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GeezerVison is showing github.com — biojava.github.io/docs/api5.0.0/deprecated-list.html at master · biojava/biojava.github.io Expand file tree/ Copy pathdeprecated-list.htmlMore file actions 279 lines (279 loc) · 13.5 KB / Copy pathdeprecated-list.htmlFile metadata and controls279 lines (279 loc) · 13.5 KB 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> <!-- NewPage --> <html lang="en"> <head> <!-- Generated by javadoc (1.8.0_162) on Fri Apr 06 16:19:09 PDT 2018 --> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <title>Deprecated List (biojava 5.0.0 API)</title> <meta name="date" content="2018-04-06"> <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style"> <script type="text/javascript" src="script.js"></script> </head> <body> <script type="text/javascript"><!-- try { if (location.href.indexOf('is-external=true') == -1) { parent.document.title="Deprecated List (biojava 5.0.0 API)"; } } catch(err) { } //--> </script> <noscript> <div>JavaScript is disabled on your browser.</div> </noscript> <!-- ========= START OF TOP NAVBAR ======= --> <div class="topNav"><a name="navbar.top"> <!-- --> </a> <div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div> <a name="navbar.top.firstrow"> <!-- --> </a> <ul class="navList" title="Navigation"> <li><a href="overview-summary.html">Overview</a></li> <li>Package</li> <li>Class</li> <li>Use</li> <li><a href="overview-tree.html">Tree</a></li> <li class="navBarCell1Rev">Deprecated</li> <li><a href="index-all.html">Index</a></li> <li><a href="help-doc.html">Help</a></li> </ul> </div> <div class="subNav"> <ul class="navList"> <li>Prev</li> <li>Next</li> </ul> <ul class="navList"> <li><a href="index.html?deprecated-list.html" target="_top">Frames</a></li> <li><a href="deprecated-list.html" target="_top">No Frames</a></li> </ul> <ul class="navList" id="allclasses_navbar_top"> <li><a href="allclasses-noframe.html">All Classes</a></li> </ul> <div> <script type="text/javascript"><!-- allClassesLink = document.getElementById("allclasses_navbar_top"); if(window==top) { allClassesLink.style.display = "block"; } else { allClassesLink.style.display = "none"; } //--> </script> </div> <a name="skip.navbar.top"> <!-- --> </a></div> <!-- ========= END OF TOP NAVBAR ========= --> <div class="header"> <h1 title="Deprecated API" class="title">Deprecated API</h1> <h2 title="Contents">Contents</h2> <ul> <li><a href="#method">Deprecated Methods</a></li> </ul> </div> <div class="contentContainer"><a name="method"> <!-- --> </a> <ul class="blockList"> <li class="blockList"> <table class="deprecatedSummary" border="0" cellpadding="3" cellspacing="0" summary="Deprecated Methods table, listing deprecated methods, and an explanation"> <caption><span>Deprecated Methods</span><span class="tabEnd"> </span></caption> <tr> <th class="colOne" scope="col">Method and Description</th> </tr> <tbody> <tr class="altColor"> <td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#findChain-java.lang.String-">org.biojava.nbio.structure.Structure.findChain(String)</a></td> </tr> <tr class="rowColor"> <td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#findChain-java.lang.String-int-">org.biojava.nbio.structure.Structure.findChain(String, int)</a></td> </tr> <tr class="altColor"> <td class="colOne"><a href="org/biojava/nbio/structure/Chain.html#getAtomLigands--">org.biojava.nbio.structure.Chain.getAtomLigands()</a> <div class="block"><span class="deprecationComment">since biojava 5.0 this does not apply anymore. Chains contain either polymeric groups or non-polymeric groups</span></div> </td> </tr> <tr class="rowColor"> <td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#getChainByPDB-java.lang.String-">org.biojava.nbio.structure.Structure.getChainByPDB(String)</a> <div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Structure.html#getPolyChainByPDB-java.lang.String-"><code>Structure.getPolyChainByPDB(String)</code></a> instead</span></div> </td> </tr> <tr