X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimUtils.java;h=1b0285cf5d9352cd350b76fe430d636cdb0c49ec;hb=3659ecfe7bb17dd25a0a6b5c94a7d9dab4525136;hp=95221d2bec39ea2b837a4ef6b4c9a680c32a7843;hpb=27ee33852181a0dc18bee27286f77f3ac99fd254;p=jalview.git diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java index 95221d2..1b0285c 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java @@ -1,9 +1,42 @@ +/* vim: set ts=2: */ +/** + * Copyright (c) 2006 The Regents of the University of California. + * All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions + * are met: + * 1. Redistributions of source code must retain the above copyright + * notice, this list of conditions, and the following disclaimer. + * 2. Redistributions in binary form must reproduce the above + * copyright notice, this list of conditions, and the following + * disclaimer in the documentation and/or other materials provided + * with the distribution. + * 3. Redistributions must acknowledge that this software was + * originally developed by the UCSF Computer Graphics Laboratory + * under support by the NIH National Center for Research Resources, + * grant P41-RR01081. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY + * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR + * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE + * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT + * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR + * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, + * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE + * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, + * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + */ package ext.edu.ucsf.rbvi.strucviz2; import java.awt.Color; import java.util.ArrayList; import java.util.HashMap; import java.util.List; +import java.util.Locale; import java.util.Map; import org.slf4j.Logger; @@ -43,8 +76,8 @@ public abstract class ChimUtils { if (decimal > 0) { - subModelNumber = Integer.parseInt(inputLine.substring(decimal - + hash + 2, space)); + subModelNumber = Integer + .parseInt(inputLine.substring(decimal + hash + 2, space)); space = decimal + hash + 1; } modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space)); @@ -87,8 +120,8 @@ public abstract class ChimUtils { if (decimal > 0) { - subModelNumber = Integer.parseInt(inputLine.substring(decimal - + hash + 2, space)); + subModelNumber = Integer + .parseInt(inputLine.substring(decimal + hash + 2, space)); space = decimal + hash + 1; } modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space)); @@ -141,7 +174,7 @@ public abstract class ChimUtils float[] rgbValues = new float[4]; for (int i = 0; i < rgbStrings.length; i++) { - Float f = new Float(rgbStrings[i]); + Float f = Float.valueOf(rgbStrings[i]); rgbValues[i] = f.floatValue(); } if (rgbStrings.length == 4) @@ -171,7 +204,7 @@ public abstract class ChimUtils */ public static Integer makeModelKey(int model, int subModel) { - return new Integer(model * MAX_SUB_MODELS + subModel); + return Integer.valueOf(model * MAX_SUB_MODELS + subModel); } // invoked by the getResdiue (parseConnectivityReplies in @@ -295,11 +328,11 @@ public abstract class ChimUtils String resType = ""; if (split.length == 2) { - resType = split[0].trim().toUpperCase(); + resType = split[0].trim().toUpperCase(Locale.ROOT); } else if (split.length == 3) { - resType = split[1].trim().toUpperCase(); + resType = split[1].trim().toUpperCase(Locale.ROOT); } if (resType.equalsIgnoreCase("HOH") || resType.equalsIgnoreCase("WAT")) { @@ -589,8 +622,8 @@ public abstract class ChimUtils { try { - chimeraModel = chimeraManager.getChimeraModel( - Integer.valueOf(model), 0); + chimeraModel = chimeraManager + .getChimeraModel(Integer.valueOf(model), 0); } catch (NumberFormatException ex) { // ignore @@ -666,8 +699,8 @@ public abstract class ChimUtils if (modelIDNoResChain[0] != null) { String modelID = modelIDNoResChain[0]; - List models = chimeraManager.getChimeraModels( - modelID, ModelType.PDB_MODEL); + List models = chimeraManager.getChimeraModels(modelID, + ModelType.PDB_MODEL); if (models.size() == 1) { // usual case with only one model chimeraModel = models.get(0); @@ -696,8 +729,8 @@ public abstract class ChimUtils // TODO: [Optional] What is this doing? try { - chimeraModel = chimeraManager.getChimeraModel( - Integer.valueOf(modelID), 0); + chimeraModel = chimeraManager + .getChimeraModel(Integer.valueOf(modelID), 0); } catch (NumberFormatException ex) { // ignore @@ -736,8 +769,8 @@ public abstract class ChimUtils } else if (chimeraModel.getChainCount() == 1) { - chimeraResidue = chimeraModel.getResidue(chimeraModel - .getChainNames().iterator().next(), residue); + chimeraResidue = chimeraModel.getResidue( + chimeraModel.getChainNames().iterator().next(), residue); } // System.out.println("ChimeraResidue = " + chimeraResidue); } @@ -913,7 +946,8 @@ public abstract class ChimUtils aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O"); aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O"); aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O"); - aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O"); + aaNames.put("PHE", + "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O"); aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O"); aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N"); aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");