRegExp)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getFormattedFasta()"><!-- --></A><H3>\r
+getFormattedFasta</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getFormattedFasta</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getOnelineFasta()"><!-- --></A><H3>\r
+getOnelineFasta</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getOnelineFasta</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>one line name, next line sequence, no matter what the sequence
+ length is</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getFormatedSequence(int)"><!-- --></A><H3>\r
+getFormatedSequence</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getFormatedSequence</B>(int width)</PRE>\r
+<DL>\r
+<DD>Format sequence per width letter in one string. Without spaces.\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>multiple line formated sequence, one line width letters length</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getLength()"><!-- --></A><H3>\r
+getLength</H3>\r
+<PRE>\r
+public int <B>getLength</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>sequence length</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toString()"><!-- --></A><H3>\r
+toString</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
+<DL>\r
+<DD>Same as oneLineFasta\r
+<P>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="hashCode()"><!-- --></A><H3>\r
+hashCode</H3>\r
+<PRE>\r
+public int <B>hashCode</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
+equals</H3>\r
+<PRE>\r
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/FastaSequence.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/FastaSequence.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="FastaSequence.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+JalviewAnnotation\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="JalviewAnnotation";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/JalviewAnnotation.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/JalviewAnnotation.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JalviewAnnotation.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.sequence</FONT>\r
+<BR>\r
+Class JalviewAnnotation</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.JalviewAnnotation</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>JalviewAnnotation</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/JalviewAnnotation.html#JalviewAnnotation()">JalviewAnnotation</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="JalviewAnnotation()"><!-- --></A><H3>\r
+JalviewAnnotation</H3>\r
+<PRE>\r
+public <B>JalviewAnnotation</B>()</PRE>\r
+<DL>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/JalviewAnnotation.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
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+</NOSCRIPT>\r
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+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+Method\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Method";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="navbar_top_firstrow"><!-- --></A>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Method.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
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+</TD>\r
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+ <SCRIPT type="text/javascript">\r
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+</NOSCRIPT>\r
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+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.sequence</FONT>\r
+<BR>\r
+Enum Method</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">java.lang.Enum</A><<A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A>>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.Method</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><<A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A>></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public enum <B>Method</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><<A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A>></DL>\r
+</PRE>\r
+\r
+<P>\r
+Enumeration listing of all the supported methods.\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Author:</B></DT>\r
+ <DD>Agnieszka Golicz & Peter Troshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
+\r
+<A NAME="enum_constant_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Enum Constant Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#ARMON">ARMON</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#GERSTEIN">GERSTEIN</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#JORES">JORES</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#KABAT">KABAT</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#KARLIN">KARLIN</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#LANDGRAF">LANDGRAF</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#MIRNY">MIRNY</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#NOT_LANCET">NOT_LANCET</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#SANDER">SANDER</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#SCHNEIDER">SCHNEIDER</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#SHENKIN">SHENKIN</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#SMERFS">SMERFS</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#TAYLOR_GAPS">TAYLOR_GAPS</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#TAYLOR_NO_GAPS">TAYLOR_NO_GAPS</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#THOMPSON">THOMPSON</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#VALDAR">VALDAR</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#WILLIAMSON">WILLIAMSON</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#ZVELIBIL">ZVELIBIL</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#getMethod(java.lang.String)">getMethod</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> meth)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#valueOf(java.lang.String)">valueOf</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ Returns the enum constant of this type with the specified name.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A>[]</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Method.html#values()">values</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns an array containing the constants of this enum type, in
+the order they are declared.</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#compareTo(E)" title="class or interface in java.lang">compareTo</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#getDeclaringClass()" title="class or interface in java.lang">getDeclaringClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#name()" title="class or interface in java.lang">name</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#ordinal()" title="class or interface in java.lang">ordinal</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#valueOf(java.lang.Class, java.lang.String)" title="class or interface in java.lang">valueOf</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
+\r
+<A NAME="enum_constant_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Enum Constant Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="KABAT"><!-- --></A><H3>\r
+KABAT</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>KABAT</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="JORES"><!-- --></A><H3>\r
+JORES</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>JORES</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="SCHNEIDER"><!-- --></A><H3>\r
+SCHNEIDER</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>SCHNEIDER</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="SHENKIN"><!-- --></A><H3>\r
+SHENKIN</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>SHENKIN</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="GERSTEIN"><!-- --></A><H3>\r
+GERSTEIN</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>GERSTEIN</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="TAYLOR_GAPS"><!-- --></A><H3>\r
+TAYLOR_GAPS</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>TAYLOR_GAPS</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="TAYLOR_NO_GAPS"><!-- --></A><H3>\r
+TAYLOR_NO_GAPS</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>TAYLOR_NO_GAPS</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="ZVELIBIL"><!-- --></A><H3>\r
+ZVELIBIL</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>ZVELIBIL</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="KARLIN"><!-- --></A><H3>\r
+KARLIN</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>KARLIN</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="ARMON"><!-- --></A><H3>\r
+ARMON</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>ARMON</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="THOMPSON"><!-- --></A><H3>\r
+THOMPSON</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>THOMPSON</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="NOT_LANCET"><!-- --></A><H3>\r
+NOT_LANCET</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>NOT_LANCET</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="MIRNY"><!-- --></A><H3>\r
+MIRNY</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>MIRNY</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="WILLIAMSON"><!-- --></A><H3>\r
+WILLIAMSON</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>WILLIAMSON</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="LANDGRAF"><!-- --></A><H3>\r
+LANDGRAF</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>LANDGRAF</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="SANDER"><!-- --></A><H3>\r
+SANDER</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>SANDER</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="VALDAR"><!-- --></A><H3>\r
+VALDAR</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>VALDAR</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="SMERFS"><!-- --></A><H3>\r
+SMERFS</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>SMERFS</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="values()"><!-- --></A><H3>\r
+values</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A>[] <B>values</B>()</PRE>\r
+<DL>\r
+<DD>Returns an array containing the constants of this enum type, in
+the order they are declared. This method may be used to iterate
+over the constants as follows:
+<pre>
+for (Method c : Method.values())
+ System.out.println(c);
+</pre>\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
+the order they are declared</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
+valueOf</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>valueOf</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</PRE>\r
+<DL>\r
+<DD>Returns the enum constant of this type with the specified name.
+The string must match <I>exactly</I> an identifier used to declare an
+enum constant in this type. (Extraneous whitespace characters are
+not permitted.)\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
+<DT><B>Returns:</B><DD>the enum constant with the specified name\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</A></CODE> - if this enum type has no constant
+with the specified name\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE> - if the argument is null</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getMethod(java.lang.String)"><!-- --></A><H3>\r
+getMethod</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>getMethod</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> meth)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Method.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/Method.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Method.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+MultiAnnotatedSequence\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="MultiAnnotatedSequence";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MultiAnnotatedSequence.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/MultiAnnotatedSequence.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="MultiAnnotatedSequence.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.sequence</FONT>\r
+<BR>\r
+Class MultiAnnotatedSequence<T extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><T>></H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.MultiAnnotatedSequence<T></B>\r
+</PRE>\r
+<DL>\r
+<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - enum type</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE><FONT SIZE="-1">@NotThreadSafe\r
+</FONT>public class <B>MultiAnnotatedSequence<T extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><T>></B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+TODO complete\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html#MultiAnnotatedSequence(java.lang.Class)">MultiAnnotatedSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><<A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html" title="type parameter in MultiAnnotatedSequence">T</A>> enumeration)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html#addAnnotation(T, java.util.ArrayList)">addAnnotation</A></B>(<A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html" title="type parameter in MultiAnnotatedSequence">T</A> type,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>> annotation)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html" title="type parameter in MultiAnnotatedSequence">T</A>,<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html#getAnnotations()">getAnnotations</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html#hashCode()">hashCode</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence">JalviewAnnotation</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html#toJalviewAnnotation()">toJalviewAnnotation</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html#toString()">toString</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="MultiAnnotatedSequence(java.lang.Class)"><!-- --></A><H3>\r
+MultiAnnotatedSequence</H3>\r
+<PRE>\r
+public <B>MultiAnnotatedSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><<A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html" title="type parameter in MultiAnnotatedSequence">T</A>> enumeration)</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="addAnnotation(java.lang.Enum,java.util.ArrayList)"><!-- --></A><A NAME="addAnnotation(T, java.util.ArrayList)"><!-- --></A><H3>\r
+addAnnotation</H3>\r
+<PRE>\r
+public void <B>addAnnotation</B>(<A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html" title="type parameter in MultiAnnotatedSequence">T</A> type,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>> annotation)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getAnnotations()"><!-- --></A><H3>\r
+getAnnotations</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html" title="type parameter in MultiAnnotatedSequence">T</A>,<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>>> <B>getAnnotations</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="hashCode()"><!-- --></A><H3>\r
+hashCode</H3>\r
+<PRE>\r
+public int <B>hashCode</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
+equals</H3>\r
+<PRE>\r
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toString()"><!-- --></A><H3>\r
+toString</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toJalviewAnnotation()"><!-- --></A><H3>\r
+toJalviewAnnotation</H3>\r
+<PRE>\r
+public <A HREF="../../../compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence">JalviewAnnotation</A> <B>toJalviewAnnotation</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MultiAnnotatedSequence.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/MultiAnnotatedSequence.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="MultiAnnotatedSequence.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+Program\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Program";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Program.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/Program.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Program.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.sequence</FONT>\r
+<BR>\r
+Enum Program</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">java.lang.Enum</A><<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.Program</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public enum <B>Program</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>></DL>\r
+</PRE>\r
+\r
+<P>\r
+The list of programmes that can produce alignments\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
+\r
+<A NAME="enum_constant_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Enum Constant Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#CLUSTAL">CLUSTAL</A></B></CODE>\r
+\r
+<BR>\r
+ ClustalW</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#MAFFT">MAFFT</A></B></CODE>\r
+\r
+<BR>\r
+ Mafft</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#MUSCLE">MUSCLE</A></B></CODE>\r
+\r
+<BR>\r
+ Muscle</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#Probcons">Probcons</A></B></CODE>\r
+\r
+<BR>\r
+ Probcons</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#Tcoffee">Tcoffee</A></B></CODE>\r
+\r
+<BR>\r
+ Tcoffee</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#valueOf(java.lang.String)">valueOf</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ Returns the enum constant of this type with the specified name.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>[]</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#values()">values</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns an array containing the constants of this enum type, in
+the order they are declared.</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#compareTo(E)" title="class or interface in java.lang">compareTo</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#getDeclaringClass()" title="class or interface in java.lang">getDeclaringClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#name()" title="class or interface in java.lang">name</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#ordinal()" title="class or interface in java.lang">ordinal</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#valueOf(java.lang.Class, java.lang.String)" title="class or interface in java.lang">valueOf</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
+\r
+<A NAME="enum_constant_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Enum Constant Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="CLUSTAL"><!-- --></A><H3>\r
+CLUSTAL</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>CLUSTAL</B></PRE>\r
+<DL>\r
+<DD>ClustalW\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="MAFFT"><!-- --></A><H3>\r
+MAFFT</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>MAFFT</B></PRE>\r
+<DL>\r
+<DD>Mafft\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="MUSCLE"><!-- --></A><H3>\r
+MUSCLE</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>MUSCLE</B></PRE>\r
+<DL>\r
+<DD>Muscle\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="Tcoffee"><!-- --></A><H3>\r
+Tcoffee</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>Tcoffee</B></PRE>\r
+<DL>\r
+<DD>Tcoffee\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="Probcons"><!-- --></A><H3>\r
+Probcons</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>Probcons</B></PRE>\r
+<DL>\r
+<DD>Probcons\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="values()"><!-- --></A><H3>\r
+values</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>[] <B>values</B>()</PRE>\r
+<DL>\r
+<DD>Returns an array containing the constants of this enum type, in
+the order they are declared. This method may be used to iterate
+over the constants as follows:
+<pre>
+for (Program c : Program.values())
+ System.out.println(c);
+</pre>\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
+the order they are declared</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
+valueOf</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>valueOf</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</PRE>\r
+<DL>\r
+<DD>Returns the enum constant of this type with the specified name.
+The string must match <I>exactly</I> an identifier used to declare an
+enum constant in this type. (Extraneous whitespace characters are
+not permitted.)\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
+<DT><B>Returns:</B><DD>the enum constant with the specified name\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</A></CODE> - if this enum type has no constant
+with the specified name\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE> - if the argument is null</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Program.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/Program.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Program.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+Score\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Score";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Score.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/Score.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Score.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.sequence</FONT>\r
+<BR>\r
+Class Score</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.Score</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE><FONT SIZE="-1">@Immutable\r
+</FONT>public class <B>Score</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#Score(compbio.data.sequence.Method, java.util.List)">Score</A></B>(<A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> method,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>> scores)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#getMethod()">getMethod</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#getScores()">getScores</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#hashCode()">hashCode</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#toString()">toString</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="Score(compbio.data.sequence.Method, java.util.List)"><!-- --></A><H3>\r
+Score</H3>\r
+<PRE>\r
+public <B>Score</B>(<A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> method,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>> scores)</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="getMethod()"><!-- --></A><H3>\r
+getMethod</H3>\r
+<PRE>\r
+public <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> <B>getMethod</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getScores()"><!-- --></A><H3>\r
+getScores</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>> <B>getScores</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toString()"><!-- --></A><H3>\r
+toString</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="hashCode()"><!-- --></A><H3>\r
+hashCode</H3>\r
+<PRE>\r
+public int <B>hashCode</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
+equals</H3>\r
+<PRE>\r
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Score.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/Score.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Score.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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+<TITLE>\r
+SequenceUtil\r
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/SequenceUtil.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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+ <A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
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+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.sequence</FONT>\r
+<BR>\r
+Class SequenceUtil</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.SequenceUtil</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public final class <B>SequenceUtil</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+Utility class for operations on sequences\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>Petr Troshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+<!-- =========== FIELD SUMMARY =========== -->\r
+\r
+<A NAME="field_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Field Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AA">AA</A></B></CODE>\r
+\r
+<BR>\r
+ Valid Amino acids</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA">AMBIGUOUS_AA</A></B></CODE>\r
+\r
+<BR>\r
+ Same as AA pattern but with two additional letters - XU</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE">AMBIGUOUS_NUCLEOTIDE</A></B></CODE>\r
+\r
+<BR>\r
+ Ambiguous nucleotide</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#DIGIT">DIGIT</A></B></CODE>\r
+\r
+<BR>\r
+ A digit</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NON_AA">NON_AA</A></B></CODE>\r
+\r
+<BR>\r
+ inversion of AA pattern</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NON_NUCLEOTIDE">NON_NUCLEOTIDE</A></B></CODE>\r
+\r
+<BR>\r
+ Non nucleotide</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NONWORD">NONWORD</A></B></CODE>\r
+\r
+<BR>\r
+ Non word</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NUCLEOTIDE">NUCLEOTIDE</A></B></CODE>\r
+\r
+<BR>\r
+ Nucleotides a, t, g, c, u</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#WHITE_SPACE">WHITE_SPACE</A></B></CODE>\r
+\r
+<BR>\r
+ A whitespace character: [\t\n\x0B\f\r]</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#cleanSequence(java.lang.String)">cleanSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence)</CODE>\r
+\r
+<BR>\r
+ Removes all whitespace chars in the sequence string</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#closeSilently(java.util.logging.Logger, java.io.Closeable)">closeSilently</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/logging/Logger.html?is-external=true" title="class or interface in java.util.logging">Logger</A> log,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/io/Closeable.html?is-external=true" title="class or interface in java.io">Closeable</A> stream)</CODE>\r
+\r
+<BR>\r
+ Closes the Closable and logs the exception if any</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#deepCleanSequence(java.lang.String)">deepCleanSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence)</CODE>\r
+\r
+<BR>\r
+ Removes all special characters and digits as well as whitespace chars
+ from the sequence</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)">isAmbiguosProtein</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence)</CODE>\r
+\r
+<BR>\r
+ Check whether the sequence confirms to amboguous protein sequence</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)">isNonAmbNucleotideSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence)</CODE>\r
+\r
+<BR>\r
+ Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
+ (!) - B char</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)">isNucleotideSequence</A></B>(<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> s)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)">isProteinSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashSet.html?is-external=true" title="class or interface in java.util">HashSet</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#readAAConResults(java.io.InputStream)">readAAConResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> results)</CODE>\r
+\r
+<BR>\r
+ Read AACon result with no alignment files.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)">readFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> inStream)</CODE>\r
+\r
+<BR>\r
+ Reads fasta sequences from inStream into the list of FastaSequence
+ objects</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.File)">readJRonn</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> result)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.InputStream)">readJRonn</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> inStream)</CODE>\r
+\r
+<BR>\r
+ Reader for JRonn horizontal file format</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)">writeFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> os,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>\r
+\r
+<BR>\r
+ Writes FastaSequence in the file, each sequence will take one line only</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)">writeFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outstream,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ int width)</CODE>\r
+\r
+<BR>\r
+ Writes list of FastaSequeces into the outstream formatting the sequence
+ so that it contains width chars on each line</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)">writeFastaKeepTheStream</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outstream,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ int width)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ FIELD DETAIL =========== -->\r
+\r
+<A NAME="field_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Field Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="WHITE_SPACE"><!-- --></A><H3>\r
+WHITE_SPACE</H3>\r
+<PRE>\r
+public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>WHITE_SPACE</B></PRE>\r
+<DL>\r
+<DD>A whitespace character: [\t\n\x0B\f\r]\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="DIGIT"><!-- --></A><H3>\r
+DIGIT</H3>\r
+<PRE>\r
+public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>DIGIT</B></PRE>\r
+<DL>\r
+<DD>A digit\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="NONWORD"><!-- --></A><H3>\r
+NONWORD</H3>\r
+<PRE>\r
+public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>NONWORD</B></PRE>\r
+<DL>\r
+<DD>Non word\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="AA"><!-- --></A><H3>\r
+AA</H3>\r
+<PRE>\r
+public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>AA</B></PRE>\r
+<DL>\r
+<DD>Valid Amino acids\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="NON_AA"><!-- --></A><H3>\r
+NON_AA</H3>\r
+<PRE>\r
+public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>NON_AA</B></PRE>\r
+<DL>\r
+<DD>inversion of AA pattern\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="AMBIGUOUS_AA"><!-- --></A><H3>\r
+AMBIGUOUS_AA</H3>\r
+<PRE>\r
+public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>AMBIGUOUS_AA</B></PRE>\r
+<DL>\r
+<DD>Same as AA pattern but with two additional letters - XU\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="NUCLEOTIDE"><!-- --></A><H3>\r
+NUCLEOTIDE</H3>\r
+<PRE>\r
+public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>NUCLEOTIDE</B></PRE>\r
+<DL>\r
+<DD>Nucleotides a, t, g, c, u\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="AMBIGUOUS_NUCLEOTIDE"><!-- --></A><H3>\r
+AMBIGUOUS_NUCLEOTIDE</H3>\r
+<PRE>\r
+public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>AMBIGUOUS_NUCLEOTIDE</B></PRE>\r
+<DL>\r
+<DD>Ambiguous nucleotide\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="NON_NUCLEOTIDE"><!-- --></A><H3>\r
+NON_NUCLEOTIDE</H3>\r
+<PRE>\r
+public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>NON_NUCLEOTIDE</B></PRE>\r
+<DL>\r
+<DD>Non nucleotide\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="isNucleotideSequence(compbio.data.sequence.FastaSequence)"><!-- --></A><H3>\r
+isNucleotideSequence</H3>\r
+<PRE>\r
+public static boolean <B>isNucleotideSequence</B>(<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> s)</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>true is the sequence contains only letters a,c, t, g, u</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="isNonAmbNucleotideSequence(java.lang.String)"><!-- --></A><H3>\r
+isNonAmbNucleotideSequence</H3>\r
+<PRE>\r
+public static boolean <B>isNonAmbNucleotideSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence)</PRE>\r
+<DL>\r
+<DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
+ (!) - B char\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="cleanSequence(java.lang.String)"><!-- --></A><H3>\r
+cleanSequence</H3>\r
+<PRE>\r
+public static <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>cleanSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence)</PRE>\r
+<DL>\r
+<DD>Removes all whitespace chars in the sequence string\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
+<DT><B>Returns:</B><DD>cleaned up sequence</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="deepCleanSequence(java.lang.String)"><!-- --></A><H3>\r
+deepCleanSequence</H3>\r
+<PRE>\r
+public static <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>deepCleanSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence)</PRE>\r
+<DL>\r
+<DD>Removes all special characters and digits as well as whitespace chars
+ from the sequence\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
+<DT><B>Returns:</B><DD>cleaned up sequence</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="isProteinSequence(java.lang.String)"><!-- --></A><H3>\r
+isProteinSequence</H3>\r
+<PRE>\r
+public static boolean <B>isProteinSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
+<DT><B>Returns:</B><DD>true is the sequence is a protein sequence, false overwise</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="isAmbiguosProtein(java.lang.String)"><!-- --></A><H3>\r
+isAmbiguosProtein</H3>\r
+<PRE>\r
+public static boolean <B>isAmbiguosProtein</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence)</PRE>\r
+<DL>\r
+<DD>Check whether the sequence confirms to amboguous protein sequence\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
+<DT><B>Returns:</B><DD>return true only if the sequence if ambiguous protein sequence
+ Return false otherwise. e.g. if the sequence is non-ambiguous
+ protein or DNA</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="writeFasta(java.io.OutputStream, java.util.List, int)"><!-- --></A><H3>\r
+writeFasta</H3>\r
+<PRE>\r
+public static void <B>writeFasta</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outstream,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ int width)\r
+ throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
+<DL>\r
+<DD>Writes list of FastaSequeces into the outstream formatting the sequence
+ so that it contains width chars on each line\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>outstream</CODE> - <DD><CODE>sequences</CODE> - <DD><CODE>width</CODE> - - the maximum number of characters to write in one line\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)"><!-- --></A><H3>\r
+writeFastaKeepTheStream</H3>\r
+<PRE>\r
+public static void <B>writeFastaKeepTheStream</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outstream,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ int width)\r
+ throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="readFasta(java.io.InputStream)"><!-- --></A><H3>\r
+readFasta</H3>\r
+<PRE>\r
+public static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> <B>readFasta</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> inStream)\r
+ throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
+<DL>\r
+<DD>Reads fasta sequences from inStream into the list of FastaSequence
+ objects\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>inStream</CODE> - from\r
+<DT><B>Returns:</B><DD>list of FastaSequence objects\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="writeFasta(java.io.OutputStream, java.util.List)"><!-- --></A><H3>\r
+writeFasta</H3>\r
+<PRE>\r
+public static void <B>writeFasta</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> os,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)\r
+ throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
+<DL>\r
+<DD>Writes FastaSequence in the file, each sequence will take one line only\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>os</CODE> - <DD><CODE>sequences</CODE> - \r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="readJRonn(java.io.File)"><!-- --></A><H3>\r
+readJRonn</H3>\r
+<PRE>\r
+public static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>> <B>readJRonn</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> result)\r
+ throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A>,\r
+ <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE>\r
+<DD><CODE><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="readJRonn(java.io.InputStream)"><!-- --></A><H3>\r
+readJRonn</H3>\r
+<PRE>\r
+public static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>> <B>readJRonn</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> inStream)\r
+ throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A>,\r
+ <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></PRE>\r
+<DL>\r
+<DD>Reader for JRonn horizontal file format
+
+ <pre>
+ >Foobar M G D T T A G 0.48 0.42
+ 0.42 0.48 0.52 0.53 0.54
+
+ <pre>
+ Where all values are tab delimited\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>inStream</CODE> - the InputStream connected to the JRonn output file\r
+<DT><B>Returns:</B><DD>List of <A HREF="../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence"><CODE>AnnotatedSequence</CODE></A> objects\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE> - is thrown if the inStream has problems accessing the data\r
+<DD><CODE><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE> - is thrown if the inStream represents an unknown source of
+ data, i.e. not a JRonn output</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="closeSilently(java.util.logging.Logger, java.io.Closeable)"><!-- --></A><H3>\r
+closeSilently</H3>\r
+<PRE>\r
+public static final void <B>closeSilently</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/logging/Logger.html?is-external=true" title="class or interface in java.util.logging">Logger</A> log,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/io/Closeable.html?is-external=true" title="class or interface in java.io">Closeable</A> stream)</PRE>\r
+<DL>\r
+<DD>Closes the Closable and logs the exception if any\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>log</CODE> - <DD><CODE>stream</CODE> - </DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="readAAConResults(java.io.InputStream)"><!-- --></A><H3>\r
+readAAConResults</H3>\r
+<PRE>\r
+public static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashSet.html?is-external=true" title="class or interface in java.util">HashSet</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> <B>readAAConResults</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> results)</PRE>\r
+<DL>\r
+<DD>Read AACon result with no alignment files. This method leaves incoming
+ the InputStream results open!\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>results</CODE> - output file of AAConservation\r
+<DT><B>Returns:</B><DD>Map with keys <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence"><CODE>Method</CODE></A> -> float[]</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/SequenceUtil.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
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+ <A HREF="../../../index.html?compbio/data/sequence/SequenceUtil.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="SequenceUtil.html" target="_top"><B>NO FRAMES</B></A> \r
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+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
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+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+UnknownFileFormatException\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="UnknownFileFormatException";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
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+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/UnknownFileFormatException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
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+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
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+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.sequence</FONT>\r
+<BR>\r
+Class UnknownFileFormatException</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">java.lang.Throwable</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">java.lang.Exception</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.UnknownFileFormatException</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>UnknownFileFormatException</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>See Also:</B><DD><A HREF="../../../serialized-form.html#compbio.data.sequence.UnknownFileFormatException">Serialized Form</A></DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException()">UnknownFileFormatException</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.io.File, java.lang.Throwable)">UnknownFileFormatException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> file,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.lang.String)">UnknownFileFormatException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.lang.String, java.lang.Throwable)">UnknownFileFormatException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.lang.Throwable)">UnknownFileFormatException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#fillInStackTrace()" title="class or interface in java.lang">fillInStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getCause()" title="class or interface in java.lang">getCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getLocalizedMessage()" title="class or interface in java.lang">getLocalizedMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getMessage()" title="class or interface in java.lang">getMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getStackTrace()" title="class or interface in java.lang">getStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#initCause(java.lang.Throwable)" title="class or interface in java.lang">initCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace()" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintStream)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintWriter)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#setStackTrace(java.lang.StackTraceElement[])" title="class or interface in java.lang">setStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="UnknownFileFormatException()"><!-- --></A><H3>\r
+UnknownFileFormatException</H3>\r
+<PRE>\r
+public <B>UnknownFileFormatException</B>()</PRE>\r
+<DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="UnknownFileFormatException(java.io.File, java.lang.Throwable)"><!-- --></A><H3>\r
+UnknownFileFormatException</H3>\r
+<PRE>\r
+public <B>UnknownFileFormatException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> file,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
+<DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="UnknownFileFormatException(java.lang.String, java.lang.Throwable)"><!-- --></A><H3>\r
+UnknownFileFormatException</H3>\r
+<PRE>\r
+public <B>UnknownFileFormatException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
+<DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="UnknownFileFormatException(java.lang.String)"><!-- --></A><H3>\r
+UnknownFileFormatException</H3>\r
+<PRE>\r
+public <B>UnknownFileFormatException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message)</PRE>\r
+<DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="UnknownFileFormatException(java.lang.Throwable)"><!-- --></A><H3>\r
+UnknownFileFormatException</H3>\r
+<PRE>\r
+public <B>UnknownFileFormatException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
+<DL>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/UnknownFileFormatException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ NEXT CLASS</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/UnknownFileFormatException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="UnknownFileFormatException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.data.sequence.Alignment\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.data.sequence.Alignment";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useAlignment.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Alignment.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.data.sequence.Alignment</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
+<TD>A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</CODE>\r
+\r
+<BR>\r
+ Return the result of the job.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.sequence"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
+<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> file)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
+<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> instream)</CODE>\r
+\r
+<BR>\r
+ Read Clustal formatted alignment.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static void</CODE></FONT></TD>\r
