1 package compbio.data.msa;
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3 import java.security.InvalidParameterException;
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4 import java.util.HashSet;
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5 import java.util.List;
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7 import javax.jws.WebMethod;
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8 import javax.jws.WebParam;
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9 import javax.jws.WebService;
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11 import compbio.data.sequence.FastaSequence;
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12 import compbio.data.sequence.Score;
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13 import compbio.metadata.JobSubmissionException;
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14 import compbio.metadata.LimitExceededException;
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15 import compbio.metadata.Option;
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16 import compbio.metadata.Preset;
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17 import compbio.metadata.ResultNotAvailableException;
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18 import compbio.metadata.UnsupportedRuntimeException;
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19 import compbio.metadata.WrongParameterException;
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22 * Interface for tools that results to one or more annotation to sequence(s)
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26 * Date November 2010
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29 * executable type / web service type
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31 @WebService(targetNamespace = "http://msa.data.compbio/01/12/2010/")
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32 public interface Annotation<T> extends JManagement, Metadata<T> {
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36 * Any dataset containing a greater number of sequences or the average
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37 * length of the sequences are greater then defined in the default Limit
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38 * will not be accepted for an alignment operation and
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39 * JobSubmissionException will be thrown.
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42 * List of FastaSequence objects. The programme does not perform
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43 * any sequence validity checks. Nor does it checks whether the
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44 * sequences names are unique. It is responsibility of the caller
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45 * to validate this information
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46 * @return jobId - unique identifier for the job
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47 * @throws JobSubmissionException
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48 * is thrown when the job could not be submitted due to the
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49 * following reasons: 1) The number of sequences in the
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50 * submission or their average length is greater then defined by
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51 * the default Limit. 2) Any problems on the server side e.g. it
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52 * is misconfigured or malfunction, is reported via this
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53 * exception. In the first case the information on the limit
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54 * could be obtained from an exception.
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55 * @throws InvalidParameterException
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56 * thrown if input list of fasta sequence is null or empty
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57 * @throws UnsupportedRuntimeException
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58 * thrown if server OS does not support native executables for a
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59 * given web service, e.g. JWS2 is deployed on Windows and Mafft
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61 * @throws LimitExceededException
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62 * is throw if the input sequences number or average length
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63 * exceeds what is defined by the limit
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67 @WebParam(name = "fastaSequences") List<FastaSequence> sequences)
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68 throws UnsupportedRuntimeException, LimitExceededException,
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69 JobSubmissionException;
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75 * Default Limit is used to decide whether the calculation will be
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76 * permitted or denied
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79 * List of FastaSequence objects. The programme does not perform
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80 * any sequence validity checks. Nor does it checks whether the
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81 * sequences names are unique. It is responsibility of the caller
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82 * to validate this information
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85 * @return jobId - unique identifier for the job
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86 * @throws JobSubmissionException. This
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87 * exception is thrown when the job could not be submitted due
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88 * to the following reasons: 1) The number of sequences in the
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89 * submission or their average length is greater then defined by
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90 * the default Limit. 2) Any problems on the server side e.g. it
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91 * is misconfigured or malfunction, is reported via this
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92 * exception. In the first case the information on the limit
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93 * could be obtained from an exception.
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94 * @throws WrongParameterException
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95 * is throws when 1) One of the Options provided is not
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96 * supported, 2) The value of the option is defined outside the
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97 * boundaries. In both cases exception object contain the
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98 * information on the violating Option.
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99 * @throws InvalidParameterException
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100 * thrown if input list of fasta sequence is null or empty
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101 * @throws UnsupportedRuntimeException
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102 * thrown if server OS does not support native executables for a
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103 * given web service, e.g. JWS2 is deployed on Windows and Mafft
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104 * service is called
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105 * @throws LimitExceededException
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106 * is throw if the input sequences number or average length
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107 * exceeds what is defined by the limit
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110 String customAnalize(
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111 @WebParam(name = "fastaSequences") List<FastaSequence> sequences,
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112 @WebParam(name = "options") List<Option<T>> options)
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113 throws UnsupportedRuntimeException, LimitExceededException,
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114 JobSubmissionException, WrongParameterException;
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119 * Limit for a presetName is used whether the calculation will be permitted
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120 * or denied. If no Limit was defined for a presetName, than default limit
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124 * List of FastaSequence objects. The programme does not perform
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125 * any sequence validity checks. Nor does it checks whether the
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126 * sequences names are unique. It is responsibility of the caller
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127 * to validate this information
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129 * A list of Options
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130 * @return String - jobId - unique identifier for the job
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131 * @throws JobSubmissionException. This
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132 * exception is thrown when the job could not be submitted due
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133 * to the following reasons: 1) The number of sequences in the
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134 * submission or their average length is greater then defined by
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135 * the default Limit. 2) Any problems on the server side e.g. it
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136 * is misconfigured or malfunction, is reported via this
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137 * exception. In the first case the information on the limit
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138 * could be obtained from an exception.
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139 * @throws WrongParameterException
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140 * is throws when 1) One of the Options provided is not
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141 * supported, 2) The value of the option is defined outside the
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142 * boundaries. In both cases exception object contain the
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143 * information on the violating Option.
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144 * @throws InvalidParameterException
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145 * thrown if input list of fasta sequence is null or empty
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146 * @throws UnsupportedRuntimeException
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147 * thrown if server OS does not support native executables for a
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148 * given web service, e.g. JWS2 is deployed on Windows and Mafft
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149 * service is called
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150 * @throws LimitExceededException
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151 * is throw if the input sequences number or average length
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152 * exceeds what is defined by the limit
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155 String presetAnalize(
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156 @WebParam(name = "fastaSequences") List<FastaSequence> sequences,
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157 @WebParam(name = "preset") Preset<T> preset)
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158 throws UnsupportedRuntimeException, LimitExceededException,
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159 JobSubmissionException, WrongParameterException;
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162 * Return the result of the job.
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165 * a unique job identifier
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167 * @throws ResultNotAvailableException
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168 * this exception is throw if the job execution was not
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169 * successful or the result of the execution could not be found.
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170 * (e.g. removed). Exception could also be thrown is dues to the
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171 * lower level problems on the server i.e. IOException,
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172 * FileNotFoundException problems as well as
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173 * UnknownFileFormatException.
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174 * @throws InvalidParameterException
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175 * thrown if jobId is empty or cannot be recognised e.g. in
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179 HashSet<Score> getConservation(@WebParam(name = "jobId") String jobId)
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180 throws ResultNotAvailableException;
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