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82 <A NAME="_I_"><!-- --></A><H2>
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85 <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#id"><B>id</B></A> -
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86 Variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>
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88 <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> -
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89 Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client">IOHelper</A>
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91 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)"><B>isAmbiguosProtein(String)</B></A> -
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92 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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93 <DD>Check whether the sequence confirms to amboguous protein sequence
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94 <DT><A HREF="../compbio/metadata/Limit.html#isDefault()"><B>isDefault()</B></A> -
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95 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>
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97 <DT><A HREF="../compbio/metadata/Limit.html#isExceeded(java.util.List)"><B>isExceeded(List<FastaSequence>)</B></A> -
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98 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>
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99 <DD>Checks if the number of sequences or their average length in the dataset
100 exceeds this limit.
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101 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)"><B>isNonAmbNucleotideSequence(String)</B></A> -
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102 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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103 <DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
105 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)"><B>isNucleotideSequence(FastaSequence)</B></A> -
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106 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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108 <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> <DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html#IsOperating()"><B>IsOperating()</B></A> -
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109 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</A>
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111 <DT><A HREF="../compbio/data/msa/RegistryWS.html#isOperating(compbio.ws.client.Services)"><B>isOperating(Services)</B></A> -
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112 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>
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113 <DD>Check whether a particular web service is working on this server
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114 <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> <DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html#IsOperatingResponse()"><B>IsOperatingResponse()</B></A> -
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115 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</A>
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117 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)"><B>isProteinSequence(String)</B></A> -
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118 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
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120 <DT><A HREF="../compbio/metadata/Option.html#isRequired()"><B>isRequired()</B></A> -
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121 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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122 <DD>Flag that indicated that this option must be specified in the command
123 line for an executable to run
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124 <DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#isReturn()"><B>isReturn()</B></A> -
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125 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</A>
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127 <DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html#isReturn()"><B>isReturn()</B></A> -
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128 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</A>
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130 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)"><B>isValidClustalFile(InputStream)</B></A> -
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131 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>
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132 <DD>Please note this method closes the input stream provided as a parameter
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133 <DT><A HREF="../compbio/ws/client/Services.html#IUPRED_INFO"><B>IUPRED_INFO</B></A> -
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134 Static variable in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>
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