+<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)">writeClustalAlignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outStream,\r
+ <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> alignment)</CODE>\r
+\r
+<BR>\r
+ Write Clustal formatted alignment Limitations: does not record the
+ consensus.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useAlignment.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Alignment.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.data.sequence.AlignmentMetadata\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.data.sequence.AlignmentMetadata";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useAlignmentMetadata.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="AlignmentMetadata.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.data.sequence.AlignmentMetadata</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
+<TD>A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.sequence"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></CODE></FONT></TD>\r
+<TD><CODE><B>Alignment.</B><B><A HREF="../../../../compbio/data/sequence/Alignment.html#getMetadata()">getMetadata</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> metadata)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useAlignmentMetadata.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="AlignmentMetadata.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.data.sequence.AnnotatedSequence\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.data.sequence.AnnotatedSequence";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useAnnotatedSequence.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="AnnotatedSequence.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.data.sequence.AnnotatedSequence</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
+<TD>A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.sequence"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return types with arguments of type <A HREF="../../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>></CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.File)">readJRonn</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> result)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>></CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.InputStream)">readJRonn</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> inStream)</CODE>\r
+\r
+<BR>\r
+ Reader for JRonn horizontal file format</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useAnnotatedSequence.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="AnnotatedSequence.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.data.sequence.ClustalAlignmentUtil\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.data.sequence.ClustalAlignmentUtil";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useClustalAlignmentUtil.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ClustalAlignmentUtil.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.data.sequence.ClustalAlignmentUtil</B></H2>\r
+</CENTER>\r
+No usage of compbio.data.sequence.ClustalAlignmentUtil\r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useClustalAlignmentUtil.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ClustalAlignmentUtil.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.data.sequence.DisemblResultAnnot\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.data.sequence.DisemblResultAnnot";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useDisemblResultAnnot.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="DisemblResultAnnot.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.data.sequence.DisemblResultAnnot</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
+<TD>A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.sequence"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A></CODE></FONT></TD>\r
+<TD><CODE><B>DisemblResultAnnot.</B><B><A HREF="../../../../compbio/data/sequence/DisemblResultAnnot.html#valueOf(java.lang.String)">valueOf</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ Returns the enum constant of this type with the specified name.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A>[]</CODE></FONT></TD>\r
+<TD><CODE><B>DisemblResultAnnot.</B><B><A HREF="../../../../compbio/data/sequence/DisemblResultAnnot.html#values()">values</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns an array containing the constants of this enum type, in
+the order they are declared.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
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+ <A HREF="DisemblResultAnnot.html" target="_top"><B>NO FRAMES</B></A> \r
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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+<HTML>\r
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+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.data.sequence.FastaSequence\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
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+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.data.sequence.FastaSequence";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
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+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
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+ <A HREF="FastaSequence.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
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+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.data.sequence.FastaSequence</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
+<TD>A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with default settings.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../../compbio/data/msa/Annotation.html#analize(java.util.List)">analize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>>> options)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with options.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../../compbio/data/msa/Annotation.html#customAnalize(java.util.List, java.util.List)">customAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>>> options)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences according to custom settings defined in options
+ list.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> preset)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with preset.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../../compbio/data/msa/Annotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>> preset)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences according to the preset settings.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.sequence"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> class</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return types with arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></FONT></TD>\r
+<TD><CODE><B>Alignment.</B><B><A HREF="../../../../compbio/data/sequence/Alignment.html#getSequences()">getSequences</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)">readFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> inStream)</CODE>\r
+\r
+<BR>\r
+ Reads fasta sequences from inStream into the list of FastaSequence
+ objects</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static boolean</CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)">isNucleotideSequence</A></B>(<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> s)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static void</CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)">writeFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> os,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>\r
+\r
+<BR>\r
+ Writes FastaSequence in the file, each sequence will take one line only</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static void</CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)">writeFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outstream,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ int width)</CODE>\r
+\r
+<BR>\r
+ Writes list of FastaSequeces into the outstream formatting the sequence
+ so that it contains width chars on each line</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static void</CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)">writeFastaKeepTheStream</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outstream,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ int width)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../../compbio/data/sequence/AnnotatedSequence.html#AnnotatedSequence(compbio.data.sequence.FastaSequence, float[])">AnnotatedSequence</A></B>(<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> fsequence,\r
+ float[] annotation)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Constructor parameters in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> metadata)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,\r
+ char gapchar)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static int</CODE></FONT></TD>\r
+<TD><CODE><B>Limit.</B><B><A HREF="../../../../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)">getAvgSequenceLength</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> data)</CODE>\r
+\r
+<BR>\r
+ Calculates an average sequence length of the dataset</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B>Limit.</B><B><A HREF="../../../../compbio/metadata/Limit.html#isExceeded(java.util.List)">isExceeded</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> data)</CODE>\r
+\r
+<BR>\r
+ Checks if the number of sequences or their average length in the dataset
+ exceeds this limit.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
+<TD><CODE><B>LimitExceededException.</B><B><A HREF="../../../../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)">newLimitExceeded</A></B>(<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><?> limit,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> seqs)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+ <A HREF="FastaSequence.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.data.sequence.JalviewAnnotation\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.data.sequence.JalviewAnnotation";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useJalviewAnnotation.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JalviewAnnotation.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.data.sequence.JalviewAnnotation</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../../compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence">JalviewAnnotation</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
+<TD>A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.sequence"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence">JalviewAnnotation</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence">JalviewAnnotation</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../../compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence">JalviewAnnotation</A></CODE></FONT></TD>\r
+<TD><CODE><B>MultiAnnotatedSequence.</B><B><A HREF="../../../../compbio/data/sequence/MultiAnnotatedSequence.html#toJalviewAnnotation()">toJalviewAnnotation</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useJalviewAnnotation.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JalviewAnnotation.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.data.sequence.Method\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.data.sequence.Method";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useMethod.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Method.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.data.sequence.Method</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
+<TD>A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.sequence"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A></CODE></FONT></TD>\r
+<TD><CODE><B>Score.</B><B><A HREF="../../../../compbio/data/sequence/Score.html#getMethod()">getMethod</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A></CODE></FONT></TD>\r
+<TD><CODE><B>Method.</B><B><A HREF="../../../../compbio/data/sequence/Method.html#getMethod(java.lang.String)">getMethod</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> meth)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A></CODE></FONT></TD>\r
+<TD><CODE><B>Method.</B><B><A HREF="../../../../compbio/data/sequence/Method.html#valueOf(java.lang.String)">valueOf</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ Returns the enum constant of this type with the specified name.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A>[]</CODE></FONT></TD>\r
+<TD><CODE><B>Method.</B><B><A HREF="../../../../compbio/data/sequence/Method.html#values()">values</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns an array containing the constants of this enum type, in
+the order they are declared.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../../compbio/data/sequence/Score.html#Score(compbio.data.sequence.Method, java.util.List)">Score</A></B>(<A HREF="../../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> method,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>> scores)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useMethod.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Method.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.data.sequence.MultiAnnotatedSequence\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.data.sequence.MultiAnnotatedSequence";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useMultiAnnotatedSequence.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="MultiAnnotatedSequence.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.data.sequence.MultiAnnotatedSequence</B></H2>\r
+</CENTER>\r
+No usage of compbio.data.sequence.MultiAnnotatedSequence\r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useMultiAnnotatedSequence.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="MultiAnnotatedSequence.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.data.sequence.Program\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.data.sequence.Program";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useProgram.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Program.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.data.sequence.Program</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
+<TD>A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.sequence"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></CODE></FONT></TD>\r
+<TD><CODE><B>AlignmentMetadata.</B><B><A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html#getProgram()">getProgram</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></CODE></FONT></TD>\r
+<TD><CODE><B>Program.</B><B><A HREF="../../../../compbio/data/sequence/Program.html#valueOf(java.lang.String)">valueOf</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ Returns the enum constant of this type with the specified name.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>[]</CODE></FONT></TD>\r
+<TD><CODE><B>Program.</B><B><A HREF="../../../../compbio/data/sequence/Program.html#values()">values</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns an array containing the constants of this enum type, in
+the order they are declared.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,\r
+ char gapchar)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html#AlignmentMetadata(compbio.data.sequence.Program, char)">AlignmentMetadata</A></B>(<A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,\r
+ char gapchar)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useProgram.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Program.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.data.sequence.Score\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.data.sequence.Score";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useScore.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Score.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.data.sequence.Score</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
+<TD>A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return types with arguments of type <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashSet.html?is-external=true" title="class or interface in java.util">HashSet</A><<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../../compbio/data/msa/Annotation.html#getAnnotation(java.lang.String)">getAnnotation</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</CODE>\r
+\r
+<BR>\r
+ Return the result of the job.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.sequence"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return types with arguments of type <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashSet.html?is-external=true" title="class or interface in java.util">HashSet</A><<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readAAConResults(java.io.InputStream)">readAAConResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> results)</CODE>\r
+\r
+<BR>\r
+ Read AACon result with no alignment files.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+ <A HREF="Score.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.data.sequence.SequenceUtil\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.data.sequence.SequenceUtil";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+ <A HREF="SequenceUtil.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.data.sequence.SequenceUtil</B></H2>\r
+</CENTER>\r
+No usage of compbio.data.sequence.SequenceUtil\r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useSequenceUtil.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="SequenceUtil.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.data.sequence.UnknownFileFormatException\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.data.sequence.UnknownFileFormatException";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/data/sequence/\class-useUnknownFileFormatException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="UnknownFileFormatException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.data.sequence.UnknownFileFormatException</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
+<TD>A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.sequence"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that throw <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
+<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> file)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
+<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> instream)</CODE>\r
+\r
+<BR>\r
+ Read Clustal formatted alignment.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>></CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.File)">readJRonn</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> result)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>></CODE></FONT></TD>\r
+<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.InputStream)">readJRonn</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> inStream)</CODE>\r
+\r
+<BR>\r
+ Reader for JRonn horizontal file format</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+compbio.data.sequence\r
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+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
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+\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white">\r
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+<A HREF="../../../compbio/data/sequence/package-summary.html" target="classFrame">compbio.data.sequence</A></FONT>\r
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+Classes</FONT> \r
+<FONT CLASS="FrameItemFont">\r
+<BR>\r
+<A HREF="Alignment.html" title="class in compbio.data.sequence" target="classFrame">Alignment</A>\r
+<BR>\r
+<A HREF="AlignmentMetadata.html" title="class in compbio.data.sequence" target="classFrame">AlignmentMetadata</A>\r
+<BR>\r
+<A HREF="AnnotatedSequence.html" title="class in compbio.data.sequence" target="classFrame">AnnotatedSequence</A>\r
+<BR>\r
+<A HREF="ClustalAlignmentUtil.html" title="class in compbio.data.sequence" target="classFrame">ClustalAlignmentUtil</A>\r
+<BR>\r
+<A HREF="FastaSequence.html" title="class in compbio.data.sequence" target="classFrame">FastaSequence</A>\r
+<BR>\r
+<A HREF="JalviewAnnotation.html" title="class in compbio.data.sequence" target="classFrame">JalviewAnnotation</A>\r
+<BR>\r
+<A HREF="MultiAnnotatedSequence.html" title="class in compbio.data.sequence" target="classFrame">MultiAnnotatedSequence</A>\r
+<BR>\r
+<A HREF="Score.html" title="class in compbio.data.sequence" target="classFrame">Score</A>\r
+<BR>\r
+<A HREF="SequenceUtil.html" title="class in compbio.data.sequence" target="classFrame">SequenceUtil</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+\r
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
+<TR>\r
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
+Enums</FONT> \r
+<FONT CLASS="FrameItemFont">\r
+<BR>\r
+<A HREF="DisemblResultAnnot.html" title="enum in compbio.data.sequence" target="classFrame">DisemblResultAnnot</A>\r
+<BR>\r
+<A HREF="Method.html" title="enum in compbio.data.sequence" target="classFrame">Method</A>\r
+<BR>\r
+<A HREF="Program.html" title="enum in compbio.data.sequence" target="classFrame">Program</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+\r
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
+<TR>\r
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
+Exceptions</FONT> \r
+<FONT CLASS="FrameItemFont">\r
+<BR>\r
+<A HREF="UnknownFileFormatException.html" title="class in compbio.data.sequence" target="classFrame">UnknownFileFormatException</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+compbio.data.sequence\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="compbio.data.sequence";\r
+ }\r
+}\r
+</SCRIPT>\r
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+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/msa/package-summary.html"><B>PREV PACKAGE</B></A> \r
+ <A HREF="../../../compbio/metadata/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/package-summary.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<H2>\r
+Package compbio.data.sequence\r
+</H2>\r
+A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model.\r
+<P>\r
+<B>See:</B>\r
+<BR>\r
+ <A HREF="#package_description"><B>Description</B></A>\r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Class Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></B></TD>\r
+<TD>Multiple sequence alignment.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></B></TD>\r
+<TD>Alignment metadata e.g.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A></B></TD>\r
+<TD>Tools to read and write clustal formated files</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></B></TD>\r
+<TD>A FASTA formatted sequence.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence">JalviewAnnotation</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence">MultiAnnotatedSequence<T extends Enum<T>></A></B></TD>\r
+<TD>TODO complete</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A></B></TD>\r
+<TD>Utility class for operations on sequences</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+\r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Enum Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A></B></TD>\r
+<TD>Enumeration listing of all the supported methods.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></B></TD>\r
+<TD>The list of programmes that can produce alignments</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+\r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Exception Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+\r
+<P>\r
+<A NAME="package_description"><!-- --></A><H2>\r
+Package compbio.data.sequence Description\r
+</H2>\r
+\r
+<P>\r
+A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model.
+ Classes in this package have no dependencies to other sources in the project.
+ They form a base layer of JAva Bioinformatics Analysis Web Services.\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 January 2010</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>Petr Troshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/data/msa/package-summary.html"><B>PREV PACKAGE</B></A> \r
+ <A HREF="../../../compbio/metadata/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/sequence/package-summary.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+compbio.data.sequence Class Hierarchy\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="compbio.data.sequence Class Hierarchy";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="navbar_top_firstrow"><!-- --></A>\r
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+<HR>\r
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+<UL>\r
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+</UL>\r
+</UL>\r
+</UL>\r
+<H2>\r
+Enum Hierarchy\r
+</H2>\r
+<UL>\r
+<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang"><B>Object</B></A><UL>\r
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+<UL>\r
+<LI TYPE="circle">compbio.data.sequence.<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>Program</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence"><B>Method</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence"><B>DisemblResultAnnot</B></A></UL>\r
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+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Package compbio.data.sequence\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
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+function windowTitle()\r
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+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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+ PREV \r
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+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
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+ }\r
+ //-->\r
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+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
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+<CENTER>\r
+<H2>\r
+<B>Uses of Package<br>compbio.data.sequence</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
+<TD>A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa"><B>Alignment</B></A></B>\r
+\r
+<BR>\r
+ Multiple sequence alignment.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa"><B>FastaSequence</B></A></B>\r
+\r
+<BR>\r
+ A FASTA formatted sequence.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/Score.html#compbio.data.msa"><B>Score</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.sequence"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.sequence"><B>Alignment</B></A></B>\r
+\r
+<BR>\r
+ Multiple sequence alignment.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/AlignmentMetadata.html#compbio.data.sequence"><B>AlignmentMetadata</B></A></B>\r
+\r
+<BR>\r
+ Alignment metadata e.g.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/AnnotatedSequence.html#compbio.data.sequence"><B>AnnotatedSequence</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/DisemblResultAnnot.html#compbio.data.sequence"><B>DisemblResultAnnot</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.sequence"><B>FastaSequence</B></A></B>\r
+\r
+<BR>\r
+ A FASTA formatted sequence.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/JalviewAnnotation.html#compbio.data.sequence"><B>JalviewAnnotation</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/Method.html#compbio.data.sequence"><B>Method</B></A></B>\r
+\r
+<BR>\r
+ Enumeration listing of all the supported methods.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/Program.html#compbio.data.sequence"><B>Program</B></A></B>\r
+\r
+<BR>\r
+ The list of programmes that can produce alignments</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/Score.html#compbio.data.sequence"><B>Score</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.data.sequence"><B>UnknownFileFormatException</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.metadata"><B>FastaSequence</B></A></B>\r
+\r
+<BR>\r
+ A FASTA formatted sequence.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
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+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
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+</SCRIPT>\r
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+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="navbar_top_firstrow"><!-- --></A>\r
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Argument.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV CLASS \r
+ <A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/Argument.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Argument.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Interface Argument<T></H2>\r
+<DL>\r
+<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type</DL>\r
+<DL>\r
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>, <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public interface <B>Argument<T></B></DL>\r
+</PRE>\r
+\r
+<P>\r
+An unmodifiable view for the options and parameters, with one exception - it
+ allows to set a value\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin
+
+ Date December 2009</DD>\r
+<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>, \r
+<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A></DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Argument.html#getDefaultValue()">getDefaultValue</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Argument.html#getDescription()">getDescription</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Argument.html#getFurtherDetails()">getFurtherDetails</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Argument.html#getName()">getName</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Argument.html#getPossibleValues()">getPossibleValues</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Argument.html#setValue(java.lang.String)">setValue</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> defaultValue)</CODE>\r
+\r
+<BR>\r
+ Set default values for the parameter or an option</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="getFurtherDetails()"><!-- --></A><H3>\r
+getFurtherDetails</H3>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A> <B>getFurtherDetails</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getDefaultValue()"><!-- --></A><H3>\r
+getDefaultValue</H3>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getDefaultValue</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getDescription()"><!-- --></A><H3>\r
+getDescription</H3>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getDescription</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getName()"><!-- --></A><H3>\r
+getName</H3>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getName</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getPossibleValues()"><!-- --></A><H3>\r
+getPossibleValues</H3>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> <B>getPossibleValues</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>List of values allowed for an Argument</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setValue(java.lang.String)"><!-- --></A><H3>\r
+setValue</H3>\r
+<PRE>\r
+void <B>setValue</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> defaultValue)\r
+ throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
+<DL>\r
+<DD>Set default values for the parameter or an option\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>defaultValue</CODE> - the value to be set\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - - when the value to be set is illegal. Wrong value for
+ numeric parameter is the value defined outside it , for
+ string type parameter, wrong value is the one which is not
+ listed in possible values list<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><CODE>ValueConstrain</CODE></A></DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Argument.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV CLASS \r
+ <A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/Argument.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Argument.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+ChunkHolder\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="ChunkHolder";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ChunkHolder.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/ChunkHolder.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ChunkHolder.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class ChunkHolder</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.ChunkHolder</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>ChunkHolder</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+Represents a chunk of a string data together with the position in a file for
+ the next read operation.\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 December 2009</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ChunkHolder.html#ChunkHolder(java.lang.String, long)">ChunkHolder</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> chunk,\r
+ long position)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ChunkHolder.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ChunkHolder.html#getChunk()">getChunk</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> long</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ChunkHolder.html#getNextPosition()">getNextPosition</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ChunkHolder.html#hashCode()">hashCode</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ChunkHolder.html#toString()">toString</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="ChunkHolder(java.lang.String, long)"><!-- --></A><H3>\r
+ChunkHolder</H3>\r
+<PRE>\r
+public <B>ChunkHolder</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> chunk,\r
+ long position)</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="getChunk()"><!-- --></A><H3>\r
+getChunk</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getChunk</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getNextPosition()"><!-- --></A><H3>\r
+getNextPosition</H3>\r
+<PRE>\r
+public long <B>getNextPosition</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
+equals</H3>\r
+<PRE>\r
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toString()"><!-- --></A><H3>\r
+toString</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="hashCode()"><!-- --></A><H3>\r
+hashCode</H3>\r
+<PRE>\r
+public int <B>hashCode</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ChunkHolder.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/ChunkHolder.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ChunkHolder.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+JobExecutionException\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="JobExecutionException";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/JobExecutionException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/JobExecutionException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JobExecutionException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class JobExecutionException</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">java.lang.Throwable</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">java.lang.Exception</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.JobExecutionException</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>JobExecutionException</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+JobExecutionException is thrown wherever the results of the calculation
+ cannot be obtained. For cluster execution it hides DrmaaException\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 October 2009</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#compbio.metadata.JobExecutionException">Serialized Form</A></DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.String)">JobExecutionException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.String, java.lang.Throwable)">JobExecutionException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.Throwable)">JobExecutionException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#fillInStackTrace()" title="class or interface in java.lang">fillInStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getCause()" title="class or interface in java.lang">getCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getLocalizedMessage()" title="class or interface in java.lang">getLocalizedMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getMessage()" title="class or interface in java.lang">getMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getStackTrace()" title="class or interface in java.lang">getStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#initCause(java.lang.Throwable)" title="class or interface in java.lang">initCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace()" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintStream)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintWriter)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#setStackTrace(java.lang.StackTraceElement[])" title="class or interface in java.lang">setStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="JobExecutionException(java.lang.String)"><!-- --></A><H3>\r
+JobExecutionException</H3>\r
+<PRE>\r
+public <B>JobExecutionException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message)</PRE>\r
+<DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="JobExecutionException(java.lang.Throwable)"><!-- --></A><H3>\r
+JobExecutionException</H3>\r
+<PRE>\r
+public <B>JobExecutionException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
+<DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="JobExecutionException(java.lang.String, java.lang.Throwable)"><!-- --></A><H3>\r
+JobExecutionException</H3>\r
+<PRE>\r
+public <B>JobExecutionException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
+<DL>\r
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+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/JobExecutionException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JobExecutionException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+JobStatus\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="JobStatus";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/JobStatus.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/JobStatus.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JobStatus.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Enum JobStatus</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">java.lang.Enum</A><<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.JobStatus</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public enum <B>JobStatus</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>></DL>\r
+</PRE>\r
+\r
+<P>\r
+The status of the job.\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 October 2009</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
+\r
+<A NAME="enum_constant_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Enum Constant Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#CANCELLED">CANCELLED</A></B></CODE>\r
+\r
+<BR>\r
+ Jobs that has been cancelled</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#COLLECTED">COLLECTED</A></B></CODE>\r
+\r
+<BR>\r
+ Results has been collected</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#FAILED">FAILED</A></B></CODE>\r
+\r
+<BR>\r
+ Failed jobs</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#FINISHED">FINISHED</A></B></CODE>\r
+\r
+<BR>\r
+ Finished jobs</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#PENDING">PENDING</A></B></CODE>\r
+\r
+<BR>\r
+ Jobs which are in the queue and awaiting execution reported for cluster
+ jobs only</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#RUNNING">RUNNING</A></B></CODE>\r
+\r
+<BR>\r
+ Jobs that are running</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#STARTED">STARTED</A></B></CODE>\r
+\r
+<BR>\r
+ Job calculation has been started.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#SUBMITTED">SUBMITTED</A></B></CODE>\r
+\r
+<BR>\r
+ Job has been submitted.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#UNDEFINED">UNDEFINED</A></B></CODE>\r
+\r
+<BR>\r
+ Represents jobs with unknown status</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#valueOf(java.lang.String)">valueOf</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ Returns the enum constant of this type with the specified name.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>[]</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#values()">values</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns an array containing the constants of this enum type, in
+the order they are declared.</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#compareTo(E)" title="class or interface in java.lang">compareTo</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#getDeclaringClass()" title="class or interface in java.lang">getDeclaringClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#name()" title="class or interface in java.lang">name</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#ordinal()" title="class or interface in java.lang">ordinal</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#valueOf(java.lang.Class, java.lang.String)" title="class or interface in java.lang">valueOf</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
+\r
+<A NAME="enum_constant_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Enum Constant Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="PENDING"><!-- --></A><H3>\r
+PENDING</H3>\r
+<PRE>\r
+public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>PENDING</B></PRE>\r
+<DL>\r
+<DD>Jobs which are in the queue and awaiting execution reported for cluster
+ jobs only\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="RUNNING"><!-- --></A><H3>\r
+RUNNING</H3>\r
+<PRE>\r
+public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>RUNNING</B></PRE>\r
+<DL>\r
+<DD>Jobs that are running\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="CANCELLED"><!-- --></A><H3>\r
+CANCELLED</H3>\r
+<PRE>\r
+public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>CANCELLED</B></PRE>\r
+<DL>\r
+<DD>Jobs that has been cancelled\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="FINISHED"><!-- --></A><H3>\r
+FINISHED</H3>\r
+<PRE>\r
+public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>FINISHED</B></PRE>\r
+<DL>\r
+<DD>Finished jobs\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="FAILED"><!-- --></A><H3>\r
+FAILED</H3>\r
+<PRE>\r
+public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>FAILED</B></PRE>\r
+<DL>\r
+<DD>Failed jobs\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="UNDEFINED"><!-- --></A><H3>\r
+UNDEFINED</H3>\r
+<PRE>\r
+public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>UNDEFINED</B></PRE>\r
+<DL>\r
+<DD>Represents jobs with unknown status\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="STARTED"><!-- --></A><H3>\r
+STARTED</H3>\r
+<PRE>\r
+public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>STARTED</B></PRE>\r
+<DL>\r
+<DD>Job calculation has been started. First status reported by the local
+ engine\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="SUBMITTED"><!-- --></A><H3>\r
+SUBMITTED</H3>\r
+<PRE>\r
+public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>SUBMITTED</B></PRE>\r
+<DL>\r
+<DD>Job has been submitted. This status is only set for cluster jobs\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="COLLECTED"><!-- --></A><H3>\r
+COLLECTED</H3>\r
+<PRE>\r
+public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>COLLECTED</B></PRE>\r
+<DL>\r
+<DD>Results has been collected\r
+<P>\r
+<DL>\r
+</DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="values()"><!-- --></A><H3>\r
+values</H3>\r
+<PRE>\r
+public static <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>[] <B>values</B>()</PRE>\r
+<DL>\r
+<DD>Returns an array containing the constants of this enum type, in
+the order they are declared. This method may be used to iterate
+over the constants as follows:
+<pre>
+for (JobStatus c : JobStatus.values())
+ System.out.println(c);
+</pre>\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
+the order they are declared</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
+valueOf</H3>\r
+<PRE>\r
+public static <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>valueOf</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</PRE>\r
+<DL>\r
+<DD>Returns the enum constant of this type with the specified name.
