updated javadoc for the system as well as new redirect address for download app
[jabaws.git] / website / full_javadoc / index-files / index-9.html
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40   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
41   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
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81 <A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
82 <A NAME="_I_"><!-- --></A><H2>\r
83 <B>I</B></H2>\r
84 <DL>\r
85 <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#id"><B>id</B></A> - \r
86 Variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
87 <DD>&nbsp;\r
88 <DT><A HREF="../compbio/engine/FilePuller.html#initPull()"><B>initPull()</B></A> - \r
89 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
90 <DD>&nbsp;\r
91 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#INPUT"><B>INPUT</B></A> - \r
92 Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
93 <DD>&nbsp;\r
94 <DT><A HREF="../compbio/stat/collector/InputFilter.html" title="class in compbio.stat.collector"><B>InputFilter</B></A> - Class in <A HREF="../compbio/stat/collector/package-summary.html">compbio.stat.collector</A><DD>&nbsp;<DT><A HREF="../compbio/stat/collector/InputFilter.html#InputFilter()"><B>InputFilter()</B></A> - \r
95 Constructor for class compbio.stat.collector.<A HREF="../compbio/stat/collector/InputFilter.html" title="class in compbio.stat.collector">InputFilter</A>\r
96 <DD>&nbsp;\r
97 <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>&nbsp;<DT><A HREF="../compbio/ws/client/IOHelper.html#IOHelper()"><B>IOHelper()</B></A> - \r
98 Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client">IOHelper</A>\r
99 <DD>&nbsp;\r
100 <DT><A HREF="../compbio/engine/Configurator.html#IS_CLUSTER_ENGINE_ENABLED"><B>IS_CLUSTER_ENGINE_ENABLED</B></A> - \r
101 Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
102 <DD>&nbsp;\r
103 <DT><A HREF="../compbio/engine/Configurator.html#IS_LOCAL_ENGINE_ENABLED"><B>IS_LOCAL_ENGINE_ENABLED</B></A> - \r
104 Static variable in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
105 <DD>&nbsp;\r
106 <DT><A HREF="../compbio/engine/client/PathValidator.html#isAbsolutePath(java.lang.String)"><B>isAbsolutePath(String)</B></A> - \r
107 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
108 <DD>Whether a certain path is absolute or not is operation system dependent!\r
109 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)"><B>isAmbiguosProtein(String)</B></A> - \r
110 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
111 <DD>Check whether the sequence confirms to amboguous protein sequence\r
112 <DT><A HREF="../compbio/stat/collector/JobStat.html#isClusterJob()"><B>isClusterJob()</B></A> - \r
113 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
114 <DD>&nbsp;\r
115 <DT><A HREF="../compbio/metadata/Limit.html#isDefault()"><B>isDefault()</B></A> - \r
116 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
117 <DD>&nbsp;\r
118 <DT><A HREF="../compbio/metadata/Limit.html#isExceeded(java.util.List)"><B>isExceeded(List&lt;FastaSequence&gt;)</B></A> - \r
119 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
120 <DD>Checks if the number of sequences or their average length in the dataset
121  exceeds this limit.\r
122 <DT><A HREF="../compbio/engine/FilePuller.html#isFileCreated()"><B>isFileCreated()</B></A> - \r
123 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
124 <DD>&nbsp;\r
125 <DT><A HREF="../compbio/engine/client/Util.html#isJavaLibrary(java.lang.Class)"><B>isJavaLibrary(Class&lt;?&gt;)</B></A> - \r
126 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
127 <DD>Returns true of executableName.jar.file property has some value in the
128  Executable.properties file, false otherwise.\r
129 <DT><A HREF="../compbio/engine/client/Util.html#isMarked(java.lang.String, compbio.metadata.JobStatus)"><B>isMarked(String, JobStatus)</B></A> - \r
130 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
131 <DD>&nbsp;\r
132 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)"><B>isNonAmbNucleotideSequence(String)</B></A> - \r
133 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
134 <DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
135  (!) - B char\r
136 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)"><B>isNucleotideSequence(FastaSequence)</B></A> - \r
137 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
138 <DD>&nbsp;\r
139 <DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws"><B>IsOperating</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html#IsOperating()"><B>IsOperating()</B></A> - \r
140 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</A>\r
141 <DD>&nbsp;\r
142 <DT><A HREF="../compbio/data/msa/RegistryWS.html#isOperating(compbio.ws.client.Services)"><B>isOperating(Services)</B></A> - \r
143 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
144 <DD>Check whether a particular web service is working on this server\r
145 <DT><A HREF="../compbio/ws/server/RegistryWS.html#isOperating(compbio.ws.client.Services)"><B>isOperating(Services)</B></A> - \r
146 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
147 <DD>&nbsp;\r
148 <DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws"><B>IsOperatingResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html#IsOperatingResponse()"><B>IsOperatingResponse()</B></A> - \r
149 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</A>\r
150 <DD>&nbsp;\r
151 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)"><B>isProteinSequence(String)</B></A> - \r
152 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
153 <DD>&nbsp;\r
154 <DT><A HREF="../compbio/metadata/Option.html#isRequired()"><B>isRequired()</B></A> - \r
155 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
156 <DD>Flag that indicated that this option must be specified in the command
157  line for an executable to run\r
158 <DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#isReturn()"><B>isReturn()</B></A> - \r
159 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</A>\r
160 <DD>&nbsp;\r
161 <DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html#isReturn()"><B>isReturn()</B></A> - \r
162 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</A>\r
163 <DD>&nbsp;\r
164 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)"><B>isValidClustalFile(InputStream)</B></A> - \r
165 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
166 <DD>Please note this method closes the input stream provided as a parameter\r
167 <DT><A HREF="../compbio/engine/client/PathValidator.html#isValidDirectory(java.lang.String)"><B>isValidDirectory(String)</B></A> - \r
168 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
169 <DD>&nbsp;\r
170 <DT><A HREF="../compbio/engine/client/PathValidator.html#isValidExecutable(java.lang.String)"><B>isValidExecutable(String)</B></A> - \r
171 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
172 <DD>&nbsp;\r
173 <DT><A HREF="../compbio/engine/client/Util.html#isValidJobId(java.lang.String)"><B>isValidJobId(String)</B></A> - \r
174 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
175 <DD>&nbsp;\r
176 <DT><A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder"><B>IUPred</B></A> - Class in <A HREF="../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A><DD>iupred sequenceFile <short long glob >
177  
178  Maximum sequence length is 40000 chars.<DT><A HREF="../compbio/runner/disorder/IUPred.html#IUPred()"><B>IUPred()</B></A> - \r
179 Constructor for class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>\r
180 <DD>&nbsp;\r
181 <DT><A HREF="../compbio/ws/client/Services.html#IUPRED_INFO"><B>IUPRED_INFO</B></A> - \r
182 Static variable in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
183 <DD>&nbsp;\r
184 <DT><A HREF="../compbio/ws/server/IUPredWS.html" title="class in compbio.ws.server"><B>IUPredWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/IUPredWS.html#IUPredWS()"><B>IUPredWS()</B></A> - \r
185 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/IUPredWS.html" title="class in compbio.ws.server">IUPredWS</A>\r
186 <DD>&nbsp;\r
187 </DL>\r
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