class="altColor"> <td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#getChainByPDB-java.lang.String-int-">org.biojava.nbio.structure.Structure.getChainByPDB(String, int)</a> <div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Structure.html#getPolyChainByPDB-java.lang.String-int-"><code>Structure.getPolyChainByPDB(String,int)</code></a> instead</span></div> </td> </tr> <tr class="rowColor"> <td class="colOne"><a href="org/biojava/nbio/structure/Chain.html#getChainID--">org.biojava.nbio.structure.Chain.getChainID()</a> <div class="block"><span class="deprecationComment">use getId() instead</span></div> </td> </tr> <tr class="altColor"> <td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#getCompoundById-int-">org.biojava.nbio.structure.Structure.getCompoundById(int)</a> <div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Structure.html#getEntityById-int-"><code>Structure.getEntityById(int)</code></a> instead</span></div> </td> </tr> <tr class="rowColor"> <td class="colOne"><a href="org/biojava/nbio/structure/contact/Grid.html#getContacts--">org.biojava.nbio.structure.contact.Grid.getContacts()</a> <div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/contact/Grid.html#getAtomContacts--"><code>Grid.getAtomContacts()</code></a> instead</span></div> </td> </tr> <tr class="altColor"> <td class="colOne"><a href="org/biojava/nbio/structure/Chain.html#getInternalChainID--">org.biojava.nbio.structure.Chain.getInternalChainID()</a> <div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Chain.html#getId--"><code>Chain.getId()</code></a> instead</span></div> </td> </tr> <tr class="rowColor"> <td class="colOne"><a href="org/biojava/nbio/structure/Chain.html#getParent--">org.biojava.nbio.structure.Chain.getParent()</a> <div class="block"><span class="deprecationComment">use getStructure(Structure) instead.</span></div> </td> </tr> <tr class="altColor"> <td class="colOne"><a href="org/biojava/nbio/structure/ChainImpl.html#getParent--">org.biojava.nbio.structure.ChainImpl.getParent()</a> <div class="block"><span class="deprecationComment">use getStructure instead.</span></div> </td> </tr> <tr class="rowColor"> <td class="colOne"><a href="org/biojava/nbio/structure/StructureImpl.html#getPdbId--">org.biojava.nbio.structure.StructureImpl.getPdbId()</a></td> </tr> <tr class="altColor"> <td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#getPdbId--">org.biojava.nbio.structure.Structure.getPdbId()</a> <div class="block"><span class="deprecationComment">From BioJava 4.2, use <a href="org/biojava/nbio/structure/Structure.html#getPDBCode--"><code>Structure.getPDBCode()</code></a> or <code>getStructureIdentifier().toCanonical().getPdbId()</code></span></div> </td> </tr> <tr class="rowColor"> <td class="colOne"><a href="org/biojava/nbio/structure/StructureTools.html#getPredominantGroupType-org.biojava.nbio.structure.Chain-">org.biojava.nbio.structure.StructureTools.getPredominantGroupType(Chain)</a> <div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Chain.html#getPredominantGroupType--"><code>Chain.getPredominantGroupType()</code></a> instead.</span></div> </td> </tr> <tr class="altColor"> <td class="colOne"><a href="org/biojava/nbio/structure/StructureImpl.html#getRanges--">org.biojava.nbio.structure.StructureImpl.getRanges()</a></td> </tr> <tr class="rowColor"> <td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#getRanges--">org.biojava.nbio.structure.Structure.getRanges()</a> <div class="block"><span class="deprecationComment">From BioJava 4.2, use <code>getStructureIdentifier().toCanonical().getRanges()</code></span></div> </td> </tr> <tr class="altColor"> <td class="colOne"><a href="org/biojava/nbio/structure/StructureTools.html#getReducedStructure-org.biojava.nbio.structure.Structure-java.lang.String-">org.biojava.nbio.structure.StructureTools.getReducedStructure(Structure, String)</a> <div class="block"><span class="deprecationComment">Use <a