+The string must match <I>exactly</I> an identifier used to declare an
+enum constant in this type. (Extraneous whitespace characters are
+not permitted.)\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
+<DT><B>Returns:</B><DD>the enum constant with the specified name\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</A></CODE> - if this enum type has no constant
+with the specified name\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE> - if the argument is null</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/JobStatus.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
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+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/JobStatus.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JobStatus.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+JobSubmissionException\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="JobSubmissionException";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
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+<!-- ========= START OF TOP NAVBAR ======= -->\r
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/JobSubmissionException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+ <A HREF="JobSubmissionException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
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+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class JobSubmissionException</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">java.lang.Throwable</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">java.lang.Exception</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.JobSubmissionException</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A></DD>\r
+</DL>\r
+<DL>\r
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>, <A HREF="../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>JobSubmissionException</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+Exception for generic problems with JobSubmission it is often thrown as a
+ wrapper for the lower level exceptions like IOException or DrmaaException. If
+ this exception is thrown the task has not been calculated\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin
+
+ Date December 2009</DD>\r
+<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#compbio.metadata.JobSubmissionException">Serialized Form</A></DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.String)">JobSubmissionException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.String, java.lang.Throwable)">JobSubmissionException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.Throwable)">JobSubmissionException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
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+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#fillInStackTrace()" title="class or interface in java.lang">fillInStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getCause()" title="class or interface in java.lang">getCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getLocalizedMessage()" title="class or interface in java.lang">getLocalizedMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getMessage()" title="class or interface in java.lang">getMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getStackTrace()" title="class or interface in java.lang">getStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#initCause(java.lang.Throwable)" title="class or interface in java.lang">initCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace()" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintStream)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintWriter)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#setStackTrace(java.lang.StackTraceElement[])" title="class or interface in java.lang">setStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="JobSubmissionException(java.lang.String)"><!-- --></A><H3>\r
+JobSubmissionException</H3>\r
+<PRE>\r
+public <B>JobSubmissionException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message)</PRE>\r
+<DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="JobSubmissionException(java.lang.Throwable)"><!-- --></A><H3>\r
+JobSubmissionException</H3>\r
+<PRE>\r
+public <B>JobSubmissionException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
+<DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="JobSubmissionException(java.lang.String, java.lang.Throwable)"><!-- --></A><H3>\r
+JobSubmissionException</H3>\r
+<PRE>\r
+public <B>JobSubmissionException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
+<DL>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
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+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+Limit\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Limit";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Limit.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/Limit.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Limit.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class Limit<T></H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.Limit<T></B>\r
+</PRE>\r
+<DL>\r
+<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - the type of an executable for which this limit is defined.</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>Limit<T></B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+A value object containing a maximum number of sequences and a maximum average
+ sequence length for a preset. Also contains static method for determining the
+ number of sequence and their average length in the List<FastaSequence>\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 January 2010</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><CODE>LimitsManager</CODE></A></DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#Limit(int, int, java.lang.String)">Limit</A></B>(int seqNumber,\r
+ int seqLength,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> preset)</CODE>\r
+\r
+<BR>\r
+ Instantiate the limit</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#Limit(int, int, java.lang.String, boolean)">Limit</A></B>(int seqNumber,\r
+ int seqLength,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> preset,\r
+ boolean isDefault)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#getAvgSeqLength()">getAvgSeqLength</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)">getAvgSequenceLength</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> data)</CODE>\r
+\r
+<BR>\r
+ Calculates an average sequence length of the dataset</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#getPreset()">getPreset</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#getSeqNumber()">getSeqNumber</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#hashCode()">hashCode</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#isDefault()">isDefault</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#isExceeded(java.util.List)">isExceeded</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> data)</CODE>\r
+\r
+<BR>\r
+ Checks if the number of sequences or their average length in the dataset
+ exceeds this limit.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#toString()">toString</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="Limit(int, int, java.lang.String)"><!-- --></A><H3>\r
+Limit</H3>\r
+<PRE>\r
+public <B>Limit</B>(int seqNumber,\r
+ int seqLength,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> preset)</PRE>\r
+<DL>\r
+<DD>Instantiate the limit\r
+<P>\r
+<DL>\r
+<DT><B>Parameters:</B><DD><CODE>seqNumber</CODE> - the maximum number of sequences allowed for calculation.
+ Required<DD><CODE>seqLength</CODE> - the average length of the sequence, optional<DD><CODE>preset</CODE> - the name of preset if any, optional\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</A></CODE> - if the seqNumber is not supplied or the seqLength is negative</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="Limit(int, int, java.lang.String, boolean)"><!-- --></A><H3>\r
+Limit</H3>\r
+<PRE>\r
+public <B>Limit</B>(int seqNumber,\r
+ int seqLength,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> preset,\r
+ boolean isDefault)</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="getPreset()"><!-- --></A><H3>\r
+getPreset</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getPreset</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getAvgSeqLength()"><!-- --></A><H3>\r
+getAvgSeqLength</H3>\r
+<PRE>\r
+public int <B>getAvgSeqLength</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>the allowed average sequence length</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getSeqNumber()"><!-- --></A><H3>\r
+getSeqNumber</H3>\r
+<PRE>\r
+public int <B>getSeqNumber</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>the maximum number of sequences allowed</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="isDefault()"><!-- --></A><H3>\r
+isDefault</H3>\r
+<PRE>\r
+public boolean <B>isDefault</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>true is this is a default limit to be used, false otherwise</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="hashCode()"><!-- --></A><H3>\r
+hashCode</H3>\r
+<PRE>\r
+public int <B>hashCode</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
+equals</H3>\r
+<PRE>\r
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toString()"><!-- --></A><H3>\r
+toString</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="isExceeded(java.util.List)"><!-- --></A><H3>\r
+isExceeded</H3>\r
+<PRE>\r
+public boolean <B>isExceeded</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> data)</PRE>\r
+<DL>\r
+<DD>Checks if the number of sequences or their average length in the dataset
+ exceeds this limit.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>data</CODE> - the dataset to measure\r
+<DT><B>Returns:</B><DD>true if a limit is exceeded (what is the dataset is larger then
+ the limit), false otherwise. First check the number of sequences
+ in the dataset and if it exceeds the limit return true
+ irrespective of the average length. If the number of sequences in
+ the dataset is less than the limit and average length is defined,
+ then check whether the total number of letters (number of
+ sequence multiplied by the average sequence length) is greater
+ then the total number of letters in the dataset. Returns true if
+ the total number of letters in the dataset is greater than the
+ limit, false otherwise.</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getAvgSequenceLength(java.util.List)"><!-- --></A><H3>\r
+getAvgSequenceLength</H3>\r
+<PRE>\r
+public static int <B>getAvgSequenceLength</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> data)</PRE>\r
+<DL>\r
+<DD>Calculates an average sequence length of the dataset\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>data</CODE> - \r
+<DT><B>Returns:</B><DD>an average sequence length in the input dataset</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Limit.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+LimitExceededException\r
+</TITLE>\r
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+ <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
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+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
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+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class LimitExceededException</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">java.lang.Throwable</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">java.lang.Exception</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">compbio.metadata.JobSubmissionException</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.LimitExceededException</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>LimitExceededException</B><DT>extends <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+This exception is thrown if the task larger in size that the limit that
+ applies to the calculation.\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 February 2010</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><CODE>Limit</CODE></A>, \r
+<A HREF="../../serialized-form.html#compbio.metadata.LimitExceededException">Serialized Form</A></DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#LimitExceededException(java.lang.String)">LimitExceededException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#getActualNumberofSequences()">getActualNumberofSequences</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#getNumberOfSequencesAllowed()">getNumberOfSequencesAllowed</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#getSequenceLenghtActual()">getSequenceLenghtActual</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#getSequenceLenghtAllowed()">getSequenceLenghtAllowed</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)">newLimitExceeded</A></B>(<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><?> limit,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> seqs)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#fillInStackTrace()" title="class or interface in java.lang">fillInStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getCause()" title="class or interface in java.lang">getCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getLocalizedMessage()" title="class or interface in java.lang">getLocalizedMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getMessage()" title="class or interface in java.lang">getMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getStackTrace()" title="class or interface in java.lang">getStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#initCause(java.lang.Throwable)" title="class or interface in java.lang">initCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace()" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintStream)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintWriter)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#setStackTrace(java.lang.StackTraceElement[])" title="class or interface in java.lang">setStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="LimitExceededException(java.lang.String)"><!-- --></A><H3>\r
+LimitExceededException</H3>\r
+<PRE>\r
+public <B>LimitExceededException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message)</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="newLimitExceeded(compbio.metadata.Limit, java.util.List)"><!-- --></A><H3>\r
+newLimitExceeded</H3>\r
+<PRE>\r
+public static <A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A> <B>newLimitExceeded</B>(<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><?> limit,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> seqs)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getNumberOfSequencesAllowed()"><!-- --></A><H3>\r
+getNumberOfSequencesAllowed</H3>\r
+<PRE>\r
+public int <B>getNumberOfSequencesAllowed</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getActualNumberofSequences()"><!-- --></A><H3>\r
+getActualNumberofSequences</H3>\r
+<PRE>\r
+public int <B>getActualNumberofSequences</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getSequenceLenghtAllowed()"><!-- --></A><H3>\r
+getSequenceLenghtAllowed</H3>\r
+<PRE>\r
+public int <B>getSequenceLenghtAllowed</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getSequenceLenghtActual()"><!-- --></A><H3>\r
+getSequenceLenghtActual</H3>\r
+<PRE>\r
+public int <B>getSequenceLenghtActual</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/LimitExceededException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
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+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
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+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+LimitsManager\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="LimitsManager";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/LimitsManager.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
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+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/LimitsManager.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="LimitsManager.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
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+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
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+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class LimitsManager<T></H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.LimitsManager<T></B>\r
+</PRE>\r
+<DL>\r
+<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>LimitsManager<T></B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+A collection of Limits\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 January 2010</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><CODE>Limit</CODE></A></DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#LimitsManager()">LimitsManager</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#getDefaultLimit()">getDefaultLimit</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#getLimitByName(java.lang.String)">getLimitByName</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> presetName)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#getLimits()">getLimits</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#toString()">toString</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#validate(compbio.metadata.PresetManager)">validate</A></B>(<A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>> presets)</CODE>\r
+\r
+<BR>\r
+ Validate Limits</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="LimitsManager()"><!-- --></A><H3>\r
+LimitsManager</H3>\r
+<PRE>\r
+public <B>LimitsManager</B>()</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="getLimits()"><!-- --></A><H3>\r
+getLimits</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>>> <B>getLimits</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>all limits defined for an executable T</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toString()"><!-- --></A><H3>\r
+toString</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getLimitByName(java.lang.String)"><!-- --></A><H3>\r
+getLimitByName</H3>\r
+<PRE>\r
+public <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>> <B>getLimitByName</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> presetName)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - \r
+<DT><B>Returns:</B><DD>Limit defined for the executable T and presetName. If no limit is
+ defined for the presetName then default Limit is returned. If
+ presetName is empty or null than the default Limit will be
+ returned. If not limit defined for the type T than NULL will be
+ returned</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getDefaultLimit()"><!-- --></A><H3>\r
+getDefaultLimit</H3>\r
+<PRE>\r
+public <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>> <B>getDefaultLimit</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>the default Limit for an executable type T</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="validate(compbio.metadata.PresetManager)"><!-- --></A><H3>\r
+validate</H3>\r
+<PRE>\r
+public void <B>validate</B>(<A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>> presets)\r
+ throws <A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></PRE>\r
+<DL>\r
+<DD>Validate Limits\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>presets</CODE> - \r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></CODE> - if any of the Limit defined is found to be invalid. That is
+ when
+
+ 1) No default limit is defined
+
+ 2) More than 1 default limit is defined
+
+ 3) Limit's preset name does not match any presets for type T<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><CODE>Limit</CODE></A>, \r
+<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/LimitsManager.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/LimitsManager.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="LimitsManager.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
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+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+Option\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Option";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Option.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
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+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
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+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class Option<T></H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.Option<T></B>\r
+</PRE>\r
+<DL>\r
+<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - type of executable</DL>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><T></DD>\r
+</DL>\r
+<DL>\r
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>Option<T></B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A><DT>implements <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><T></DL>\r
+</PRE>\r
+\r
+<P>\r
+Command line option/flag or multiple exclusive options with no value. Example
+ -protein, -dna, -auto\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 October 2009</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#Option(java.lang.String, java.lang.String)">Option</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> description)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#addOptionNames(java.lang.String...)">addOptionNames</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>... value)</CODE>\r
+\r
+<BR>\r
+ Adds an option to the optionName list</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getDefaultValue()">getDefaultValue</A></B>()</CODE>\r
+\r
+<BR>\r
+ A default value of the option.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getDescription()">getDescription</A></B>()</CODE>\r
+\r
+<BR>\r
+ A long description of the Option</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getFurtherDetails()">getFurtherDetails</A></B>()</CODE>\r
+\r
+<BR>\r
+ The URL where further details about the option can be found</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getName()">getName</A></B>()</CODE>\r
+\r
+<BR>\r
+ Human readable name of the option</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getOptionNames()">getOptionNames</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getPossibleValues()">getPossibleValues</A></B>()</CODE>\r
+\r
+<BR>\r
+ List of possible optionNames</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#hashCode()">hashCode</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#isRequired()">isRequired</A></B>()</CODE>\r
+\r
+<BR>\r
+ Flag that indicated that this option must be specified in the command
+ line for an executable to run</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setDefaultValue(java.lang.String)">setDefaultValue</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> defaultVal)</CODE>\r
+\r
+<BR>\r
+ Sets one of the values defined in optionList as default.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setDescription(java.lang.String)">setDescription</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> description)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setFurtherDetails(java.net.URL)">setFurtherDetails</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A> furtherDetails)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setName(java.lang.String)">setName</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setOptionNames(java.util.Set)">setOptionNames</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> optionNames)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setRequired(boolean)">setRequired</A></B>(boolean isRequired)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setValue(java.lang.String)">setValue</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> dValue)</CODE>\r
+\r
+<BR>\r
+ Set default values for the parameter or an option</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#toCommand(java.lang.String)">toCommand</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> nameValueSeparator)</CODE>\r
+\r
+<BR>\r
+ Convert the option to the command string.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#toString()">toString</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="Option(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
+Option</H3>\r
+<PRE>\r
+public <B>Option</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> description)</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="getName()"><!-- --></A><H3>\r
+getName</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getName</B>()</PRE>\r
+<DL>\r
+<DD>Human readable name of the option\r
+<P>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getName()">getName</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setName(java.lang.String)"><!-- --></A><H3>\r
+setName</H3>\r
+<PRE>\r
+public void <B>setName</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getDescription()"><!-- --></A><H3>\r
+getDescription</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getDescription</B>()</PRE>\r
+<DL>\r
+<DD>A long description of the Option\r
+<P>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getDescription()">getDescription</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setDescription(java.lang.String)"><!-- --></A><H3>\r
+setDescription</H3>\r
+<PRE>\r
+public void <B>setDescription</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> description)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getFurtherDetails()"><!-- --></A><H3>\r
+getFurtherDetails</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A> <B>getFurtherDetails</B>()</PRE>\r
+<DL>\r
+<DD>The URL where further details about the option can be found\r
+<P>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getFurtherDetails()">getFurtherDetails</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setFurtherDetails(java.net.URL)"><!-- --></A><H3>\r
+setFurtherDetails</H3>\r
+<PRE>\r
+public void <B>setFurtherDetails</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A> furtherDetails)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getDefaultValue()"><!-- --></A><H3>\r
+getDefaultValue</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getDefaultValue</B>()</PRE>\r
+<DL>\r
+<DD>A default value of the option. Defaults to command line argument name
+ e.g. -auto\r
+<P>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getDefaultValue()">getDefaultValue</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setDefaultValue(java.lang.String)"><!-- --></A><H3>\r
+setDefaultValue</H3>\r
+<PRE>\r
+public void <B>setDefaultValue</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> defaultVal)\r
+ throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
+<DL>\r
+<DD>Sets one of the values defined in optionList as default. Attempting set
+ the value not listed there will result in WrongParameter exception\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>defaultVal</CODE> - \r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is thrown if the defaultValue is not found in optionList</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="isRequired()"><!-- --></A><H3>\r
+isRequired</H3>\r
+<PRE>\r
+public boolean <B>isRequired</B>()</PRE>\r
+<DL>\r
+<DD>Flag that indicated that this option must be specified in the command
+ line for an executable to run\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>true is the option is required, false otherwise</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setRequired(boolean)"><!-- --></A><H3>\r
+setRequired</H3>\r
+<PRE>\r
+public void <B>setRequired</B>(boolean isRequired)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getOptionNames()"><!-- --></A><H3>\r
+getOptionNames</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> <B>getOptionNames</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>List of option names</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setOptionNames(java.util.Set)"><!-- --></A><H3>\r
+setOptionNames</H3>\r
+<PRE>\r
+public void <B>setOptionNames</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> optionNames)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="addOptionNames(java.lang.String...)"><!-- --></A><H3>\r
+addOptionNames</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> <B>addOptionNames</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>... value)</PRE>\r
+<DL>\r
+<DD>Adds an option to the optionName list\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>value</CODE> - \r
+<DT><B>Returns:</B><DD>modified optionName list</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toString()"><!-- --></A><H3>\r
+toString</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toCommand(java.lang.String)"><!-- --></A><H3>\r
+toCommand</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toCommand</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> nameValueSeparator)</PRE>\r
+<DL>\r
+<DD>Convert the option to the command string.\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>If only one optionName is defined, than it is returned, if many
+ option names are defined, then the defaultValue is returned.
+ Option must have a default value if there are many optionNames to
+ be valid.</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
+equals</H3>\r
+<PRE>\r
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="hashCode()"><!-- --></A><H3>\r
+hashCode</H3>\r
+<PRE>\r
+public int <B>hashCode</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getPossibleValues()"><!-- --></A><H3>\r
+getPossibleValues</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> <B>getPossibleValues</B>()</PRE>\r
+<DL>\r
+<DD>List of possible optionNames\r
+<P>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getPossibleValues()">getPossibleValues</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>List of values allowed for an Argument</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setValue(java.lang.String)"><!-- --></A><H3>\r
+setValue</H3>\r
+<PRE>\r
+public void <B>setValue</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> dValue)\r
+ throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
+<DL>\r
+<DD><B>Description copied from interface: <CODE><A HREF="../../compbio/metadata/Argument.html#setValue(java.lang.String)">Argument</A></CODE></B></DD>\r
+<DD>Set default values for the parameter or an option\r
+<P>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#setValue(java.lang.String)">setValue</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>dValue</CODE> - the value to be set\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - - when the value to be set is illegal. Wrong value for
+ numeric parameter is the value defined outside it , for
+ string type parameter, wrong value is the one which is not
+ listed in possible values list<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><CODE>ValueConstrain</CODE></A></DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/Option.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Option.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
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+ }\r
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+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
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+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
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+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+Parameter\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Parameter";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Parameter.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/Parameter.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Parameter.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class Parameter<T></H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">compbio.metadata.Option</A><T>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.Parameter<T></B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><T></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>Parameter<T></B><DT>extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><T></DL>\r
+</PRE>\r
+\r
+<P>\r
+A single value containing an option supported by the web service e.g.
+ seqType=protein. Where seqType is a optionName and protein is one of
+ possibleValues\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 November 2009</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>, \r
+<A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A></DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#Parameter(java.lang.String, java.lang.String)">Parameter</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> description)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#addOptionNames(java.lang.String...)">addOptionNames</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>... value)</CODE>\r
+\r
+<BR>\r
+ Adds an option to the optionName list</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#addPossibleValues(java.lang.String...)">addPossibleValues</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>... value)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#getOptionName()">getOptionName</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#getPossibleValues()">getPossibleValues</A></B>()</CODE>\r
+\r
+<BR>\r
+ List is more convenient to work with</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#getValidValue()">getValidValue</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#hashCode()">hashCode</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)">setDefaultValue</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> defaultVal)</CODE>\r
+\r
+<BR>\r
+ Sets one of the values defined in optionList as default.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#setOptionName(java.lang.String)">setOptionName</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> optionName)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#setOptionNames(java.util.Set)">setOptionNames</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> optionName)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#setPossibleValues(java.util.Set)">setPossibleValues</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> possibleValues)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#setValidValue(compbio.metadata.ValueConstrain)">setValidValue</A></B>(<A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A> validValue)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#toCommand(java.lang.String)">toCommand</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> nameValueSeparator)</CODE>\r
+\r
+<BR>\r
+ Convert the option to the command string.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#toString()">toString</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_compbio.metadata.Option"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class compbio.metadata.<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="../../compbio/metadata/Option.html#getDefaultValue()">getDefaultValue</A>, <A HREF="../../compbio/metadata/Option.html#getDescription()">getDescription</A>, <A HREF="../../compbio/metadata/Option.html#getFurtherDetails()">getFurtherDetails</A>, <A HREF="../../compbio/metadata/Option.html#getName()">getName</A>, <A HREF="../../compbio/metadata/Option.html#getOptionNames()">getOptionNames</A>, <A HREF="../../compbio/metadata/Option.html#isRequired()">isRequired</A>, <A HREF="../../compbio/metadata/Option.html#setDescription(java.lang.String)">setDescription</A>, <A HREF="../../compbio/metadata/Option.html#setFurtherDetails(java.net.URL)">setFurtherDetails</A>, <A HREF="../../compbio/metadata/Option.html#setName(java.lang.String)">setName</A>, <A HREF="../../compbio/metadata/Option.html#setRequired(boolean)">setRequired</A>, <A HREF="../../compbio/metadata/Option.html#setValue(java.lang.String)">setValue</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="Parameter(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
+Parameter</H3>\r
+<PRE>\r
+public <B>Parameter</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> description)</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="getValidValue()"><!-- --></A><H3>\r
+getValidValue</H3>\r
+<PRE>\r
+public <A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A> <B>getValidValue</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setValidValue(compbio.metadata.ValueConstrain)"><!-- --></A><H3>\r
+setValidValue</H3>\r
+<PRE>\r
+public void <B>setValidValue</B>(<A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A> validValue)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toString()"><!-- --></A><H3>\r
+toString</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#toString()">toString</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toCommand(java.lang.String)"><!-- --></A><H3>\r
+toCommand</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toCommand</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> nameValueSeparator)</PRE>\r
+<DL>\r
+<DD><B>Description copied from class: <CODE><A HREF="../../compbio/metadata/Option.html#toCommand(java.lang.String)">Option</A></CODE></B></DD>\r
+<DD>Convert the option to the command string.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#toCommand(java.lang.String)">toCommand</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>If only one optionName is defined, than it is returned, if many
+ option names are defined, then the defaultValue is returned.
+ Option must have a default value if there are many optionNames to
+ be valid.</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
+equals</H3>\r
+<PRE>\r
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#equals(java.lang.Object)">equals</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getPossibleValues()"><!-- --></A><H3>\r
+getPossibleValues</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> <B>getPossibleValues</B>()</PRE>\r
+<DL>\r
+<DD>List is more convenient to work with\r
+<P>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getPossibleValues()">getPossibleValues</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#getPossibleValues()">getPossibleValues</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>List of String</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setPossibleValues(java.util.Set)"><!-- --></A><H3>\r
+setPossibleValues</H3>\r
+<PRE>\r
+public void <B>setPossibleValues</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> possibleValues)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="addPossibleValues(java.lang.String...)"><!-- --></A><H3>\r
+addPossibleValues</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> <B>addPossibleValues</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>... value)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="hashCode()"><!-- --></A><H3>\r
+hashCode</H3>\r
+<PRE>\r
+public int <B>hashCode</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#hashCode()">hashCode</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setOptionNames(java.util.Set)"><!-- --></A><H3>\r
+setOptionNames</H3>\r
+<PRE>\r
+public void <B>setOptionNames</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> optionName)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#setOptionNames(java.util.Set)">setOptionNames</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="addOptionNames(java.lang.String...)"><!-- --></A><H3>\r
+addOptionNames</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> <B>addOptionNames</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>... value)</PRE>\r
+<DL>\r
+<DD><B>Description copied from class: <CODE><A HREF="../../compbio/metadata/Option.html#addOptionNames(java.lang.String...)">Option</A></CODE></B></DD>\r
+<DD>Adds an option to the optionName list\r
+<P>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#addOptionNames(java.lang.String...)">addOptionNames</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>modified optionName list</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getOptionName()"><!-- --></A><H3>\r
+getOptionName</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getOptionName</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setOptionName(java.lang.String)"><!-- --></A><H3>\r
+setOptionName</H3>\r
+<PRE>\r
+public void <B>setOptionName</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> optionName)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setDefaultValue(java.lang.String)"><!-- --></A><H3>\r
+setDefaultValue</H3>\r
+<PRE>\r
+public void <B>setDefaultValue</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> defaultVal)\r
+ throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
+<DL>\r
+<DD><B>Description copied from class: <CODE><A HREF="../../compbio/metadata/Option.html#setDefaultValue(java.lang.String)">Option</A></CODE></B></DD>\r
+<DD>Sets one of the values defined in optionList as default. Attempting set
+ the value not listed there will result in WrongParameter exception\r
+<P>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#setDefaultValue(java.lang.String)">setDefaultValue</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is thrown if the defaultValue is not found in optionList</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Parameter.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/Parameter.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Parameter.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+Preset\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Preset";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Preset.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/Preset.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Preset.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class Preset<T></H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.Preset<T></B>\r
+</PRE>\r
+<DL>\r
+<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>Preset<T></B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+Collection of Options and Parameters with their values\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 December 2009</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>, \r
+<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A></DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#Preset()">Preset</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>> rconfig)</CODE>\r
+\r
+<BR>\r
+ Converts list of options as String to type Option</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#getDescription()">getDescription</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#getName()">getName</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#getOptions()">getOptions</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#hashCode()">hashCode</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#setDescription(java.lang.String)">setDescription</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> description)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#setName(java.lang.String)">setName</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#setOptions(java.util.List)">setOptions</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> option)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#toString()">toString</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="Preset()"><!-- --></A><H3>\r
+Preset</H3>\r
+<PRE>\r
+public <B>Preset</B>()</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="setOptions(java.util.List)"><!-- --></A><H3>\r
+setOptions</H3>\r
+<PRE>\r
+public void <B>setOptions</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> option)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setName(java.lang.String)"><!-- --></A><H3>\r
+setName</H3>\r
+<PRE>\r
+public void <B>setName</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setDescription(java.lang.String)"><!-- --></A><H3>\r
+setDescription</H3>\r
+<PRE>\r
+public void <B>setDescription</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> description)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getOptions()"><!-- --></A><H3>\r
+getOptions</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> <B>getOptions</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>a List of Options as a String</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getName()"><!-- --></A><H3>\r
+getName</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getName</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>- name of the Preset</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getDescription()"><!-- --></A><H3>\r
+getDescription</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getDescription</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>- a long description of the Preset</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getArguments(compbio.metadata.RunnerConfig)"><!-- --></A><H3>\r
+getArguments</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>>> <B>getArguments</B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>> rconfig)\r
+ throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
+<DL>\r
+<DD>Converts list of options as String to type Option\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>rconfig</CODE> - \r
+<DT><B>Returns:</B><DD>List of Options\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - if the value of the parameter is invalid @see
+ <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toString()"><!-- --></A><H3>\r
+toString</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="hashCode()"><!-- --></A><H3>\r
+hashCode</H3>\r
+<PRE>\r
+public int <B>hashCode</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
+equals</H3>\r
+<PRE>\r
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Preset.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/Preset.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Preset.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+PresetManager\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="PresetManager";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/PresetManager.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/PresetManager.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="PresetManager.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class PresetManager<T></H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.PresetManager<T></B>\r
+</PRE>\r
+<DL>\r
+<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - type of executable.</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>PresetManager<T></B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A>\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 December 2009</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+<!-- =========== FIELD SUMMARY =========== -->\r
+\r
+<A NAME="field_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Field Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET">LOCAL_ENGINE_LIMIT_PRESET</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#PresetManager()">PresetManager</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)">getPresetByName</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> presetName)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#getPresets()">getPresets</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#getRunnerClassName()">getRunnerClassName</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#setPresets(java.util.List)">setPresets</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>>> presets)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#setRunnerClassName(java.lang.String)">setRunnerClassName</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> runnerClassName)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#toString()">toString</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#validate(compbio.metadata.RunnerConfig)">validate</A></B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>> options)</CODE>\r
+\r
+<BR>\r
+ Checks whether preset option and parameter are defined in RunnerConfig
+ object.</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ FIELD DETAIL =========== -->\r
+\r
+<A NAME="field_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Field Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="LOCAL_ENGINE_LIMIT_PRESET"><!-- --></A><H3>\r
+LOCAL_ENGINE_LIMIT_PRESET</H3>\r
+<PRE>\r
+public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>LOCAL_ENGINE_LIMIT_PRESET</B></PRE>\r
+<DL>\r
+<DL>\r
+<DT><B>See Also:</B><DD><A HREF="../../constant-values.html#compbio.metadata.PresetManager.LOCAL_ENGINE_LIMIT_PRESET">Constant Field Values</A></DL>\r
+</DL>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="PresetManager()"><!-- --></A><H3>\r
+PresetManager</H3>\r
+<PRE>\r
+public <B>PresetManager</B>()</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="getPresets()"><!-- --></A><H3>\r
+getPresets</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>>> <B>getPresets</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setPresets(java.util.List)"><!-- --></A><H3>\r
+setPresets</H3>\r
+<PRE>\r
+public void <B>setPresets</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>>> presets)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getRunnerClassName()"><!-- --></A><H3>\r
+getRunnerClassName</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getRunnerClassName</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>fully qualified class name of type T</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setRunnerClassName(java.lang.String)"><!-- --></A><H3>\r
+setRunnerClassName</H3>\r
+<PRE>\r
+public void <B>setRunnerClassName</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> runnerClassName)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getPresetByName(java.lang.String)"><!-- --></A><H3>\r
+getPresetByName</H3>\r
+<PRE>\r
+public <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>> <B>getPresetByName</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> presetName)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - \r
+<DT><B>Returns:</B><DD>preset by its name, null if no preset found</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="validate(compbio.metadata.RunnerConfig)"><!-- --></A><H3>\r
+validate</H3>\r
+<PRE>\r
+public void <B>validate</B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>> options)\r
+ throws <A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></PRE>\r
+<DL>\r
+<DD>Checks whether preset option and parameter are defined in RunnerConfig
+ object.
+
+ TODO handle parameters with values properly!\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></CODE> - if preset is found to be invalid.</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toString()"><!-- --></A><H3>\r
+toString</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
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+</DD>\r
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+<!-- ========= END OF CLASS DATA ========= -->\r
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+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/PresetManager.html" target="_top"><B>FRAMES</B></A> \r
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+ <SCRIPT type="text/javascript">\r
+ <!--\r
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+ }\r
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+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
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+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+ResultNotAvailableException\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="ResultNotAvailableException";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ResultNotAvailableException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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+</TABLE>\r
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+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
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+ <SCRIPT type="text/javascript">\r
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+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
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+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
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+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
+</TR>\r
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+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class ResultNotAvailableException</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">java.lang.Throwable</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">java.lang.Exception</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.ResultNotAvailableException</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>ResultNotAvailableException</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+ResultNotAvailableException is thrown wherever the results of the calculation
+ cannot be obtained. For cluster execution it hides lower level exceptions
+ like DrmaaException\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin
+
+ Date October 2009</DD>\r
+<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#compbio.metadata.ResultNotAvailableException">Serialized Form</A></DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String)">ResultNotAvailableException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String, java.lang.Throwable)">ResultNotAvailableException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.Throwable)">ResultNotAvailableException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#fillInStackTrace()" title="class or interface in java.lang">fillInStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getCause()" title="class or interface in java.lang">getCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getLocalizedMessage()" title="class or interface in java.lang">getLocalizedMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getMessage()" title="class or interface in java.lang">getMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getStackTrace()" title="class or interface in java.lang">getStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#initCause(java.lang.Throwable)" title="class or interface in java.lang">initCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace()" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintStream)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintWriter)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#setStackTrace(java.lang.StackTraceElement[])" title="class or interface in java.lang">setStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="ResultNotAvailableException(java.lang.String)"><!-- --></A><H3>\r
+ResultNotAvailableException</H3>\r
+<PRE>\r
+public <B>ResultNotAvailableException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message)</PRE>\r
+<DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="ResultNotAvailableException(java.lang.Throwable)"><!-- --></A><H3>\r
+ResultNotAvailableException</H3>\r
+<PRE>\r
+public <B>ResultNotAvailableException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
+<DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="ResultNotAvailableException(java.lang.String, java.lang.Throwable)"><!-- --></A><H3>\r
+ResultNotAvailableException</H3>\r
+<PRE>\r
+public <B>ResultNotAvailableException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
+<DL>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/ResultNotAvailableException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ResultNotAvailableException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
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+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+RunnerConfig\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="RunnerConfig";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
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+<A NAME="navbar_top_firstrow"><!-- --></A>\r
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/RunnerConfig.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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+</TD>\r
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/RunnerConfig.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="RunnerConfig.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
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+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
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+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
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+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class RunnerConfig<T></H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.RunnerConfig<T></B>\r
+</PRE>\r
+<DL>\r
+<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - type of an Executable</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE><FONT SIZE="-1">@NotThreadSafe\r
+</FONT>public class <B>RunnerConfig<T></B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.
+ The lists is defined in and loaded from <ExecutableName>Parameters.xml file.\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 October 2009</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#RunnerConfig()">RunnerConfig</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)">addOption</A></B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> option)</CODE>\r
+\r
+<BR>\r
+ Adds Option to the internal list of options</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#addParameter(compbio.metadata.Parameter)">addParameter</A></B>(<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> param)</CODE>\r
+\r
+<BR>\r
+ Adds parameter to the internal parameter list</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)">copyAndValidateRConfig</A></B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><?> runnerConf)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)">getArgument</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ Returns the argument by its name if found, NULL otherwise.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)">getArgumentByOptionName</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> optionName)</CODE>\r
+\r
+<BR>\r
+ Returns the argument by option name, NULL if the argument is not found</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArguments()">getArguments</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
+ runner</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getOptions()">getOptions</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns the list of the Options supported by the executable of type T</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getParameters()">getParameters</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns the list of parameters supported executable of type T.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getPrmSeparator()">getPrmSeparator</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getRunnerClassName()">getRunnerClassName</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#removeArgument(java.lang.String)">removeArgument</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ Removes the argument <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#removeArgumentByOptionName(java.lang.String)">removeArgumentByOptionName</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> optionName)</CODE>\r
+\r
+<BR>\r
+ Removes the argument which can be a Parameter or an Option instance by
+ the value in <optionNames> element of the runner configuration
+ descriptor.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)">setOptions</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</CODE>\r
+\r
+<BR>\r
+ Adds the list of options or parameters to the internal list of options</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)">setParameters</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</CODE>\r
+\r
+<BR>\r
+ Sets the list of parameters as internal list</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setPrmSeparator(java.lang.String)">setPrmSeparator</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> prmSeparator)</CODE>\r
+\r
+<BR>\r
+ Sets name value separator character</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setRunnerClassName(java.lang.String)">setRunnerClassName</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> runnerClassName)</CODE>\r
+\r
+<BR>\r
+ Set the name of a runner class</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#toString()">toString</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#validate()">validate</A></B>()</CODE>\r
+\r
+<BR>\r
+ Validate the value of the argument.</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="RunnerConfig()"><!-- --></A><H3>\r
+RunnerConfig</H3>\r
+<PRE>\r
+public <B>RunnerConfig</B>()</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="copyAndValidateRConfig(compbio.metadata.RunnerConfig)"><!-- --></A><H3>\r
+copyAndValidateRConfig</H3>\r
+<PRE>\r
+public <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> <B>copyAndValidateRConfig</B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><?> runnerConf)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getOptions()"><!-- --></A><H3>\r
+getOptions</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> <B>getOptions</B>()</PRE>\r
+<DL>\r
+<DD>Returns the list of the Options supported by the executable of type T\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>list of <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by type T<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="addParameter(compbio.metadata.Parameter)"><!-- --></A><H3>\r
+addParameter</H3>\r
+<PRE>\r
+public void <B>addParameter</B>(<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> param)</PRE>\r
+<DL>\r
+<DD>Adds parameter to the internal parameter list\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>param</CODE> - the <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> to add<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="addOption(compbio.metadata.Option)"><!-- --></A><H3>\r
+addOption</H3>\r
+<PRE>\r
+public void <B>addOption</B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> option)</PRE>\r
+<DL>\r
+<DD>Adds Option to the internal list of options\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>option</CODE> - the <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> to add</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getArguments()"><!-- --></A><H3>\r
+getArguments</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> <B>getArguments</B>()</PRE>\r
+<DL>\r
+<DD>Returns list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
+ runner\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>list of <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> and <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> supported by type T</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getPrmSeparator()"><!-- --></A><H3>\r
+getPrmSeparator</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getPrmSeparator</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>name value separator character</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setPrmSeparator(java.lang.String)"><!-- --></A><H3>\r
+setPrmSeparator</H3>\r
+<PRE>\r
+public void <B>setPrmSeparator</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> prmSeparator)</PRE>\r
+<DL>\r
+<DD>Sets name value separator character\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>prmSeparator</CODE> - the separator char</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setOptions(java.util.List)"><!-- --></A><H3>\r
+setOptions</H3>\r
+<PRE>\r
+public void <B>setOptions</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</PRE>\r
+<DL>\r
+<DD>Adds the list of options or parameters to the internal list of options\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>parameters</CODE> - the list of parameters to add</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getRunnerClassName()"><!-- --></A><H3>\r
+getRunnerClassName</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getRunnerClassName</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>fully qualified class name for type T</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setRunnerClassName(java.lang.String)"><!-- --></A><H3>\r
+setRunnerClassName</H3>\r
+<PRE>\r
+public void <B>setRunnerClassName</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> runnerClassName)</PRE>\r
+<DL>\r
+<DD>Set the name of a runner class\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>runnerClassName</CODE> - the name of the executable wrapping class</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setParameters(java.util.List)"><!-- --></A><H3>\r
+setParameters</H3>\r
+<PRE>\r
+public void <B>setParameters</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</PRE>\r
+<DL>\r
+<DD>Sets the list of parameters as internal list\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>parameters</CODE> - the list of parameters</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getParameters()"><!-- --></A><H3>\r
+getParameters</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> <B>getParameters</B>()</PRE>\r
+<DL>\r
+<DD>Returns the list of parameters supported executable of type T. Where
+ <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> is an <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> with value.\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>List of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> supported by type T.</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toString()"><!-- --></A><H3>\r
+toString</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
+equals</H3>\r
+<PRE>\r
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getArgument(java.lang.String)"><!-- --></A><H3>\r
+getArgument</H3>\r
+<PRE>\r
+public <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> <B>getArgument</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</PRE>\r
+<DL>\r
+<DD>Returns the argument by its name if found, NULL otherwise. Where the
+ Argument is a common interface for <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> and <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>
+ therefore this method can return either. If you need to retrieve the
+ Option by its optionNames use @link
+ <A HREF="../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)"><CODE>getArgumentByOptionName(String)</CODE></A> method. The
+ difference between option name and optionName is explained by the
+ following example:
+
+ <pre>
+ <name>Sequence type</name>
+ <description>
+ --nuc - Assume the sequences are nucleotide.
+ --amino - Assume the sequences are amino acid. </description>
+ <optionNames>--amino</optionNames>
+ <optionNames>--nuc</optionNames>
+ <optionNames>--auto</optionNames>
+ </pre>
+
+ In the example, the "Sequence type" is a name whereas --amino, --nuc and
+ --auto are all optionNames. This dichotomy only manifests in
+ <code>Option</code> never in <code>Parameters</code> as the latter can
+ only have single <optioNames> element\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>name</CODE> - the Parameter of Option name\r
+<DT><B>Returns:</B><DD><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="removeArgument(java.lang.String)"><!-- --></A><H3>\r
+removeArgument</H3>\r
+<PRE>\r
+public boolean <B>removeArgument</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</PRE>\r
+<DL>\r
+<DD>Removes the argument <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found. Where Argument is either
+ <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> or <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>name</CODE> - of the argument\r
+<DT><B>Returns:</B><DD>true if argument was removed, false otherwise</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getArgumentByOptionName(java.lang.String)"><!-- --></A><H3>\r
+getArgumentByOptionName</H3>\r
+<PRE>\r
+public <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> <B>getArgumentByOptionName</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> optionName)</PRE>\r
+<DL>\r
+<DD>Returns the argument by option name, NULL if the argument is not found\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>optionName</CODE> - - the optionName. This is not the same as an Option name.
+
+ For example:
+
+ <pre>
+ <name>Output sequences order</name>
+ <description>--inputorder - Output order: same as input.