href="org/biojava/nbio/structure/StructureIdentifier.html#reduce-org.biojava.nbio.structure.Structure-"><code>StructureIdentifier.reduce(Structure)</code></a> instead (v. 4.2.0)</span></div> </td> </tr> <tr class="rowColor"> <td class="colOne"><a href="org/biojava/nbio/structure/StructureImpl.html#getResidueRanges--">org.biojava.nbio.structure.StructureImpl.getResidueRanges()</a></td> </tr> <tr class="altColor"> <td class="colOne"><a href="org/biojava/nbio/structure/Structure.html#getResidueRanges--">org.biojava.nbio.structure.Structure.getResidueRanges()</a> <div class="block"><span class="deprecationComment">From BioJava 4.2, use <code>getStructureIdentifier().toCanonical().getResidueRanges()</code></span></div> </td> </tr> <tr class="rowColor"> <td class="colOne"><a href="org/biojava/nbio/structure/StructureTools.html#isChainPureNonPolymer-org.biojava.nbio.structure.Chain-">org.biojava.nbio.structure.StructureTools.isChainPureNonPolymer(Chain)</a> <div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Chain.html#isPureNonPolymer--"><code>Chain.isPureNonPolymer()</code></a> instead.</span></div> </td> </tr> <tr class="altColor"> <td class="colOne"><a href="org/biojava/nbio/structure/StructureTools.html#isChainWaterOnly-org.biojava.nbio.structure.Chain-">org.biojava.nbio.structure.StructureTools.isChainWaterOnly(Chain)</a> <div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Chain.html#isWaterOnly--"><code>Chain.isWaterOnly()</code></a> instead.</span></div> </td> </tr> <tr class="rowColor"> <td class="colOne"><a href="org/biojava/nbio/structure/StructureTools.html#isNucleicAcid-org.biojava.nbio.structure.Chain-">org.biojava.nbio.structure.StructureTools.isNucleicAcid(Chain)</a> <div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Chain.html#isNucleicAcid--"><code>Chain.isNucleicAcid()</code></a> instead.</span></div> </td> </tr> <tr class="altColor"> <td class="colOne"><a href="org/biojava/nbio/structure/StructureTools.html#isProtein-org.biojava.nbio.structure.Chain-">org.biojava.nbio.structure.StructureTools.isProtein(Chain)</a> <div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Chain.html#isProtein--"><code>Chain.isProtein()</code></a> instead.</span></div> </td> </tr> <tr class="rowColor"> <td class="colOne"><a href="org/biojava/nbio/genome/parsers/gff/LocIterator.html#main-java.lang.String:A-">org.biojava.nbio.genome.parsers.gff.LocIterator.main(String[])</a> </td> </tr> <tr class="altColor"> <td class="colOne"><a href="org/biojava/nbio/structure/Chain.html#setChainID-java.lang.String-">org.biojava.nbio.structure.Chain.setChainID(String)</a> <div class="block"><span class="deprecationComment">use <a href="org/biojava/nbio/structure/Chain.html#setId-java.lang.String-"><code>Chain.setId(String asymId)</code></a> instead</span></div> </td> </tr> <tr class="rowColor"> <td class="colOne"><a href="org/biojava/nbio/structure/Chain.html#setInternalChainID-java.lang.String-">org.biojava.nbio.structure.Chain.setInternalChainID(String)</a> <div class="block"><span class="deprecationComment">use <code>#setId()</code> instead</span></div> </td> </tr> <tr class="altColor"> <td class="colOne"><a href="org/biojava/nbio/structure/Chain.html#setParent-org.biojava.nbio.structure.Structure-">org.biojava.nbio.structure.Chain.setParent(Structure)</a> <div class="block"><span class="deprecationComment">use setStructure instead</span></div> </td> </tr> <tr class="rowColor"> <td class="colOne"><a href="org/biojava/nbio/structure/ChainImpl.html#setParent-org.biojava.nbio.structure.Structure-">org.biojava.nbio.structure.ChainImpl.setParent(Structure)</a></td> </tr> <tr class="altColor"> <td class="colOne"><a href="org/biojava/nbio/structure/symmetry/internal/CESymmParameters.html#setRefineResult-boolean-">org.biojava.nbio.structure.symmetry.internal.CESymmParameters.setRefineResult(boolean)</a></td> </tr> </tbody> </table> </li> </ul> </div> <!-- ======= START OF BOTTOM NAVBAR ====== --> <div class="bottomNav"><a name="navbar.bottom"> <!-- --> </a> <div class="skipNav"><a 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