+ --reorder - Output order: aligned. Default: same as input</description>
+ <optionNames>--inputorder</optionNames>
+ <optionNames>--reorder</optionNames>
+ </pre>
+
+ The name of the option in the example is
+ "Output sequences order" whereas optionNames are
+ "--inputorder" and "--reorder". If you need to retrieve the
+ Option or Parameter by its names use
+ <A HREF="../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)"><CODE>getArgument(String)</CODE></A> method\r
+<DT><B>Returns:</B><DD>Option</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="removeArgumentByOptionName(java.lang.String)"><!-- --></A><H3>\r
+removeArgumentByOptionName</H3>\r
+<PRE>\r
+public boolean <B>removeArgumentByOptionName</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> optionName)</PRE>\r
+<DL>\r
+<DD>Removes the argument which can be a Parameter or an Option instance by
+ the value in <optionNames> element of the runner configuration
+ descriptor.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>optionName</CODE> - the optionName of the option, do not confuse with the name!\r
+<DT><B>Returns:</B><DD>true if argument with optionName exists and was removed, false
+ otherwise<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)"><CODE>for destinctions
+ between optionNames and the name of the Option</CODE></A></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="validate()"><!-- --></A><H3>\r
+validate</H3>\r
+<PRE>\r
+public void <B>validate</B>()\r
+ throws <A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></PRE>\r
+<DL>\r
+<DD>Validate the value of the argument. Checks whether the argument value is
+ in the valid values range.\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></CODE> - if any of the arguments found invalid which is when
+ <dl>
+ <li>Parameter value outside <A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><CODE>ValueConstrain</CODE></A> boundary</li>
+ <li>Parameter name is not listed in possible values</li>
+ </dl></DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/RunnerConfig.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/RunnerConfig.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="RunnerConfig.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+UnsupportedRuntimeException\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="UnsupportedRuntimeException";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/UnsupportedRuntimeException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/UnsupportedRuntimeException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="UnsupportedRuntimeException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class UnsupportedRuntimeException</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">java.lang.Throwable</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">java.lang.Exception</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">compbio.metadata.JobSubmissionException</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.UnsupportedRuntimeException</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>UnsupportedRuntimeException</B><DT>extends <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+Indicates that the server could not execute native executables. e.g. If Mafft
+ (unix executable) is asked to be run on Windows. In context of JABAWS this
+ exception indicates that the service is deployed but is not able to run.\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin
+
+ Date February 2010</DD>\r
+<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#compbio.metadata.UnsupportedRuntimeException">Serialized Form</A></DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/UnsupportedRuntimeException.html#UnsupportedRuntimeException(java.lang.String)">UnsupportedRuntimeException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/UnsupportedRuntimeException.html#UnsupportedRuntimeException(java.lang.Throwable)">UnsupportedRuntimeException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
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+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A></B></TH>\r
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+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
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+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="UnsupportedRuntimeException(java.lang.String)"><!-- --></A><H3>\r
+UnsupportedRuntimeException</H3>\r
+<PRE>\r
+public <B>UnsupportedRuntimeException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message)</PRE>\r
+<DL>\r
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+<HR>\r
+\r
+<A NAME="UnsupportedRuntimeException(java.lang.Throwable)"><!-- --></A><H3>\r
+UnsupportedRuntimeException</H3>\r
+<PRE>\r
+public <B>UnsupportedRuntimeException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
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+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+ValueConstrain.Type\r
+</TITLE>\r
+\r
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+function windowTitle()\r
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+ if (location.href.indexOf('is-external=true') == -1) {\r
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+ }\r
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+ <A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
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+ SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
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+DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Enum ValueConstrain.Type</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">java.lang.Enum</A><<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.ValueConstrain.Type</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>></DD>\r
+</DL>\r
+<DL>\r
+<DT><B>Enclosing class:</B><DD><A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public static enum <B>ValueConstrain.Type</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>></DL>\r
+</PRE>\r
+\r
+<P>\r
+<HR>\r
+\r
+<P>\r
+<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
+\r
+<A NAME="enum_constant_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Enum Constant Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html#Float">Float</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html#Integer">Integer</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html#valueOf(java.lang.String)">valueOf</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ Returns the enum constant of this type with the specified name.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>[]</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html#values()">values</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns an array containing the constants of this enum type, in
+the order they are declared.</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#compareTo(E)" title="class or interface in java.lang">compareTo</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#getDeclaringClass()" title="class or interface in java.lang">getDeclaringClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#name()" title="class or interface in java.lang">name</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#ordinal()" title="class or interface in java.lang">ordinal</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#valueOf(java.lang.Class, java.lang.String)" title="class or interface in java.lang">valueOf</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
+\r
+<A NAME="enum_constant_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Enum Constant Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="Integer"><!-- --></A><H3>\r
+Integer</H3>\r
+<PRE>\r
+public static final <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> <B>Integer</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="Float"><!-- --></A><H3>\r
+Float</H3>\r
+<PRE>\r
+public static final <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> <B>Float</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="values()"><!-- --></A><H3>\r
+values</H3>\r
+<PRE>\r
+public static <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>[] <B>values</B>()</PRE>\r
+<DL>\r
+<DD>Returns an array containing the constants of this enum type, in
+the order they are declared. This method may be used to iterate
+over the constants as follows:
+<pre>
+for (ValueConstrain.Type c : ValueConstrain.Type.values())
+ System.out.println(c);
+</pre>\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
+the order they are declared</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
+valueOf</H3>\r
+<PRE>\r
+public static <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> <B>valueOf</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</PRE>\r
+<DL>\r
+<DD>Returns the enum constant of this type with the specified name.
+The string must match <I>exactly</I> an identifier used to declare an
+enum constant in this type. (Extraneous whitespace characters are
+not permitted.)\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
+<DT><B>Returns:</B><DD>the enum constant with the specified name\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</A></CODE> - if this enum type has no constant
+with the specified name\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE> - if the argument is null</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+ <A HREF="ValueConstrain.Type.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+ValueConstrain\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="ValueConstrain";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
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+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/ValueConstrain.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
+ <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/ValueConstrain.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ValueConstrain.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class ValueConstrain</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.ValueConstrain</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>ValueConstrain</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+The type and the lower and upper boundaries for numerical value.\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 November 2009</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+<!-- ======== NESTED CLASS SUMMARY ======== -->\r
+\r
+<A NAME="nested_class_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Nested Class Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static class</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#ValueConstrain()">ValueConstrain</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Number.html?is-external=true" title="class or interface in java.lang">Number</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#getMax()">getMax</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Number.html?is-external=true" title="class or interface in java.lang">Number</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#getMin()">getMin</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#getType()">getType</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#hashCode()">hashCode</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#setMax(java.lang.String)">setMax</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> max)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#setMin(java.lang.String)">setMin</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> min)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#setType(compbio.metadata.ValueConstrain.Type)">setType</A></B>(<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> type)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#toString()">toString</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="ValueConstrain()"><!-- --></A><H3>\r
+ValueConstrain</H3>\r
+<PRE>\r
+public <B>ValueConstrain</B>()</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="getType()"><!-- --></A><H3>\r
+getType</H3>\r
+<PRE>\r
+public <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> <B>getType</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setType(compbio.metadata.ValueConstrain.Type)"><!-- --></A><H3>\r
+setType</H3>\r
+<PRE>\r
+public void <B>setType</B>(<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> type)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getMax()"><!-- --></A><H3>\r
+getMax</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Number.html?is-external=true" title="class or interface in java.lang">Number</A> <B>getMax</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setMax(java.lang.String)"><!-- --></A><H3>\r
+setMax</H3>\r
+<PRE>\r
+public void <B>setMax</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> max)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getMin()"><!-- --></A><H3>\r
+getMin</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Number.html?is-external=true" title="class or interface in java.lang">Number</A> <B>getMin</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setMin(java.lang.String)"><!-- --></A><H3>\r
+setMin</H3>\r
+<PRE>\r
+public void <B>setMin</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> min)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
+equals</H3>\r
+<PRE>\r
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="toString()"><!-- --></A><H3>\r
+toString</H3>\r
+<PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="hashCode()"><!-- --></A><H3>\r
+hashCode</H3>\r
+<PRE>\r
+public int <B>hashCode</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
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+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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+\r
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--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+WrongParameterException\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
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+ }\r
+}\r
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+</TD>\r
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
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+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class WrongParameterException</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">java.lang.Throwable</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">java.lang.Exception</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.WrongParameterException</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>WrongParameterException</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
+ does not match the actual runnable or then attempting to set the value of
+ <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 October 2009</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#compbio.metadata.WrongParameterException">Serialized Form</A></DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/WrongParameterException.html#WrongParameterException(compbio.metadata.Option)">WrongParameterException</A></B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?> option)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String)">WrongParameterException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String, java.lang.Throwable)">WrongParameterException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.Throwable)">WrongParameterException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#fillInStackTrace()" title="class or interface in java.lang">fillInStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getCause()" title="class or interface in java.lang">getCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getLocalizedMessage()" title="class or interface in java.lang">getLocalizedMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getMessage()" title="class or interface in java.lang">getMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getStackTrace()" title="class or interface in java.lang">getStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#initCause(java.lang.Throwable)" title="class or interface in java.lang">initCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace()" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintStream)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintWriter)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#setStackTrace(java.lang.StackTraceElement[])" title="class or interface in java.lang">setStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="WrongParameterException(compbio.metadata.Option)"><!-- --></A><H3>\r
+WrongParameterException</H3>\r
+<PRE>\r
+public <B>WrongParameterException</B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?> option)</PRE>\r
+<DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="WrongParameterException(java.lang.String)"><!-- --></A><H3>\r
+WrongParameterException</H3>\r
+<PRE>\r
+public <B>WrongParameterException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message)</PRE>\r
+<DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="WrongParameterException(java.lang.Throwable)"><!-- --></A><H3>\r
+WrongParameterException</H3>\r
+<PRE>\r
+public <B>WrongParameterException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
+<DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="WrongParameterException(java.lang.String, java.lang.Throwable)"><!-- --></A><H3>\r
+WrongParameterException</H3>\r
+<PRE>\r
+public <B>WrongParameterException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> message,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
+<DL>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><B>PREV CLASS</B></A> \r
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+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Interface compbio.metadata.Argument\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Interface compbio.metadata.Argument";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useArgument.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Argument.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Interface<br>compbio.metadata.Argument</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that implement <A HREF="../../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> class</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option<T></A></B></CODE>\r
+\r
+<BR>\r
+ Command line option/flag or multiple exclusive options with no value.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> class</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter<T></A></B></CODE>\r
+\r
+<BR>\r
+ A single value containing an option supported by the web service e.g.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useArgument.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Argument.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.ChunkHolder\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.ChunkHolder";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useChunkHolder.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ChunkHolder.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.ChunkHolder</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
+<TD><CODE><B>JManagement.</B><B><A HREF="../../../compbio/data/msa/JManagement.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId,\r
+ long position)</CODE>\r
+\r
+<BR>\r
+ Reads 1kb chunk from the statistics file which is specific to a given web
+ service from the <code>position</code>.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useChunkHolder.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ChunkHolder.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.JobExecutionException\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.JobExecutionException";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useJobExecutionException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JobExecutionException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.JobExecutionException</B></H2>\r
+</CENTER>\r
+No usage of compbio.metadata.JobExecutionException\r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useJobExecutionException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JobExecutionException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.JobStatus\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.JobStatus";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useJobStatus.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JobStatus.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.JobStatus</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
+<TD><CODE><B>JManagement.</B><B><A HREF="../../../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</CODE>\r
+\r
+<BR>\r
+ Return the status of the job.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
+<TD><CODE><B>JobStatus.</B><B><A HREF="../../../compbio/metadata/JobStatus.html#valueOf(java.lang.String)">valueOf</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ Returns the enum constant of this type with the specified name.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>[]</CODE></FONT></TD>\r
+<TD><CODE><B>JobStatus.</B><B><A HREF="../../../compbio/metadata/JobStatus.html#values()">values</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns an array containing the constants of this enum type, in
+the order they are declared.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useJobStatus.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JobStatus.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.JobSubmissionException\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.JobSubmissionException";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useJobSubmissionException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JobSubmissionException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.JobSubmissionException</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with default settings.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../compbio/data/msa/Annotation.html#analize(java.util.List)">analize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>>> options)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with options.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../compbio/data/msa/Annotation.html#customAnalize(java.util.List, java.util.List)">customAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>>> options)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences according to custom settings defined in options
+ list.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> preset)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with preset.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../compbio/data/msa/Annotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>> preset)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences according to the preset settings.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> class</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></B></CODE>\r
+\r
+<BR>\r
+ This exception is thrown if the task larger in size that the limit that
+ applies to the calculation.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> class</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></B></CODE>\r
+\r
+<BR>\r
+ Indicates that the server could not execute native executables.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useJobSubmissionException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="JobSubmissionException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.Limit\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.Limit";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useLimit.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Limit.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.Limit</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B>Metadata.</B><B><A HREF="../../../compbio/data/msa/Metadata.html#getLimit(java.lang.String)">getLimit</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> presetName)</CODE>\r
+\r
+<BR>\r
+ Get a Limit for a preset.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B>LimitsManager.</B><B><A HREF="../../../compbio/metadata/LimitsManager.html#getDefaultLimit()">getDefaultLimit</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B>LimitsManager.</B><B><A HREF="../../../compbio/metadata/LimitsManager.html#getLimitByName(java.lang.String)">getLimitByName</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> presetName)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>>></CODE></FONT></TD>\r
+<TD><CODE><B>LimitsManager.</B><B><A HREF="../../../compbio/metadata/LimitsManager.html#getLimits()">getLimits</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
+<TD><CODE><B>LimitExceededException.</B><B><A HREF="../../../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)">newLimitExceeded</A></B>(<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><?> limit,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> seqs)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useLimit.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Limit.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.LimitExceededException\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.LimitExceededException";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useLimitExceededException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="LimitExceededException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.LimitExceededException</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with default settings.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../compbio/data/msa/Annotation.html#analize(java.util.List)">analize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>>> options)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with options.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../compbio/data/msa/Annotation.html#customAnalize(java.util.List, java.util.List)">customAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>>> options)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences according to custom settings defined in options
+ list.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> preset)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with preset.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../compbio/data/msa/Annotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>> preset)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences according to the preset settings.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
+<TD><CODE><B>LimitExceededException.</B><B><A HREF="../../../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)">newLimitExceeded</A></B>(<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><?> limit,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> seqs)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useLimitExceededException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="LimitExceededException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.LimitsManager\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.LimitsManager";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useLimitsManager.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="LimitsManager.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.LimitsManager</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B>Metadata.</B><B><A HREF="../../../compbio/data/msa/Metadata.html#getLimits()">getLimits</A></B>()</CODE>\r
+\r
+<BR>\r
+ List Limits supported by a web service.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useLimitsManager.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="LimitsManager.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.Option\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.Option";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useOption.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Option.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.Option</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>>> options)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with options.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../compbio/data/msa/Annotation.html#customAnalize(java.util.List, java.util.List)">customAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>>> options)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences according to custom settings defined in options
+ list.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> class</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter<T></A></B></CODE>\r
+\r
+<BR>\r
+ A single value containing an option supported by the web service e.g.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)">getArgument</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ Returns the argument by its name if found, NULL otherwise.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)">getArgumentByOptionName</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> optionName)</CODE>\r
+\r
+<BR>\r
+ Returns the argument by option name, NULL if the argument is not found</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>\r
+<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArguments()">getArguments</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns list of <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
+ runner</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>>></CODE></FONT></TD>\r
+<TD><CODE><B>Preset.</B><B><A HREF="../../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>> rconfig)</CODE>\r
+\r
+<BR>\r
+ Converts list of options as String to type Option</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>\r
+<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getOptions()">getOptions</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns the list of the Options supported by the executable of type T</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)">addOption</A></B>(<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> option)</CODE>\r
+\r
+<BR>\r
+ Adds Option to the internal list of options</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)">setOptions</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</CODE>\r
+\r
+<BR>\r
+ Adds the list of options or parameters to the internal list of options</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/metadata/WrongParameterException.html#WrongParameterException(compbio.metadata.Option)">WrongParameterException</A></B>(<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?> option)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useOption.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Option.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.Parameter\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.Parameter";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useParameter.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Parameter.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.Parameter</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>\r
+<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getParameters()">getParameters</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns the list of parameters supported executable of type T.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#addParameter(compbio.metadata.Parameter)">addParameter</A></B>(<A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> param)</CODE>\r
+\r
+<BR>\r
+ Adds parameter to the internal parameter list</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)">setParameters</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</CODE>\r
+\r
+<BR>\r
+ Sets the list of parameters as internal list</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useParameter.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Parameter.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.Preset\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.Preset";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-usePreset.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Preset.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.Preset</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> with parameters of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> preset)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with preset.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../compbio/data/msa/Annotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>> preset)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences according to the preset settings.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)">getPresetByName</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> presetName)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>>></CODE></FONT></TD>\r
+<TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#getPresets()">getPresets</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#setPresets(java.util.List)">setPresets</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>>> presets)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-usePreset.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Preset.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.PresetManager\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.PresetManager";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-usePresetManager.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="PresetManager.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.PresetManager</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B>Metadata.</B><B><A HREF="../../../compbio/data/msa/Metadata.html#getPresets()">getPresets</A></B>()</CODE>\r
+\r
+<BR>\r
+ Get presets supported by a web service</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B>LimitsManager.</B><B><A HREF="../../../compbio/metadata/LimitsManager.html#validate(compbio.metadata.PresetManager)">validate</A></B>(<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>> presets)</CODE>\r
+\r
+<BR>\r
+ Validate Limits</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-usePresetManager.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="PresetManager.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.ResultNotAvailableException\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.ResultNotAvailableException";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useResultNotAvailableException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ResultNotAvailableException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.ResultNotAvailableException</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashSet.html?is-external=true" title="class or interface in java.util">HashSet</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../compbio/data/msa/Annotation.html#getAnnotation(java.lang.String)">getAnnotation</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</CODE>\r
+\r
+<BR>\r
+ Return the result of the job.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> jobId)</CODE>\r
+\r
+<BR>\r
+ Return the result of the job.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useResultNotAvailableException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ResultNotAvailableException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.RunnerConfig\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.RunnerConfig";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useRunnerConfig.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="RunnerConfig.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.RunnerConfig</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B>Metadata.</B><B><A HREF="../../../compbio/data/msa/Metadata.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
+\r
+<BR>\r
+ Get options supported by a web service</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)">copyAndValidateRConfig</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><?> runnerConf)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)">copyAndValidateRConfig</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><?> runnerConf)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>>></CODE></FONT></TD>\r
+<TD><CODE><B>Preset.</B><B><A HREF="../../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>> rconfig)</CODE>\r
+\r
+<BR>\r
+ Converts list of options as String to type Option</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#validate(compbio.metadata.RunnerConfig)">validate</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>> options)</CODE>\r
+\r
+<BR>\r
+ Checks whether preset option and parameter are defined in RunnerConfig
+ object.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useRunnerConfig.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="RunnerConfig.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.UnsupportedRuntimeException\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.UnsupportedRuntimeException";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useUnsupportedRuntimeException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="UnsupportedRuntimeException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.UnsupportedRuntimeException</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with default settings.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../compbio/data/msa/Annotation.html#analize(java.util.List)">analize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>>> options)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with options.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../compbio/data/msa/Annotation.html#customAnalize(java.util.List, java.util.List)">customAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>>> options)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences according to custom settings defined in options
+ list.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> preset)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with preset.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../compbio/data/msa/Annotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>> preset)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences according to the preset settings.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useUnsupportedRuntimeException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="UnsupportedRuntimeException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.ValueConstrain.Type\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.ValueConstrain.Type";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+ <A HREF="ValueConstrain.Type.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.ValueConstrain.Type</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></CODE></FONT></TD>\r
+<TD><CODE><B>ValueConstrain.</B><B><A HREF="../../../compbio/metadata/ValueConstrain.html#getType()">getType</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></CODE></FONT></TD>\r
+<TD><CODE><B>ValueConstrain.Type.</B><B><A HREF="../../../compbio/metadata/ValueConstrain.Type.html#valueOf(java.lang.String)">valueOf</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ Returns the enum constant of this type with the specified name.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>[]</CODE></FONT></TD>\r
+<TD><CODE><B>ValueConstrain.Type.</B><B><A HREF="../../../compbio/metadata/ValueConstrain.Type.html#values()">values</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns an array containing the constants of this enum type, in
+the order they are declared.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B>ValueConstrain.</B><B><A HREF="../../../compbio/metadata/ValueConstrain.html#setType(compbio.metadata.ValueConstrain.Type)">setType</A></B>(<A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> type)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useValueConstrain.Type.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ValueConstrain.Type.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.ValueConstrain\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.ValueConstrain";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useValueConstrain.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ValueConstrain.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.ValueConstrain</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></CODE></FONT></TD>\r
+<TD><CODE><B>Parameter.</B><B><A HREF="../../../compbio/metadata/Parameter.html#getValidValue()">getValidValue</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B>Parameter.</B><B><A HREF="../../../compbio/metadata/Parameter.html#setValidValue(compbio.metadata.ValueConstrain)">setValidValue</A></B>(<A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A> validValue)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useValueConstrain.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ValueConstrain.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.metadata.WrongParameterException\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.metadata.WrongParameterException";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+ <A HREF="WrongParameterException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.metadata.WrongParameterException</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>>> options)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with options.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../compbio/data/msa/Annotation.html#customAnalize(java.util.List, java.util.List)">customAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>>> options)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences according to custom settings defined in options
+ list.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> preset)</CODE>\r
+\r
+<BR>\r
+ Align a list of sequences with preset.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B>Annotation.</B><B><A HREF="../../../compbio/data/msa/Annotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>> preset)</CODE>\r
+\r
+<BR>\r
+ Analyse the sequences according to the preset settings.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that throw <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>>></CODE></FONT></TD>\r
+<TD><CODE><B>Preset.</B><B><A HREF="../../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>> rconfig)</CODE>\r
+\r
+<BR>\r
+ Converts list of options as String to type Option</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B>Option.</B><B><A HREF="../../../compbio/metadata/Option.html#setDefaultValue(java.lang.String)">setDefaultValue</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> defaultVal)</CODE>\r
+\r
+<BR>\r
+ Sets one of the values defined in optionList as default.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B>Parameter.</B><B><A HREF="../../../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)">setDefaultValue</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> defaultVal)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B>Argument.</B><B><A HREF="../../../compbio/metadata/Argument.html#setValue(java.lang.String)">setValue</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> defaultValue)</CODE>\r
+\r
+<BR>\r
+ Set default values for the parameter or an option</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B>Option.</B><B><A HREF="../../../compbio/metadata/Option.html#setValue(java.lang.String)">setValue</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> dValue)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/metadata/\class-useWrongParameterException.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="WrongParameterException.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+compbio.metadata\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white">\r
+<FONT size="+1" CLASS="FrameTitleFont">\r
+<A HREF="../../compbio/metadata/package-summary.html" target="classFrame">compbio.metadata</A></FONT>\r
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
+<TR>\r
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
+Interfaces</FONT> \r
+<FONT CLASS="FrameItemFont">\r
+<BR>\r
+<A HREF="Argument.html" title="interface in compbio.metadata" target="classFrame"><I>Argument</I></A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+\r
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
+<TR>\r
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
+Classes</FONT> \r
+<FONT CLASS="FrameItemFont">\r
+<BR>\r
+<A HREF="ChunkHolder.html" title="class in compbio.metadata" target="classFrame">ChunkHolder</A>\r
+<BR>\r
+<A HREF="Limit.html" title="class in compbio.metadata" target="classFrame">Limit</A>\r
+<BR>\r
+<A HREF="LimitsManager.html" title="class in compbio.metadata" target="classFrame">LimitsManager</A>\r
+<BR>\r
+<A HREF="Option.html" title="class in compbio.metadata" target="classFrame">Option</A>\r
+<BR>\r
+<A HREF="Parameter.html" title="class in compbio.metadata" target="classFrame">Parameter</A>\r
+<BR>\r
+<A HREF="Preset.html" title="class in compbio.metadata" target="classFrame">Preset</A>\r
+<BR>\r
+<A HREF="PresetManager.html" title="class in compbio.metadata" target="classFrame">PresetManager</A>\r
+<BR>\r
+<A HREF="RunnerConfig.html" title="class in compbio.metadata" target="classFrame">RunnerConfig</A>\r
+<BR>\r
+<A HREF="ValueConstrain.html" title="class in compbio.metadata" target="classFrame">ValueConstrain</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+\r
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
+<TR>\r
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
+Enums</FONT> \r
+<FONT CLASS="FrameItemFont">\r
+<BR>\r
+<A HREF="JobStatus.html" title="enum in compbio.metadata" target="classFrame">JobStatus</A>\r
+<BR>\r
+<A HREF="ValueConstrain.Type.html" title="enum in compbio.metadata" target="classFrame">ValueConstrain.Type</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+\r
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
+<TR>\r
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
+Exceptions</FONT> \r
+<FONT CLASS="FrameItemFont">\r
+<BR>\r
+<A HREF="JobExecutionException.html" title="class in compbio.metadata" target="classFrame">JobExecutionException</A>\r
+<BR>\r
+<A HREF="JobSubmissionException.html" title="class in compbio.metadata" target="classFrame">JobSubmissionException</A>\r
+<BR>\r
+<A HREF="LimitExceededException.html" title="class in compbio.metadata" target="classFrame">LimitExceededException</A>\r
+<BR>\r
+<A HREF="ResultNotAvailableException.html" title="class in compbio.metadata" target="classFrame">ResultNotAvailableException</A>\r
+<BR>\r
+<A HREF="UnsupportedRuntimeException.html" title="class in compbio.metadata" target="classFrame">UnsupportedRuntimeException</A>\r
+<BR>\r
+<A HREF="WrongParameterException.html" title="class in compbio.metadata" target="classFrame">WrongParameterException</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+compbio.metadata\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="compbio.metadata";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/data/sequence/package-summary.html"><B>PREV PACKAGE</B></A> \r
+ <A HREF="../../compbio/ws/client/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/package-summary.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<H2>\r
+Package compbio.metadata\r
+</H2>\r
+A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project.\r
+<P>\r
+<B>See:</B>\r
+<BR>\r
+ <A HREF="#package_description"><B>Description</B></A>\r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Interface Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument<T></A></B></TD>\r
+<TD>An unmodifiable view for the options and parameters, with one exception - it
+ allows to set a value</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+\r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Class Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></B></TD>\r
+<TD>Represents a chunk of a string data together with the position in a file for
+ the next read operation.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit<T></A></B></TD>\r
+<TD>A value object containing a maximum number of sequences and a maximum average
+ sequence length for a preset.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager<T></A></B></TD>\r
+<TD>A collection of Limits</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option<T></A></B></TD>\r
+<TD>Command line option/flag or multiple exclusive options with no value.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter<T></A></B></TD>\r
+<TD>A single value containing an option supported by the web service e.g.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset<T></A></B></TD>\r
+<TD>Collection of Options and Parameters with their values</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager<T></A></B></TD>\r
+<TD>Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig<T></A></B></TD>\r
+<TD>The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></B></TD>\r
+<TD>The type and the lower and upper boundaries for numerical value.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+\r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Enum Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></B></TD>\r
+<TD>The status of the job.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+\r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Exception Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></B></TD>\r
+<TD>JobExecutionException is thrown wherever the results of the calculation
+ cannot be obtained.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></B></TD>\r
+<TD>Exception for generic problems with JobSubmission it is often thrown as a
+ wrapper for the lower level exceptions like IOException or DrmaaException.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></B></TD>\r
+<TD>This exception is thrown if the task larger in size that the limit that
+ applies to the calculation.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></B></TD>\r
+<TD>ResultNotAvailableException is thrown wherever the results of the calculation
+ cannot be obtained.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></B></TD>\r
+<TD>Indicates that the server could not execute native executables.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></B></TD>\r
+<TD>WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
+ does not match the actual runnable or then attempting to set the value of
+ <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+\r
+<P>\r
+<A NAME="package_description"><!-- --></A><H2>\r
+Package compbio.metadata Description\r
+</H2>\r
+\r
+<P>\r
+A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project.
+ They form a base layer of JAva Bioinformatics Analysis Web Services (JABAWS)\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 January 2010</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>Peter Troshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/data/sequence/package-summary.html"><B>PREV PACKAGE</B></A> \r
+ <A HREF="../../compbio/ws/client/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/package-summary.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+compbio.metadata Class Hierarchy\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="compbio.metadata Class Hierarchy";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/data/sequence/package-tree.html"><B>PREV</B></A> \r
+ <A HREF="../../compbio/ws/client/package-tree.html"><B>NEXT</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/package-tree.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+Hierarchy For Package compbio.metadata\r
+</H2>\r
+</CENTER>\r
+<DL>\r
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../overview-tree.html">All Packages</A></DL>\r
+<HR>\r
+<H2>\r
+Class Hierarchy\r
+</H2>\r
+<UL>\r
+<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang"><B>Object</B></A><UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>ChunkHolder</B></A><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>Limit</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>LimitsManager</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><B>Option</B></A><T> (implements compbio.metadata.<A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><T>)\r
+<UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>Parameter</B></A><T></UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>Preset</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PresetManager</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>RunnerConfig</B></A><T><LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>)\r
+<UL>\r
+<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang"><B>Exception</B></A><UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>JobExecutionException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>JobSubmissionException</B></A><UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>LimitExceededException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><B>UnsupportedRuntimeException</B></A></UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>ResultNotAvailableException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><B>WrongParameterException</B></A></UL>\r
+</UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><B>ValueConstrain</B></A></UL>\r
+</UL>\r
+<H2>\r
+Interface Hierarchy\r
+</H2>\r
+<UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>Argument</B></A><T></UL>\r
+<H2>\r
+Enum Hierarchy\r
+</H2>\r
+<UL>\r
+<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang"><B>Object</B></A><UL>\r
+<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang"><B>Enum</B></A><E> (implements java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><T>, java.io.<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>)\r
+<UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>JobStatus</B></A><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><B>ValueConstrain.Type</B></A></UL>\r
+</UL>\r
+</UL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>\r
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+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/data/sequence/package-tree.html"><B>PREV</B></A> \r
+ <A HREF="../../compbio/ws/client/package-tree.html"><B>NEXT</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+ <A HREF="package-tree.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Package compbio.metadata\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Package compbio.metadata";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/package-use.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Package<br>compbio.metadata</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.data.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.data.msa"><B>ChunkHolder</B></A></B>\r
+\r
+<BR>\r
+ Represents a chunk of a string data together with the position in a file for
+ the next read operation.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.data.msa"><B>JobStatus</B></A></B>\r
+\r
+<BR>\r
+ The status of the job.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.data.msa"><B>JobSubmissionException</B></A></B>\r
+\r
+<BR>\r
+ Exception for generic problems with JobSubmission it is often thrown as a
+ wrapper for the lower level exceptions like IOException or DrmaaException.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.data.msa"><B>Limit</B></A></B>\r
+\r
+<BR>\r
+ A value object containing a maximum number of sequences and a maximum average
+ sequence length for a preset.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.data.msa"><B>LimitExceededException</B></A></B>\r
+\r
+<BR>\r
+ This exception is thrown if the task larger in size that the limit that
+ applies to the calculation.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.data.msa"><B>LimitsManager</B></A></B>\r
+\r
+<BR>\r
+ A collection of Limits</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.data.msa"><B>Option</B></A></B>\r
+\r
+<BR>\r
+ Command line option/flag or multiple exclusive options with no value.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.data.msa"><B>Preset</B></A></B>\r
+\r
+<BR>\r
+ Collection of Options and Parameters with their values</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.data.msa"><B>PresetManager</B></A></B>\r
+\r
+<BR>\r
+ Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.data.msa"><B>ResultNotAvailableException</B></A></B>\r
+\r
+<BR>\r
+ ResultNotAvailableException is thrown wherever the results of the calculation
+ cannot be obtained.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.data.msa"><B>RunnerConfig</B></A></B>\r
+\r
+<BR>\r
+ The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/UnsupportedRuntimeException.html#compbio.data.msa"><B>UnsupportedRuntimeException</B></A></B>\r
+\r
+<BR>\r
+ Indicates that the server could not execute native executables.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.data.msa"><B>WrongParameterException</B></A></B>\r
+\r
+<BR>\r
+ WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
+ does not match the actual runnable or then attempting to set the value of
+ <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/Argument.html#compbio.metadata"><B>Argument</B></A></B>\r
+\r
+<BR>\r
+ An unmodifiable view for the options and parameters, with one exception - it
+ allows to set a value</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.metadata"><B>JobStatus</B></A></B>\r
+\r
+<BR>\r
+ The status of the job.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.metadata"><B>JobSubmissionException</B></A></B>\r
+\r
+<BR>\r
+ Exception for generic problems with JobSubmission it is often thrown as a
+ wrapper for the lower level exceptions like IOException or DrmaaException.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.metadata"><B>Limit</B></A></B>\r
+\r
+<BR>\r
+ A value object containing a maximum number of sequences and a maximum average
+ sequence length for a preset.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.metadata"><B>LimitExceededException</B></A></B>\r
+\r
+<BR>\r
+ This exception is thrown if the task larger in size that the limit that
+ applies to the calculation.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.metadata"><B>Option</B></A></B>\r
+\r
+<BR>\r
+ Command line option/flag or multiple exclusive options with no value.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/Parameter.html#compbio.metadata"><B>Parameter</B></A></B>\r
+\r
+<BR>\r
+ A single value containing an option supported by the web service e.g.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.metadata"><B>Preset</B></A></B>\r
+\r
+<BR>\r
+ Collection of Options and Parameters with their values</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.metadata"><B>PresetManager</B></A></B>\r
+\r
+<BR>\r
+ Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.metadata"><B>RunnerConfig</B></A></B>\r
+\r
+<BR>\r
+ The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/ValueConstrain.html#compbio.metadata"><B>ValueConstrain</B></A></B>\r
+\r
+<BR>\r
+ The type and the lower and upper boundaries for numerical value.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/ValueConstrain.Type.html#compbio.metadata"><B>ValueConstrain.Type</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.metadata"><B>WrongParameterException</B></A></B>\r
+\r
+<BR>\r
+ WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
+ does not match the actual runnable or then attempting to set the value of
+ <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
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+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/metadata/package-use.html" target="_top"><B>FRAMES</B></A> \r
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+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+IOHelper\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
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+ if (location.href.indexOf('is-external=true') == -1) {\r
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+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV CLASS \r
+ <A HREF="../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
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+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.ws.client</FONT>\r
+<BR>\r
+Class IOHelper</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.IOHelper</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>IOHelper</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/IOHelper.html#IOHelper()">IOHelper</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="IOHelper()"><!-- --></A><H3>\r
+IOHelper</H3>\r
+<PRE>\r
+public <B>IOHelper</B>()</PRE>\r
+<DL>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/IOHelper.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV CLASS \r
+ <A HREF="../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/ws/client/IOHelper.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="IOHelper.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+Jws2Client\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Jws2Client";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Jws2Client.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/ws/client/Jws2Client.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Jws2Client.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.ws.client</FONT>\r
+<BR>\r
+Class Jws2Client</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.Jws2Client</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>Jws2Client</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+A command line client for JAva Bioinformatics Analysis Web Services\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Services)">connect</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> host,\r
+ <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service)</CODE>\r
+\r
+<BR>\r
+ Connects to a web service by the host and the service name</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>[] args)</CODE>\r
+\r
+<BR>\r
+ Starts command line client, if no parameter are supported print help.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#validURL(java.lang.String)">validURL</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> urlstr)</CODE>\r
+\r
+<BR>\r
+ Attempt to construct the URL object from the string</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="validURL(java.lang.String)"><!-- --></A><H3>\r
+validURL</H3>\r
+<PRE>\r
+public static boolean <B>validURL</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> urlstr)</PRE>\r
+<DL>\r
+<DD>Attempt to construct the URL object from the string\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>urlstr</CODE> - \r
+<DT><B>Returns:</B><DD>true if it succeed false otherwise</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="connect(java.lang.String, compbio.ws.client.Services)"><!-- --></A><H3>\r
+connect</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A> <B>connect</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> host,\r
+ <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service)\r
+ throws <A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/ws/WebServiceException.html?is-external=true" title="class or interface in javax.xml.ws">WebServiceException</A></PRE>\r
+<DL>\r
+<DD>Connects to a web service by the host and the service name\r
+<P>\r
+<DD><DL>\r
+<DT><B>Type Parameters:</B><DD><CODE>T</CODE> - web service type<DT><B>Parameters:</B><DD><CODE>host</CODE> - <DD><CODE>service</CODE> - \r
+<DT><B>Returns:</B><DD>MsaWS<T>\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/ws/WebServiceException.html?is-external=true" title="class or interface in javax.xml.ws">WebServiceException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>\r
+main</H3>\r
+<PRE>\r
+public static void <B>main</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>[] args)</PRE>\r
+<DL>\r
+<DD>Starts command line client, if no parameter are supported print help. Two
+ parameters are required for successfull call the JWS2 host name and a
+ service name.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>args</CODE> - Usage: <Class or Jar file name> -h=host_and_context
+ -s=serviceName ACTION [OPTIONS]
+
+ -h=<host_and_context> - a full URL to the JWS2 web server
+ including context path e.g. http://10.31.1.159:8080/ws
+
+ -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,
+ TcoffeeWS, ProbconsWS] ACTIONS:
+
+ -i=<inputFile> - full path to fasta formatted sequence file,
+ from which to align sequences
+
+ -parameters - lists parameters supported by web service
+
+ -presets - lists presets supported by web service
+
+ -limits - lists web services limits Please note that if input
+ file is specified other actions are ignored
+
+ OPTIONS: (only for use with -i action):
+
+ -r=<presetName> - name of the preset to use
+
+ -o=<outputFile> - full path to the file where to write an
+ alignment -f=<parameterInputFile> - the name of the file with
+ the list of parameters to use. Please note that -r and -f
+ options cannot be used together. Alignment is done with either
+ preset or a parameters from the file, but not both!</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Jws2Client.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/ws/client/Jws2Client.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Jws2Client.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+MetadataHelper\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="MetadataHelper";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MetadataHelper.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/ws/client/MetadataHelper.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="MetadataHelper.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.ws.client</FONT>\r
+<BR>\r
+Class MetadataHelper</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.MetadataHelper</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>MetadataHelper</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/MetadataHelper.html#MetadataHelper()">MetadataHelper</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="MetadataHelper()"><!-- --></A><H3>\r
+MetadataHelper</H3>\r
+<PRE>\r
+public <B>MetadataHelper</B>()</PRE>\r
+<DL>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MetadataHelper.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/ws/client/MetadataHelper.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="MetadataHelper.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+Services\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Services";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Services.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/ws/client/Services.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Services.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.ws.client</FONT>\r
+<BR>\r
+Enum Services</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">java.lang.Enum</A><<A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.Services</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><<A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public enum <B>Services</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><<A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>></DL>\r
+</PRE>\r
+\r
+<P>\r
+List of web services currently supported by JABAWS version 2\r
+<P>\r
+\r
+<P>\r
+<HR>\r
+\r
+<P>\r
+<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
+\r
+<A NAME="enum_constant_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Enum Constant Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#AAConWS">AAConWS</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#ClustalWS">ClustalWS</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#MafftWS">MafftWS</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#MuscleWS">MuscleWS</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#ProbconsWS">ProbconsWS</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#TcoffeeWS">TcoffeeWS</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#getService(java.lang.String)">getService</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> servName)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#valueOf(java.lang.String)">valueOf</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ Returns the enum constant of this type with the specified name.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>[]</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#values()">values</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns an array containing the constants of this enum type, in
+the order they are declared.</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#compareTo(E)" title="class or interface in java.lang">compareTo</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#getDeclaringClass()" title="class or interface in java.lang">getDeclaringClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#name()" title="class or interface in java.lang">name</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#ordinal()" title="class or interface in java.lang">ordinal</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#valueOf(java.lang.Class, java.lang.String)" title="class or interface in java.lang">valueOf</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
+\r
+<A NAME="enum_constant_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Enum Constant Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="MafftWS"><!-- --></A><H3>\r
+MafftWS</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>MafftWS</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="MuscleWS"><!-- --></A><H3>\r
+MuscleWS</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>MuscleWS</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="ClustalWS"><!-- --></A><H3>\r
+ClustalWS</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>ClustalWS</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="TcoffeeWS"><!-- --></A><H3>\r
+TcoffeeWS</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>TcoffeeWS</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="ProbconsWS"><!-- --></A><H3>\r
+ProbconsWS</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>ProbconsWS</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="AAConWS"><!-- --></A><H3>\r
+AAConWS</H3>\r
+<PRE>\r
+public static final <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>AAConWS</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="values()"><!-- --></A><H3>\r
+values</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>[] <B>values</B>()</PRE>\r
+<DL>\r
+<DD>Returns an array containing the constants of this enum type, in
+the order they are declared. This method may be used to iterate
+over the constants as follows:
+<pre>
+for (Services c : Services.values())
+ System.out.println(c);
+</pre>\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
+the order they are declared</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
+valueOf</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>valueOf</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</PRE>\r
+<DL>\r
+<DD>Returns the enum constant of this type with the specified name.
+The string must match <I>exactly</I> an identifier used to declare an
+enum constant in this type. (Extraneous whitespace characters are
+not permitted.)\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
+<DT><B>Returns:</B><DD>the enum constant with the specified name\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</A></CODE> - if this enum type has no constant
+with the specified name\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE> - if the argument is null</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getService(java.lang.String)"><!-- --></A><H3>\r
+getService</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>getService</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> servName)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Services.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/ws/client/Services.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Services.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 GMT 2010 -->\r
+<TITLE>\r
+WSTester\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="WSTester";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/WSTester.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>PREV CLASS</B></A> \r
+ NEXT CLASS</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/ws/client/WSTester.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="WSTester.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.ws.client</FONT>\r
+<BR>\r
+Class WSTester</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.WSTester</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>WSTester</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+Class for testing web services\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 February 2010</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/WSTester.html#WSTester()">WSTester</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
+<TR ALIGN="right" VALIGN="">\r
+<TD NOWRAP><FONT SIZE="-1">\r
+<CODE><T> void</CODE></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/WSTester.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>[] args)</CODE>\r
+\r
+<BR>\r
+ Test JWS2 web services</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="WSTester()"><!-- --></A><H3>\r
+WSTester</H3>\r
+<PRE>\r
+public <B>WSTester</B>()</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>\r
+main</H3>\r
+<PRE>\r
+public static <T> void <B>main</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>[] args)\r
+ throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
+<DL>\r
+<DD>Test JWS2 web services\r
+<P>\r
+<DD><DL>\r
+<DT><B>Type Parameters:</B><DD><CODE>T</CODE> - web service type<DT><B>Parameters:</B><DD><CODE>args</CODE> - -h=<Your web application server host name, port and JWS2
+ context path>
+
+ -s=<ServiceName> which is optional. If service name is not
+ provided then all known JWS2 web services are tested\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/WSTester.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>PREV CLASS</B></A> \r
+ NEXT CLASS</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/ws/client/WSTester.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="WSTester.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.ws.client.IOHelper\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.ws.client.IOHelper";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/ws/client/\class-useIOHelper.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="IOHelper.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.ws.client.IOHelper</B></H2>\r
+</CENTER>\r
+No usage of compbio.ws.client.IOHelper\r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/ws/client/\class-useIOHelper.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="IOHelper.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.ws.client.Jws2Client\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.ws.client.Jws2Client";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/ws/client/\class-useJws2Client.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Jws2Client.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.ws.client.Jws2Client</B></H2>\r
+</CENTER>\r
+No usage of compbio.ws.client.Jws2Client\r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/ws/client/\class-useJws2Client.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Jws2Client.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.ws.client.MetadataHelper\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.ws.client.MetadataHelper";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/ws/client/\class-useMetadataHelper.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="MetadataHelper.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.ws.client.MetadataHelper</B></H2>\r
+</CENTER>\r
+No usage of compbio.ws.client.MetadataHelper\r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/ws/client/\class-useMetadataHelper.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="MetadataHelper.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.ws.client.Services\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.ws.client.Services";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/ws/client/\class-useServices.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Services.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.ws.client.Services</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.ws.client"><B>compbio.ws.client</B></A></TD>\r
+<TD>A command line client and web services testing client for
+ JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.ws.client"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A> that return <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></CODE></FONT></TD>\r
+<TD><CODE><B>Services.</B><B><A HREF="../../../../compbio/ws/client/Services.html#getService(java.lang.String)">getService</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> servName)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></CODE></FONT></TD>\r
+<TD><CODE><B>Services.</B><B><A HREF="../../../../compbio/ws/client/Services.html#valueOf(java.lang.String)">valueOf</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> name)</CODE>\r
+\r
+<BR>\r
+ Returns the enum constant of this type with the specified name.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>[]</CODE></FONT></TD>\r
+<TD><CODE><B>Services.</B><B><A HREF="../../../../compbio/ws/client/Services.html#values()">values</A></B>()</CODE>\r
+\r
+<BR>\r
+ Returns an array containing the constants of this enum type, in
+the order they are declared.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A> with parameters of type <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></CODE></FONT></TD>\r
+<TD><CODE><B>Jws2Client.</B><B><A HREF="../../../../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Services)">connect</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> host,\r
+ <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service)</CODE>\r
+\r
+<BR>\r
+ Connects to a web service by the host and the service name</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/ws/client/\class-useServices.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Services.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Class compbio.ws.client.WSTester\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.ws.client.WSTester";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/ws/client/\class-useWSTester.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="WSTester.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.ws.client.WSTester</B></H2>\r
+</CENTER>\r
+No usage of compbio.ws.client.WSTester\r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/ws/client/\class-useWSTester.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="WSTester.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+compbio.ws.client\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white">\r
+<FONT size="+1" CLASS="FrameTitleFont">\r
+<A HREF="../../../compbio/ws/client/package-summary.html" target="classFrame">compbio.ws.client</A></FONT>\r
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
+<TR>\r
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
+Classes</FONT> \r
+<FONT CLASS="FrameItemFont">\r
+<BR>\r
+<A HREF="IOHelper.html" title="class in compbio.ws.client" target="classFrame">IOHelper</A>\r
+<BR>\r
+<A HREF="Jws2Client.html" title="class in compbio.ws.client" target="classFrame">Jws2Client</A>\r
+<BR>\r
+<A HREF="MetadataHelper.html" title="class in compbio.ws.client" target="classFrame">MetadataHelper</A>\r
+<BR>\r
+<A HREF="WSTester.html" title="class in compbio.ws.client" target="classFrame">WSTester</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+\r
+<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
+<TR>\r
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
+Enums</FONT> \r
+<FONT CLASS="FrameItemFont">\r
+<BR>\r
+<A HREF="Services.html" title="enum in compbio.ws.client" target="classFrame">Services</A></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+compbio.ws.client\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
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+function windowTitle()\r
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+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="compbio.ws.client";\r
+ }\r
+}\r
+</SCRIPT>\r
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+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
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+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/metadata/package-summary.html"><B>PREV PACKAGE</B></A> \r
+ NEXT PACKAGE</FONT></TD>\r
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+ <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
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+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<H2>\r
+Package compbio.ws.client\r
+</H2>\r
+A command line client and web services testing client for
+ JAva Bioinformatics Analysis Web Services.\r
+<P>\r
+<B>See:</B>\r
+<BR>\r
+ <A HREF="#package_description"><B>Description</B></A>\r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Class Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client">IOHelper</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A></B></TD>\r
+<TD>A command line client for JAva Bioinformatics Analysis Web Services</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A></B></TD>\r
+<TD>Class for testing web services</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+\r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Enum Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></B></TD>\r
+<TD>List of web services currently supported by JABAWS version 2</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+\r
+<P>\r
+<A NAME="package_description"><!-- --></A><H2>\r
+Package compbio.ws.client Description\r
+</H2>\r
+\r
+<P>\r
+A command line client and web services testing client for
+ JAva Bioinformatics Analysis Web Services.\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0 April 2010</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>Peter Troshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/metadata/package-summary.html"><B>PREV PACKAGE</B></A> \r
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+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+compbio.ws.client Class Hierarchy\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="compbio.ws.client Class Hierarchy";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/metadata/package-tree.html"><B>PREV</B></A> \r
+ NEXT</FONT></TD>\r
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+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
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+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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+\r
+\r
+</FONT></TD>\r
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+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+Hierarchy For Package compbio.ws.client\r
+</H2>\r
+</CENTER>\r
+<DL>\r
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../overview-tree.html">All Packages</A></DL>\r
+<HR>\r
+<H2>\r
+Class Hierarchy\r
+</H2>\r
+<UL>\r
+<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang"><B>Object</B></A><UL>\r
+<LI TYPE="circle">compbio.ws.client.<A HREF="../../../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client"><B>IOHelper</B></A><LI TYPE="circle">compbio.ws.client.<A HREF="../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><B>Jws2Client</B></A><LI TYPE="circle">compbio.ws.client.<A HREF="../../../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client"><B>MetadataHelper</B></A><LI TYPE="circle">compbio.ws.client.<A HREF="../../../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>WSTester</B></A></UL>\r
+</UL>\r
+<H2>\r
+Enum Hierarchy\r
+</H2>\r
+<UL>\r
+<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang"><B>Object</B></A><UL>\r
+<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang"><B>Enum</B></A><E> (implements java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><T>, java.io.<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>)\r
+<UL>\r
+<LI TYPE="circle">compbio.ws.client.<A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>Services</B></A></UL>\r
+</UL>\r
+</UL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../compbio/metadata/package-tree.html"><B>PREV</B></A> \r
+ NEXT</FONT></TD>\r
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+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
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+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
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+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Uses of Package compbio.ws.client\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
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+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Package compbio.ws.client";\r
+ }\r
+}\r
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+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+<H2>\r
+<B>Uses of Package<br>compbio.ws.client</B></H2>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Packages that use <A HREF="../../../compbio/ws/client/package-summary.html">compbio.ws.client</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.ws.client"><B>compbio.ws.client</B></A></TD>\r
+<TD>A command line client and web services testing client for
+ JAva Bioinformatics Analysis Web Services. </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.ws.client"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Classes in <A HREF="../../../compbio/ws/client/package-summary.html">compbio.ws.client</A> used by <A HREF="../../../compbio/ws/client/package-summary.html">compbio.ws.client</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/ws/client/class-use/Services.html#compbio.ws.client"><B>Services</B></A></B>\r
+\r
+<BR>\r
+ List of web services currently supported by JABAWS version 2</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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+ <!--\r
+ if(window==top) {\r
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+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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+\r
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--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Constant Field Values\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">\r
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+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
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+\r
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+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<H1>\r
+Constant Field Values</H1>\r
+</CENTER>\r
+<HR SIZE="4" NOSHADE>\r
+<B>Contents</B><UL>\r
+<LI><A HREF="#compbio.data">compbio.data.*</A>\r
+<LI><A HREF="#compbio.metadata">compbio.metadata.*</A>\r
+</UL>\r
+\r
+<A NAME="compbio.data"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left"><FONT SIZE="+2">\r
+compbio.data.*</FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+\r
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<A NAME="compbio.data.sequence.ClustalAlignmentUtil.gapchar"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
+<CODE>public static final char</CODE></FONT></TD>\r
+<TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</A></CODE></TD>\r
+<TD ALIGN="right"><CODE>45</CODE></TD>\r
+</TR>\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+\r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left"><FONT SIZE="+2">\r
+compbio.metadata.*</FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+\r
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="3">compbio.metadata.<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<A NAME="compbio.metadata.PresetManager.LOCAL_ENGINE_LIMIT_PRESET"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
+<CODE>public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD ALIGN="left"><CODE><A HREF="compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET">LOCAL_ENGINE_LIMIT_PRESET</A></CODE></TD>\r
+<TD ALIGN="right"><CODE>"# LocalEngineExecutionLimit #"</CODE></TD>\r
+</TR>\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+\r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
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+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
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+\r
+<META NAME="date" CONTENT="2010-12-09">\r
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+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Deprecated List";\r
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+}\r
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+\r
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+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
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+<!-- ========= START OF TOP NAVBAR ======= -->\r
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+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
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+\r
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+<CENTER>\r
+<H1>\r
+How This API Document Is Organized</H1>\r
+</CENTER>\r
+This API (Application Programming Interface) document has pages corresponding to the items in the navigation bar, described as follows.<H3>\r
+Overview</H3>\r
+<BLOCKQUOTE>\r
+\r
+<P>\r
+The <A HREF="overview-summary.html">Overview</A> page is the front page of this API document and provides a list of all packages with a summary for each. This page can also contain an overall description of the set of packages.</BLOCKQUOTE>\r
+<H3>\r
+Package</H3>\r
+<BLOCKQUOTE>\r
+\r
+<P>\r
+Each package has a page that contains a list of its classes and interfaces, with a summary for each. This page can contain four categories:<UL>\r
+<LI>Interfaces (italic)<LI>Classes<LI>Enums<LI>Exceptions<LI>Errors<LI>Annotation Types</UL>\r
+</BLOCKQUOTE>\r
+<H3>\r
+Class/Interface</H3>\r
+<BLOCKQUOTE>\r
+\r
+<P>\r
+Each class, interface, nested class and nested interface has its own separate page. Each of these pages has three sections consisting of a class/interface description, summary tables, and detailed member descriptions:<UL>\r
+<LI>Class inheritance diagram<LI>Direct Subclasses<LI>All Known Subinterfaces<LI>All Known Implementing Classes<LI>Class/interface declaration<LI>Class/interface description\r
+<P>\r
+<LI>Nested Class Summary<LI>Field Summary<LI>Constructor Summary<LI>Method Summary\r
+<P>\r
+<LI>Field Detail<LI>Constructor Detail<LI>Method Detail</UL>\r
+Each summary entry contains the first sentence from the detailed description for that item. The summary entries are alphabetical, while the detailed descriptions are in the order they appear in the source code. This preserves the logical groupings established by the programmer.</BLOCKQUOTE>\r
+</BLOCKQUOTE>\r
+<H3>\r
+Annotation Type</H3>\r
+<BLOCKQUOTE>\r
+\r
+<P>\r
+Each annotation type has its own separate page with the following sections:<UL>\r
+<LI>Annotation Type declaration<LI>Annotation Type description<LI>Required Element Summary<LI>Optional Element Summary<LI>Element Detail</UL>\r
+</BLOCKQUOTE>\r
+</BLOCKQUOTE>\r
+<H3>\r
+Enum</H3>\r
+<BLOCKQUOTE>\r
+\r
+<P>\r
+Each enum has its own separate page with the following sections:<UL>\r
+<LI>Enum declaration<LI>Enum description<LI>Enum Constant Summary<LI>Enum Constant Detail</UL>\r
+</BLOCKQUOTE>\r
+<H3>\r
+Use</H3>\r
+<BLOCKQUOTE>\r
+Each documented package, class and interface has its own Use page. This page describes what packages, classes, methods, constructors and fields use any part of the given class or package. Given a class or interface A, its Use page includes subclasses of A, fields declared as A, methods that return A, and methods and constructors with parameters of type A. You can access this page by first going to the package, class or interface, then clicking on the "Use" link in the navigation bar.</BLOCKQUOTE>\r
+<H3>\r
+Tree (Class Hierarchy)</H3>\r
+<BLOCKQUOTE>\r
+There is a <A HREF="overview-tree.html">Class Hierarchy</A> page for all packages, plus a hierarchy for each package. Each hierarchy page contains a list of classes and a list of interfaces. The classes are organized by inheritance structure starting with <code>java.lang.Object</code>. The interfaces do not inherit from <code>java.lang.Object</code>.<UL>\r
+<LI>When viewing the Overview page, clicking on "Tree" displays the hierarchy for all packages.<LI>When viewing a particular package, class or interface page, clicking "Tree" displays the hierarchy for only that package.</UL>\r
+</BLOCKQUOTE>\r
+<H3>\r
+Deprecated API</H3>\r
+<BLOCKQUOTE>\r
+The <A HREF="deprecated-list.html">Deprecated API</A> page lists all of the API that have been deprecated. A deprecated API is not recommended for use, generally due to improvements, and a replacement API is usually given. Deprecated APIs may be removed in future implementations.</BLOCKQUOTE>\r
+<H3>\r
+Index</H3>\r
+<BLOCKQUOTE>\r
+The <A HREF="index-files/index-1.html">Index</A> contains an alphabetic list of all classes, interfaces, constructors, methods, and fields.</BLOCKQUOTE>\r
+<H3>\r
+Prev/Next</H3>\r
+These links take you to the next or previous class, interface, package, or related page.<H3>\r
+Frames/No Frames</H3>\r
+These links show and hide the HTML frames. All pages are available with or without frames.\r
+<P>\r
+<H3>\r
+Serialized Form</H3>\r
+Each serializable or externalizable class has a description of its serialization fields and methods. This information is of interest to re-implementors, not to developers using the API. While there is no link in the navigation bar, you can get to this information by going to any serialized class and clicking "Serialized Form" in the "See also" section of the class description.\r
+<P>\r
+<H3>\r
+Constant Field Values</H3>\r
+The <a href="constant-values.html">Constant Field Values</a> page lists the static final fields and their values.\r
+<P>\r
+<FONT SIZE="-1">\r
+<EM>\r
+This help file applies to API documentation generated using the standard doclet.</EM>\r
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+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_A_"><!-- --></A><H2>\r
+<B>A</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AA"><B>AA</B></A> - \r
+Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Valid Amino acids\r
+<DT><A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html#addAnnotation(T, java.util.ArrayList)"><B>addAnnotation(T, ArrayList<Float>)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence">MultiAnnotatedSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)"><B>addOption(Option<T>)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Adds Option to the internal list of options\r
+<DT><A HREF="../compbio/metadata/Option.html#addOptionNames(java.lang.String...)"><B>addOptionNames(String...)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>Adds an option to the optionName list\r
+<DT><A HREF="../compbio/metadata/Parameter.html#addOptionNames(java.lang.String...)"><B>addOptionNames(String...)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#addParameter(compbio.metadata.Parameter)"><B>addParameter(Parameter<T>)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Adds parameter to the internal parameter list\r
+<DT><A HREF="../compbio/metadata/Parameter.html#addPossibleValues(java.lang.String...)"><B>addPossibleValues(String...)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/MsaWS.html#align(java.util.List)"><B>align(List<FastaSequence>)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DD>Align a list of sequences with default settings.\r
+<DT><A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><B>Alignment</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Multiple sequence alignment.<DT><A HREF="../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)"><B>Alignment(List<FastaSequence>, Program, char)</B></A> - \r
+Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)"><B>Alignment(List<FastaSequence>, AlignmentMetadata)</B></A> - \r
+Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>AlignmentMetadata</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Alignment metadata e.g.<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#AlignmentMetadata(compbio.data.sequence.Program, char)"><B>AlignmentMetadata(Program, char)</B></A> - \r
+Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA"><B>AMBIGUOUS_AA</B></A> - \r
+Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Same as AA pattern but with two additional letters - XU\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE"><B>AMBIGUOUS_NUCLEOTIDE</B></A> - \r
+Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Ambiguous nucleotide\r
+<DT><A HREF="../compbio/data/msa/Annotation.html#analize(java.util.List)"><B>analize(List<FastaSequence>)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa">Annotation</A>\r
+<DD>Analyse the sequences.\r
+<DT><A HREF="../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence"><B>AnnotatedSequence</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD> <DT><A HREF="../compbio/data/sequence/AnnotatedSequence.html#AnnotatedSequence(java.lang.String, java.lang.String, float[])"><B>AnnotatedSequence(String, String, float[])</B></A> - \r
+Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/AnnotatedSequence.html#AnnotatedSequence(compbio.data.sequence.FastaSequence, float[])"><B>AnnotatedSequence(FastaSequence, float[])</B></A> - \r
+Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><B>Annotation</B></A><<A HREF="../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>> - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>Interface for tools that results to one or more annotation to sequence(s)<DT><A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>Argument</B></A><<A HREF="../compbio/metadata/Argument.html" title="type parameter in Argument">T</A>> - Interface in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>An unmodifiable view for the options and parameters, with one exception - it
+ allows to set a value</DL>\r
+<HR>\r
+\r
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+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+L-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="L-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-9.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-11.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-10.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-10.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_L_"><!-- --></A><H2>\r
+<B>L</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>Limit</B></A><<A HREF="../compbio/metadata/Limit.html" title="type parameter in Limit">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>A value object containing a maximum number of sequences and a maximum average
+ sequence length for a preset.<DT><A HREF="../compbio/metadata/Limit.html#Limit(int, int, java.lang.String)"><B>Limit(int, int, String)</B></A> - \r
+Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
+<DD>Instantiate the limit\r
+<DT><A HREF="../compbio/metadata/Limit.html#Limit(int, int, java.lang.String, boolean)"><B>Limit(int, int, String, boolean)</B></A> - \r
+Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>LimitExceededException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>This exception is thrown if the task larger in size that the limit that
+ applies to the calculation.<DT><A HREF="../compbio/metadata/LimitExceededException.html#LimitExceededException(java.lang.String)"><B>LimitExceededException(String)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>LimitsManager</B></A><<A HREF="../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>A collection of Limits<DT><A HREF="../compbio/metadata/LimitsManager.html#LimitsManager()"><B>LimitsManager()</B></A> - \r
+Constructor for class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET"><B>LOCAL_ENGINE_LIMIT_PRESET</B></A> - \r
+Static variable in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
+<DD> \r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-9.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-11.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-10.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-10.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+M-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="M-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-10.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-12.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-11.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-11.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_M_"><!-- --></A><H2>\r
+<B>M</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/ws/client/Jws2Client.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
+Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
+<DD>Starts command line client, if no parameter are supported print help.\r
+<DT><A HREF="../compbio/ws/client/WSTester.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
+Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
+<DD>Test JWS2 web services\r
+<DT><A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><B>Metadata</B></A><<A HREF="../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>> - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD> <DT><A HREF="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client"><B>MetadataHelper</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD> <DT><A HREF="../compbio/ws/client/MetadataHelper.html#MetadataHelper()"><B>MetadataHelper()</B></A> - \r
+Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence"><B>Method</B></A> - Enum in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Enumeration listing of all the supported methods.<DT><A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A><<A HREF="../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>Multiple Sequence Alignment (MSA) Web Services Interface<DT><A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence"><B>MultiAnnotatedSequence</B></A><<A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html" title="type parameter in MultiAnnotatedSequence">T</A> extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><<A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html" title="type parameter in MultiAnnotatedSequence">T</A>>> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>TODO complete<DT><A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html#MultiAnnotatedSequence(java.lang.Class)"><B>MultiAnnotatedSequence(Class<T>)</B></A> - \r
+Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence">MultiAnnotatedSequence</A>\r
+<DD> \r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-10.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-12.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-11.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-11.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+N-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="N-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-11.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-13.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-12.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-12.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_N_"><!-- --></A><H2>\r
+<B>N</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)"><B>newLimitExceeded(Limit<?>, List<FastaSequence>)</B></A> - \r
+Static method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NON_AA"><B>NON_AA</B></A> - \r
+Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>inversion of AA pattern\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NON_NUCLEOTIDE"><B>NON_NUCLEOTIDE</B></A> - \r
+Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Non nucleotide\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NONWORD"><B>NONWORD</B></A> - \r
+Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Non word\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NUCLEOTIDE"><B>NUCLEOTIDE</B></A> - \r
+Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Nucleotides a, t, g, c, u\r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-11.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-13.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-12.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-12.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+O-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="O-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-12.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-14.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-13.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-13.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_O_"><!-- --></A><H2>\r
+<B>O</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata"><B>Option</B></A><<A HREF="../compbio/metadata/Option.html" title="type parameter in Option">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Command line option/flag or multiple exclusive options with no value.<DT><A HREF="../compbio/metadata/Option.html#Option(java.lang.String, java.lang.String)"><B>Option(String, String)</B></A> - \r
+Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD> \r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-12.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-14.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-13.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-13.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+P-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="P-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-13.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-15.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-14.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-14.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_P_"><!-- --></A><H2>\r
+<B>P</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>Parameter</B></A><<A HREF="../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>A single value containing an option supported by the web service e.g.<DT><A HREF="../compbio/metadata/Parameter.html#Parameter(java.lang.String, java.lang.String)"><B>Parameter(String, String)</B></A> - \r
+Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>Preset</B></A><<A HREF="../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Collection of Options and Parameters with their values<DT><A HREF="../compbio/metadata/Preset.html#Preset()"><B>Preset()</B></A> - \r
+Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List<FastaSequence>, Preset<T>)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DD>Align a list of sequences with preset.\r
+<DT><A HREF="../compbio/data/msa/Annotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)"><B>presetAnalize(List<FastaSequence>, Preset<T>)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa">Annotation</A>\r
+<DD>Analyse the sequences according to the preset settings.\r
+<DT><A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PresetManager</B></A><<A HREF="../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Collection of presets and methods to manipulate them @see <A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A><DT><A HREF="../compbio/metadata/PresetManager.html#PresetManager()"><B>PresetManager()</B></A> - \r
+Constructor for class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>Program</B></A> - Enum in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>The list of programmes that can produce alignments<DT><A HREF="../compbio/data/msa/JManagement.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>\r
+<DD>Reads 1kb chunk from the statistics file which is specific to a given web
+ service from the <code>position</code>.\r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-13.html"><B>PREV LETTER</B></A> \r
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+ <A HREF="index-14.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+R-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="R-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-14.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-16.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-15.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-15.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_R_"><!-- --></A><H2>\r
+<B>R</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readAAConResults(java.io.InputStream)"><B>readAAConResults(InputStream)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Read AACon result with no alignment files.\r
+<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)"><B>readClustalFile(InputStream)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
+<DD>Read Clustal formatted alignment.\r
+<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)"><B>readClustalFile(File)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)"><B>readFasta(InputStream)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Reads fasta sequences from inStream into the list of FastaSequence
+ objects\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.File)"><B>readJRonn(File)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.InputStream)"><B>readJRonn(InputStream)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Reader for JRonn horizontal file format\r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgument(java.lang.String)"><B>removeArgument(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Removes the argument <A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found.\r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgumentByOptionName(java.lang.String)"><B>removeArgumentByOptionName(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Removes the argument which can be a Parameter or an Option instance by
+ the value in <optionNames> element of the runner configuration
+ descriptor.\r
+<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>ResultNotAvailableException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>ResultNotAvailableException is thrown wherever the results of the calculation
+ cannot be obtained.<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String)"><B>ResultNotAvailableException(String)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.Throwable)"><B>ResultNotAvailableException(Throwable)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String, java.lang.Throwable)"><B>ResultNotAvailableException(String, Throwable)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>RunnerConfig</B></A><<A HREF="../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>The list of <A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.<DT><A HREF="../compbio/metadata/RunnerConfig.html#RunnerConfig()"><B>RunnerConfig()</B></A> - \r
+Constructor for class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD> \r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-14.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-16.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-15.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-15.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+S-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="S-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-15.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-17.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-16.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-16.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_S_"><!-- --></A><H2>\r
+<B>S</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><B>Score</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD> <DT><A HREF="../compbio/data/sequence/Score.html#Score(compbio.data.sequence.Method, java.util.List)"><B>Score(Method, List<Float>)</B></A> - \r
+Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>SequenceUtil</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Utility class for operations on sequences<DT><A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>Services</B></A> - Enum in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>List of web services currently supported by JABAWS version 2<DT><A HREF="../compbio/metadata/Option.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>Sets one of the values defined in optionList as default.\r
+<DT><A HREF="../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Option.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Preset.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Option.html#setFurtherDetails(java.net.URL)"><B>setFurtherDetails(URL)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/ValueConstrain.html#setMax(java.lang.String)"><B>setMax(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/ValueConstrain.html#setMin(java.lang.String)"><B>setMin(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Option.html#setName(java.lang.String)"><B>setName(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Preset.html#setName(java.lang.String)"><B>setName(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Parameter.html#setOptionName(java.lang.String)"><B>setOptionName(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Option.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set<String>)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Parameter.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set<String>)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Preset.html#setOptions(java.util.List)"><B>setOptions(List<String>)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)"><B>setOptions(List<Option<T>>)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Adds the list of options or parameters to the internal list of options\r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)"><B>setParameters(List<Parameter<T>>)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Sets the list of parameters as internal list\r
+<DT><A HREF="../compbio/metadata/Parameter.html#setPossibleValues(java.util.Set)"><B>setPossibleValues(Set<String>)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/PresetManager.html#setPresets(java.util.List)"><B>setPresets(List<Preset<T>>)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#setPrmSeparator(java.lang.String)"><B>setPrmSeparator(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Sets name value separator character\r
+<DT><A HREF="../compbio/metadata/Option.html#setRequired(boolean)"><B>setRequired(boolean)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/PresetManager.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Set the name of a runner class\r
+<DT><A HREF="../compbio/metadata/ValueConstrain.html#setType(compbio.metadata.ValueConstrain.Type)"><B>setType(ValueConstrain.Type)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Parameter.html#setValidValue(compbio.metadata.ValueConstrain)"><B>setValidValue(ValueConstrain)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Argument.html#setValue(java.lang.String)"><B>setValue(String)</B></A> - \r
+Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
+<DD>Set default values for the parameter or an option\r
+<DT><A HREF="../compbio/metadata/Option.html#setValue(java.lang.String)"><B>setValue(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD> \r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
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+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
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+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
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+\r
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+</FONT></TD>\r
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+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+T-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
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+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
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+function windowTitle()\r
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+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-16.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-18.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-17.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-17.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_T_"><!-- --></A><H2>\r
+<B>T</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/metadata/Option.html#toCommand(java.lang.String)"><B>toCommand(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>Convert the option to the command string.\r
+<DT><A HREF="../compbio/metadata/Parameter.html#toCommand(java.lang.String)"><B>toCommand(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html#toJalviewAnnotation()"><B>toJalviewAnnotation()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence">MultiAnnotatedSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/Alignment.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/AnnotatedSequence.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/FastaSequence.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
+<DD>Same as oneLineFasta\r
+<DT><A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence">MultiAnnotatedSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/Score.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/ChunkHolder.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Limit.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/LimitsManager.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Option.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Parameter.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Preset.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/PresetManager.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/ValueConstrain.html#toString()"><B>toString()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
+<DD> \r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-16.html"><B>PREV LETTER</B></A> \r
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+ <A HREF="../index.html?index-filesindex-17.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-17.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
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+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+U-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="U-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-17.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-19.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-18.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-18.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_U_"><!-- --></A><H2>\r
+<B>U</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence"><B>UnknownFileFormatException</B></A> - Exception in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD> <DT><A HREF="../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException()"><B>UnknownFileFormatException()</B></A> - \r
+Constructor for exception compbio.data.sequence.<A HREF="../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.io.File, java.lang.Throwable)"><B>UnknownFileFormatException(File, Throwable)</B></A> - \r
+Constructor for exception compbio.data.sequence.<A HREF="../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.lang.String, java.lang.Throwable)"><B>UnknownFileFormatException(String, Throwable)</B></A> - \r
+Constructor for exception compbio.data.sequence.<A HREF="../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.lang.String)"><B>UnknownFileFormatException(String)</B></A> - \r
+Constructor for exception compbio.data.sequence.<A HREF="../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.lang.Throwable)"><B>UnknownFileFormatException(Throwable)</B></A> - \r
+Constructor for exception compbio.data.sequence.<A HREF="../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><B>UnsupportedRuntimeException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Indicates that the server could not execute native executables.<DT><A HREF="../compbio/metadata/UnsupportedRuntimeException.html#UnsupportedRuntimeException(java.lang.String)"><B>UnsupportedRuntimeException(String)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/UnsupportedRuntimeException.html#UnsupportedRuntimeException(java.lang.Throwable)"><B>UnsupportedRuntimeException(Throwable)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>\r
+<DD> \r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-17.html"><B>PREV LETTER</B></A> \r
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+ <A HREF="index-18.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+V-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="V-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-18.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-20.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-19.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-19.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_V_"><!-- --></A><H2>\r
+<B>V</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/metadata/LimitsManager.html#validate(compbio.metadata.PresetManager)"><B>validate(PresetManager<T>)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
+<DD>Validate Limits\r
+<DT><A HREF="../compbio/metadata/PresetManager.html#validate(compbio.metadata.RunnerConfig)"><B>validate(RunnerConfig<T>)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
+<DD>Checks whether preset option and parameter are defined in RunnerConfig
+ object.\r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#validate()"><B>validate()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Validate the value of the argument.\r
+<DT><A HREF="../compbio/ws/client/Jws2Client.html#validURL(java.lang.String)"><B>validURL(String)</B></A> - \r
+Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
+<DD>Attempt to construct the URL object from the string\r
+<DT><A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><B>ValueConstrain</B></A> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>The type and the lower and upper boundaries for numerical value.<DT><A HREF="../compbio/metadata/ValueConstrain.html#ValueConstrain()"><B>ValueConstrain()</B></A> - \r
+Constructor for class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><B>ValueConstrain.Type</B></A> - Enum in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD> <DT><A HREF="../compbio/data/sequence/DisemblResultAnnot.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
+Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A>\r
+<DD>Returns the enum constant of this type with the specified name.\r
+<DT><A HREF="../compbio/data/sequence/Method.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
+Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A>\r
+<DD>Returns the enum constant of this type with the specified name.\r
+<DT><A HREF="../compbio/data/sequence/Program.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
+Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>\r
+<DD>Returns the enum constant of this type with the specified name.\r
+<DT><A HREF="../compbio/metadata/JobStatus.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
+Static method in enum compbio.metadata.<A HREF="../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>\r
+<DD>Returns the enum constant of this type with the specified name.\r
+<DT><A HREF="../compbio/metadata/ValueConstrain.Type.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
+Static method in enum compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>\r
+<DD>Returns the enum constant of this type with the specified name.\r
+<DT><A HREF="../compbio/ws/client/Services.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
+Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
+<DD>Returns the enum constant of this type with the specified name.\r
+<DT><A HREF="../compbio/data/sequence/DisemblResultAnnot.html#values()"><B>values()</B></A> - \r
+Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence">DisemblResultAnnot</A>\r
+<DD>Returns an array containing the constants of this enum type, in
+the order they are declared.\r
+<DT><A HREF="../compbio/data/sequence/Method.html#values()"><B>values()</B></A> - \r
+Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A>\r
+<DD>Returns an array containing the constants of this enum type, in
+the order they are declared.\r
+<DT><A HREF="../compbio/data/sequence/Program.html#values()"><B>values()</B></A> - \r
+Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>\r
+<DD>Returns an array containing the constants of this enum type, in
+the order they are declared.\r
+<DT><A HREF="../compbio/metadata/JobStatus.html#values()"><B>values()</B></A> - \r
+Static method in enum compbio.metadata.<A HREF="../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>\r
+<DD>Returns an array containing the constants of this enum type, in
+the order they are declared.\r
+<DT><A HREF="../compbio/metadata/ValueConstrain.Type.html#values()"><B>values()</B></A> - \r
+Static method in enum compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>\r
+<DD>Returns an array containing the constants of this enum type, in
+the order they are declared.\r
+<DT><A HREF="../compbio/ws/client/Services.html#values()"><B>values()</B></A> - \r
+Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
+<DD>Returns an array containing the constants of this enum type, in
+the order they are declared.\r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-18.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-20.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-19.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-19.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+C-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="C-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-1.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-3.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-2.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-2.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_C_"><!-- --></A><H2>\r
+<B>C</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/data/msa/JManagement.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>\r
+<DD>Stop running the job <code>jobId</code> but leave its output untouched\r
+<DT><A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>ChunkHolder</B></A> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Represents a chunk of a string data together with the position in a file for
+ the next read operation.<DT><A HREF="../compbio/metadata/ChunkHolder.html#ChunkHolder(java.lang.String, long)"><B>ChunkHolder(String, long)</B></A> - \r
+Constructor for class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#cleanSequence(java.lang.String)"><B>cleanSequence(String)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Removes all whitespace chars in the sequence string\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#closeSilently(java.util.logging.Logger, java.io.Closeable)"><B>closeSilently(Logger, Closeable)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Closes the Closable and logs the exception if any\r
+<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>ClustalAlignmentUtil</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Tools to read and write clustal formated files<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#ClustalAlignmentUtil()"><B>ClustalAlignmentUtil()</B></A> - \r
+Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/package-summary.html"><B>compbio.data.msa</B></A> - package compbio.data.msa<DD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.<DT><A HREF="../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Services)"><B>connect(String, Services)</B></A> - \r
+Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
+<DD>Connects to a web service by the host and the service name\r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)"><B>copyAndValidateRConfig(RunnerConfig<?>)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)"><B>countMatchesInSequence(String, String)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List<FastaSequence>, List<Option<T>>)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DD>Align a list of sequences with options.\r
+<DT><A HREF="../compbio/data/msa/Annotation.html#customAnalize(java.util.List, java.util.List)"><B>customAnalize(List<FastaSequence>, List<Option<T>>)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa">Annotation</A>\r
+<DD>Analyse the sequences according to custom settings defined in options
+ list.\r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-1.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-3.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-2.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-2.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+W-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="W-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-19.html"><B>PREV LETTER</B></A> \r
+ NEXT LETTER</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-20.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-20.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_W_"><!-- --></A><H2>\r
+<B>W</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#WHITE_SPACE"><B>WHITE_SPACE</B></A> - \r
+Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>A whitespace character: [\t\n\x0B\f\r]\r
+<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)"><B>writeClustalAlignment(OutputStream, Alignment)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
+<DD>Write Clustal formatted alignment Limitations: does not record the
+ consensus.\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)"><B>writeFasta(OutputStream, List<FastaSequence>, int)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Writes list of FastaSequeces into the outstream formatting the sequence
+ so that it contains width chars on each line\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)"><B>writeFasta(OutputStream, List<FastaSequence>)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Writes FastaSequence in the file, each sequence will take one line only\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)"><B>writeFastaKeepTheStream(OutputStream, List<FastaSequence>, int)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><B>WrongParameterException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>WrongParameterException is thrown wherever the <A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
+ does not match the actual runnable or then attempting to set the value of
+ <A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.<DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(compbio.metadata.Option)"><B>WrongParameterException(Option<?>)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String)"><B>WrongParameterException(String)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.Throwable)"><B>WrongParameterException(Throwable)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String, java.lang.Throwable)"><B>WrongParameterException(String, Throwable)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>WSTester</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>Class for testing web services<DT><A HREF="../compbio/ws/client/WSTester.html#WSTester()"><B>WSTester()</B></A> - \r
+Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
+<DD> \r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-19.html"><B>PREV LETTER</B></A> \r
+ NEXT LETTER</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-20.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-20.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+D-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="D-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-2.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-4.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-3.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-3.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_D_"><!-- --></A><H2>\r
+<B>D</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#deepCleanSequence(java.lang.String)"><B>deepCleanSequence(String)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Removes all special characters and digits as well as whitespace chars
+ from the sequence\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#DIGIT"><B>DIGIT</B></A> - \r
+Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>A digit\r
+<DT><A HREF="../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence"><B>DisemblResultAnnot</B></A> - Enum in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD> </DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-2.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-4.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-3.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-3.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+E-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="E-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-3.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-5.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-4.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-4.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_E_"><!-- --></A><H2>\r
+<B>E</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/data/sequence/Alignment.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
+<DD>Please note that this implementation does not take the order of sequences
+ into account!\r
+<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/AnnotatedSequence.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence">MultiAnnotatedSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/Score.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/ChunkHolder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Limit.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Option.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Parameter.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Preset.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/ValueConstrain.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
+<DD> \r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-3.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-5.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-4.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-4.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+F-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="F-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-4.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-6.html"><B>NEXT LETTER</B></A></FONT></TD>\r
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+ <A HREF="index-5.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_F_"><!-- --></A><H2>\r
+<B>F</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>FastaSequence</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>A FASTA formatted sequence.<DT><A HREF="../compbio/data/sequence/FastaSequence.html#FastaSequence(java.lang.String, java.lang.String)"><B>FastaSequence(String, String)</B></A> - \r
+Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
+<DD>Upon construction the any whitespace characters are removed from the
+ sequence\r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-4.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-6.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-5.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-5.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+G-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="G-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-5.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-7.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-6.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-6.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_G_"><!-- --></A><H2>\r
+<B>G</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#gapchar"><B>gapchar</B></A> - \r
+Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
+<DD>Dash char to be used as gap char in the alignments\r
+<DT><A HREF="../compbio/metadata/LimitExceededException.html#getActualNumberofSequences()"><B>getActualNumberofSequences()</B></A> - \r
+Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/Annotation.html#getAnnotation(java.lang.String)"><B>getAnnotation(String)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa">Annotation</A>\r
+<DD>Return the result of the job.\r
+<DT><A HREF="../compbio/data/sequence/AnnotatedSequence.html#getAnnotation()"><B>getAnnotation()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html#getAnnotations()"><B>getAnnotations()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence">MultiAnnotatedSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)"><B>getArgument(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Returns the argument by its name if found, NULL otherwise.\r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)"><B>getArgumentByOptionName(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Returns the argument by option name, NULL if the argument is not found\r
+<DT><A HREF="../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)"><B>getArguments(RunnerConfig<T>)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
+<DD>Converts list of options as String to type Option\r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#getArguments()"><B>getArguments()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Returns list of <A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
+ runner\r
+<DT><A HREF="../compbio/metadata/Limit.html#getAvgSeqLength()"><B>getAvgSeqLength()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)"><B>getAvgSequenceLength(List<FastaSequence>)</B></A> - \r
+Static method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
+<DD>Calculates an average sequence length of the dataset\r
+<DT><A HREF="../compbio/metadata/ChunkHolder.html#getChunk()"><B>getChunk()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/LimitsManager.html#getDefaultLimit()"><B>getDefaultLimit()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Argument.html#getDefaultValue()"><B>getDefaultValue()</B></A> - \r
+Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Option.html#getDefaultValue()"><B>getDefaultValue()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>A default value of the option.\r
+<DT><A HREF="../compbio/metadata/Argument.html#getDescription()"><B>getDescription()</B></A> - \r
+Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Option.html#getDescription()"><B>getDescription()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>A long description of the Option\r
+<DT><A HREF="../compbio/metadata/Preset.html#getDescription()"><B>getDescription()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)"><B>getFormatedSequence(int)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
+<DD>Format sequence per width letter in one string.\r
+<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getFormattedFasta()"><B>getFormattedFasta()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Argument.html#getFurtherDetails()"><B>getFurtherDetails()</B></A> - \r
+Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Option.html#getFurtherDetails()"><B>getFurtherDetails()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>The URL where further details about the option can be found\r
+<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getGapchar()"><B>getGapchar()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getId()"><B>getId()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
+<DD>Gets the value of id\r
+<DT><A HREF="../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>\r
+<DD>Return the status of the job.\r
+<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getLength()"><B>getLength()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/Metadata.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
+<DD>Get a Limit for a preset.\r
+<DT><A HREF="../compbio/metadata/LimitsManager.html#getLimitByName(java.lang.String)"><B>getLimitByName(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/Metadata.html#getLimits()"><B>getLimits()</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
+<DD>List Limits supported by a web service.\r
+<DT><A HREF="../compbio/metadata/LimitsManager.html#getLimits()"><B>getLimits()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/ValueConstrain.html#getMax()"><B>getMax()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/Alignment.html#getMetadata()"><B>getMetadata()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/Method.html#getMethod(java.lang.String)"><B>getMethod(String)</B></A> - \r
+Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/Score.html#getMethod()"><B>getMethod()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/ValueConstrain.html#getMin()"><B>getMin()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Argument.html#getName()"><B>getName()</B></A> - \r
+Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Option.html#getName()"><B>getName()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>Human readable name of the option\r
+<DT><A HREF="../compbio/metadata/Preset.html#getName()"><B>getName()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/ChunkHolder.html#getNextPosition()"><B>getNextPosition()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/LimitExceededException.html#getNumberOfSequencesAllowed()"><B>getNumberOfSequencesAllowed()</B></A> - \r
+Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getOnelineFasta()"><B>getOnelineFasta()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Parameter.html#getOptionName()"><B>getOptionName()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Option.html#getOptionNames()"><B>getOptionNames()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Preset.html#getOptions()"><B>getOptions()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#getOptions()"><B>getOptions()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Returns the list of the Options supported by the executable of type T\r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#getParameters()"><B>getParameters()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Returns the list of parameters supported executable of type T.\r
+<DT><A HREF="../compbio/metadata/Argument.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
+Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Option.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>List of possible optionNames\r
+<DT><A HREF="../compbio/metadata/Parameter.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD>List is more convenient to work with\r
+<DT><A HREF="../compbio/metadata/Limit.html#getPreset()"><B>getPreset()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)"><B>getPresetByName(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/Metadata.html#getPresets()"><B>getPresets()</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
+<DD>Get presets supported by a web service\r
+<DT><A HREF="../compbio/metadata/PresetManager.html#getPresets()"><B>getPresets()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#getPrmSeparator()"><B>getPrmSeparator()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getProgram()"><B>getProgram()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/MsaWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DD>Return the result of the job.\r
+<DT><A HREF="../compbio/metadata/PresetManager.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/Metadata.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
+<DD>Get options supported by a web service\r
+<DT><A HREF="../compbio/data/sequence/Score.html#getScores()"><B>getScores()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Limit.html#getSeqNumber()"><B>getSeqNumber()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getSequence()"><B>getSequence()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
+<DD>Gets the value of sequence\r
+<DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtActual()"><B>getSequenceLenghtActual()</B></A> - \r
+Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtAllowed()"><B>getSequenceLenghtAllowed()</B></A> - \r
+Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/Alignment.html#getSequences()"><B>getSequences()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
+<DD> \r
+<DT><A HREF="../compbio/ws/client/Services.html#getService(java.lang.String)"><B>getService(String)</B></A> - \r
+Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/Alignment.html#getSize()"><B>getSize()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/ValueConstrain.html#getType()"><B>getType()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Parameter.html#getValidValue()"><B>getValidValue()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD> \r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
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+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
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+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-5.html"><B>PREV LETTER</B></A> \r
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+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+H-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
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+function windowTitle()\r
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+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="H-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-6.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-8.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-7.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-7.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_H_"><!-- --></A><H2>\r
+<B>H</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/data/sequence/Alignment.html#hashCode()"><B>hashCode()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#hashCode()"><B>hashCode()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/AnnotatedSequence.html#hashCode()"><B>hashCode()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/FastaSequence.html#hashCode()"><B>hashCode()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html#hashCode()"><B>hashCode()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence">MultiAnnotatedSequence</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/Score.html#hashCode()"><B>hashCode()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/ChunkHolder.html#hashCode()"><B>hashCode()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Limit.html#hashCode()"><B>hashCode()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Option.html#hashCode()"><B>hashCode()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Parameter.html#hashCode()"><B>hashCode()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Preset.html#hashCode()"><B>hashCode()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/ValueConstrain.html#hashCode()"><B>hashCode()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
+<DD> \r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-6.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-8.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-7.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-7.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+I-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="I-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-7.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-9.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-8.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-8.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_I_"><!-- --></A><H2>\r
+<B>I</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client"><B>IOHelper</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD> <DT><A HREF="../compbio/ws/client/IOHelper.html#IOHelper()"><B>IOHelper()</B></A> - \r
+Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client">IOHelper</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)"><B>isAmbiguosProtein(String)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Check whether the sequence confirms to amboguous protein sequence\r
+<DT><A HREF="../compbio/metadata/Limit.html#isDefault()"><B>isDefault()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Limit.html#isExceeded(java.util.List)"><B>isExceeded(List<FastaSequence>)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
+<DD>Checks if the number of sequences or their average length in the dataset
+ exceeds this limit.\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)"><B>isNonAmbNucleotideSequence(String)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
+ (!) - B char\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)"><B>isNucleotideSequence(FastaSequence)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)"><B>isProteinSequence(String)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/Option.html#isRequired()"><B>isRequired()</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
+<DD>Flag that indicated that this option must be specified in the command
+ line for an executable to run\r
+<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)"><B>isValidClustalFile(InputStream)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
+<DD>Please note this method closes the input stream provided as a parameter\r
+</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-7.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-9.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-8.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-8.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+J-Index\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="J-Index";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-8.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-10.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-9.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-9.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_J_"><!-- --></A><H2>\r
+<B>J</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><B>JABAService</B></A> - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>This is a marker interface, contains no methods<DT><A HREF="../compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence"><B>JalviewAnnotation</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD> <DT><A HREF="../compbio/data/sequence/JalviewAnnotation.html#JalviewAnnotation()"><B>JalviewAnnotation()</B></A> - \r
+Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence">JalviewAnnotation</A>\r
+<DD> \r
+<DT><A HREF="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><B>JManagement</B></A> - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD> <DT><A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>JobExecutionException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>JobExecutionException is thrown wherever the results of the calculation
+ cannot be obtained.<DT><A HREF="../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.String)"><B>JobExecutionException(String)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.Throwable)"><B>JobExecutionException(Throwable)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.String, java.lang.Throwable)"><B>JobExecutionException(String, Throwable)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>JobStatus</B></A> - Enum in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>The status of the job.<DT><A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>JobSubmissionException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Exception for generic problems with JobSubmission it is often thrown as a
+ wrapper for the lower level exceptions like IOException or DrmaaException.<DT><A HREF="../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.String)"><B>JobSubmissionException(String)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.Throwable)"><B>JobSubmissionException(Throwable)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.String, java.lang.Throwable)"><B>JobSubmissionException(String, Throwable)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
+<DD> \r
+<DT><A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><B>Jws2Client</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>A command line client for JAva Bioinformatics Analysis Web Services</DL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index-8.html"><B>PREV LETTER</B></A> \r
+ <A HREF="index-10.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../index.html?index-filesindex-9.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="index-9.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Frameset//EN" "http://www.w3.org/TR/html4/frameset.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc on Thu Dec 09 12:00:29 GMT 2010-->\r
+<TITLE>\r
+Generated Documentation (Untitled)\r
+</TITLE>\r
+<SCRIPT type="text/javascript">\r
+ targetPage = "" + window.location.search;\r
+ if (targetPage != "" && targetPage != "undefined")\r
+ targetPage = targetPage.substring(1);\r
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+ if (targetPage != "" && targetPage != "undefined")\r
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+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+ }\r
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+\r
+<HR>\r
+<CENTER>\r
+<H1>\r
+JABAWS datamodel and web services client Javadoc\r
+</H1>\r
+</CENTER>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Packages</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/data/msa/package-summary.html">compbio.data.msa</A></B></TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/data/sequence/package-summary.html">compbio.data.sequence</A></B></TD>\r
+<TD>A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/metadata/package-summary.html">compbio.metadata</A></B></TD>\r
+<TD>A meta-data model for multiple sequence alignment web services
+ Classes in this package have no dependencies to other sources in the project.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="20%"><B><A HREF="compbio/ws/client/package-summary.html">compbio.ws.client</A></B></TD>\r
+<TD>A command line client and web services testing client for
+ JAva Bioinformatics Analysis Web Services.</TD>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+ <HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
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+ if(window==top) {\r
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+ }\r
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+<NOSCRIPT>\r
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
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+\r
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+</BODY>\r
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--- /dev/null
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+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Class Hierarchy\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Class Hierarchy";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
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+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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+ if(window==top) {\r
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+\r
+<HR>\r
+<CENTER>\r
+<H2>\r
+Hierarchy For All Packages</H2>\r
+</CENTER>\r
+<DL>\r
+<DT><B>Package Hierarchies:</B><DD><A HREF="compbio/data/msa/package-tree.html">compbio.data.msa</A>, <A HREF="compbio/data/sequence/package-tree.html">compbio.data.sequence</A>, <A HREF="compbio/metadata/package-tree.html">compbio.metadata</A>, <A HREF="compbio/ws/client/package-tree.html">compbio.ws.client</A></DL>\r
+<HR>\r
+<H2>\r
+Class Hierarchy\r
+</H2>\r
+<UL>\r
+<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang"><B>Object</B></A><UL>\r
+<LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><B>Alignment</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>AlignmentMetadata</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>ChunkHolder</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>ClustalAlignmentUtil</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>FastaSequence</B></A><UL>\r
+<LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence"><B>AnnotatedSequence</B></A></UL>\r
+<LI TYPE="circle">compbio.ws.client.<A HREF="compbio/ws/client/IOHelper.html" title="class in compbio.ws.client"><B>IOHelper</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/JalviewAnnotation.html" title="class in compbio.data.sequence"><B>JalviewAnnotation</B></A><LI TYPE="circle">compbio.ws.client.<A HREF="compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><B>Jws2Client</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/Limit.html" title="class in compbio.metadata"><B>Limit</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>LimitsManager</B></A><T><LI TYPE="circle">compbio.ws.client.<A HREF="compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client"><B>MetadataHelper</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence"><B>MultiAnnotatedSequence</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/Option.html" title="class in compbio.metadata"><B>Option</B></A><T> (implements compbio.metadata.<A HREF="compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><T>)\r
+<UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>Parameter</B></A><T></UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/Preset.html" title="class in compbio.metadata"><B>Preset</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PresetManager</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>RunnerConfig</B></A><T><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><B>Score</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>SequenceUtil</B></A><LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>)\r
+<UL>\r
+<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang"><B>Exception</B></A><UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>JobExecutionException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>JobSubmissionException</B></A><UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>LimitExceededException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><B>UnsupportedRuntimeException</B></A></UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>ResultNotAvailableException</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence"><B>UnknownFileFormatException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><B>WrongParameterException</B></A></UL>\r
+</UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><B>ValueConstrain</B></A><LI TYPE="circle">compbio.ws.client.<A HREF="compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>WSTester</B></A></UL>\r
+</UL>\r
+<H2>\r
+Interface Hierarchy\r
+</H2>\r
+<UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>Argument</B></A><T><LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><B>JABAService</B></A><UL>\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><B>Annotation</B></A><T> (also extends compbio.data.msa.<A HREF="compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>, compbio.data.msa.<A HREF="compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T>)\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A><T> (also extends compbio.data.msa.<A HREF="compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>, compbio.data.msa.<A HREF="compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T>)\r
+</UL>\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><B>JManagement</B></A><UL>\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><B>Annotation</B></A><T> (also extends compbio.data.msa.<A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, compbio.data.msa.<A HREF="compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T>)\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A><T> (also extends compbio.data.msa.<A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, compbio.data.msa.<A HREF="compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T>)\r
+</UL>\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><B>Metadata</B></A><T><UL>\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/Annotation.html" title="interface in compbio.data.msa"><B>Annotation</B></A><T> (also extends compbio.data.msa.<A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, compbio.data.msa.<A HREF="compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>)\r
+<LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A><T> (also extends compbio.data.msa.<A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, compbio.data.msa.<A HREF="compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>)\r
+</UL>\r
+</UL>\r
+<H2>\r
+Enum Hierarchy\r
+</H2>\r
+<UL>\r
+<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang"><B>Object</B></A><UL>\r
+<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang"><B>Enum</B></A><E> (implements java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><T>, java.io.<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>)\r
+<UL>\r
+<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>JobStatus</B></A><LI TYPE="circle">compbio.ws.client.<A HREF="compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>Services</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>Program</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><B>ValueConstrain.Type</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/Method.html" title="enum in compbio.data.sequence"><B>Method</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence"><B>DisemblResultAnnot</B></A></UL>\r
+</UL>\r
+</UL>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index.html?overview-tree.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="overview-tree.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+compbio.data.msa\r
+compbio.data.sequence\r
+compbio.metadata\r
+compbio.ws.client\r
--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<TITLE>\r
+Serialized Form\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-09">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Serialized Form";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index.html?serialized-form.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="serialized-form.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<CENTER>\r
+<H1>\r
+Serialized Form</H1>\r
+</CENTER>\r
+<HR SIZE="4" NOSHADE>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="center"><FONT SIZE="+2">\r
+<B>Package</B> <B>compbio.data.sequence</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+<A NAME="compbio.data.sequence.UnknownFileFormatException"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Class <A HREF="compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">compbio.data.sequence.UnknownFileFormatException</A> extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A> implements Serializable</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+<B>serialVersionUID: </B>196629543695636854L\r
+\r
+<P>\r
+<A NAME="serializedForm"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Serialized Fields</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<H3>\r
+file</H3>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> <B>file</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR SIZE="4" NOSHADE>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="center"><FONT SIZE="+2">\r
+<B>Package</B> <B>compbio.metadata</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+<A NAME="compbio.metadata.JobExecutionException"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Class <A HREF="compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">compbio.metadata.JobExecutionException</A> extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A> implements Serializable</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+<B>serialVersionUID: </B>-5477751361755778769L\r
+\r
+<P>\r
+\r
+<P>\r
+<A NAME="compbio.metadata.JobSubmissionException"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Class <A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">compbio.metadata.JobSubmissionException</A> extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A> implements Serializable</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+<B>serialVersionUID: </B>607986894357895572L\r
+\r
+<P>\r
+\r
+<P>\r
+<A NAME="compbio.metadata.LimitExceededException"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Class <A HREF="compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">compbio.metadata.LimitExceededException</A> extends <A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> implements Serializable</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+<B>serialVersionUID: </B>15066952180013505L\r
+\r
+<P>\r
+<A NAME="serializedForm"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Serialized Fields</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<H3>\r
+numberOfSequencesAllowed</H3>\r
+<PRE>\r
+int <B>numberOfSequencesAllowed</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+<H3>\r
+actualNumberofSequences</H3>\r
+<PRE>\r
+int <B>actualNumberofSequences</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+<H3>\r
+aSequenceLenghtAllowed</H3>\r
+<PRE>\r
+int <B>aSequenceLenghtAllowed</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+<H3>\r
+aSequenceLenghtActual</H3>\r
+<PRE>\r
+int <B>aSequenceLenghtActual</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+\r
+<P>\r
+<A NAME="compbio.metadata.ResultNotAvailableException"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Class <A HREF="compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">compbio.metadata.ResultNotAvailableException</A> extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A> implements Serializable</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+<B>serialVersionUID: </B>-5475613614578761L\r
+\r
+<P>\r
+\r
+<P>\r
+<A NAME="compbio.metadata.UnsupportedRuntimeException"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Class <A HREF="compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">compbio.metadata.UnsupportedRuntimeException</A> extends <A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> implements Serializable</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+<B>serialVersionUID: </B>-86624836785110293L\r
+\r
+<P>\r
+\r
+<P>\r
+<A NAME="compbio.metadata.WrongParameterException"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Class <A HREF="compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">compbio.metadata.WrongParameterException</A> extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A> implements Serializable</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+<B>serialVersionUID: </B>-547775417557345769L\r
+\r
+<P>\r
+\r
+<P>\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="index.html?serialized-form.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="serialized-form.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
--- /dev/null
+/* Javadoc style sheet */\r
+\r
+/* Define colors, fonts and other style attributes here to override the defaults */\r
+\r
+/* Page background color */\r
+body { background-color: #FFFFFF; color:#000000 }\r
+\r
+/* Headings */\r
+h1 { font-size: 145% }\r
+\r
+/* Table colors */\r
+.TableHeadingColor { background: #CCCCFF; color:#000000 } /* Dark mauve */\r
+.TableSubHeadingColor { background: #EEEEFF; color:#000000 } /* Light mauve */\r
+.TableRowColor { background: #FFFFFF; color:#000000 } /* White */\r
+\r
+/* Font used in left-hand frame lists */\r
+.FrameTitleFont { font-size: 100%; font-family: Helvetica, Arial, sans-serif; color:#000000 }\r
+.FrameHeadingFont { font-size: 90%; font-family: Helvetica, Arial, sans-serif; color:#000000 }\r
+.FrameItemFont { font-size: 90%; font-family: Helvetica, Arial, sans-serif; color:#000000 }\r
+\r
+/* Navigation bar fonts and colors */\r
+.NavBarCell1 { background-color:#EEEEFF; color:#000000} /* Light mauve */\r
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+\r
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+.NavBarCell3 { font-family: Arial, Helvetica, sans-serif; background-color:#FFFFFF; color:#000000}\r
+\r
git://source.jalview.org / jabaws.git / commitdiff
