X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FStructureManager.java;h=c1d04c475aa6e4523c41bf5be58f3106ac470014;hb=586ade46bdcd05ff028a1cff82c3c527326d28ec;hp=12086382b08a108da35911045dff6c821b9b0fa7;hpb=739296345a62ffba3edcd23c1213d60db89e7c7e;p=jalview.git diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java index 1208638..c1d04c4 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java @@ -1,7 +1,41 @@ +/* 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 jalview.bin.Cache; import jalview.gui.Preferences; +import jalview.util.FileUtils; +import jalview.util.Platform; import java.io.File; import java.io.IOException; @@ -24,15 +58,15 @@ import org.slf4j.LoggerFactory; public class StructureManager { - static final String[] defaultStructureKeys = - { "Structure", "pdb", "pdbFileName", "PDB ID", "structure", - "biopax.xref.PDB", "pdb_ids", "ModelName", "ModelNumber" }; + static final String[] defaultStructureKeys = { "Structure", "pdb", + "pdbFileName", "PDB ID", "structure", "biopax.xref.PDB", "pdb_ids", + "ModelName", "ModelNumber" }; - static final String[] defaultChemStructKeys = - { "Smiles", "smiles", "SMILES" }; + static final String[] defaultChemStructKeys = { "Smiles", "smiles", + "SMILES" }; - static final String[] defaultResidueKeys = - { "FunctionalResidues", "ResidueList", "Residues" }; + static final String[] defaultResidueKeys = { "FunctionalResidues", + "ResidueList", "Residues" }; public enum ModelType { @@ -65,7 +99,7 @@ public class StructureManager this.haveGUI = haveGUI; // Create the Chimera interface chimeraManager = new ChimeraManager(this); - chimSelectionList = new ArrayList(); + chimSelectionList = new ArrayList<>(); pathProps = new Properties(); } @@ -78,7 +112,7 @@ public class StructureManager ModelType type) { // new models - Map> newModels = new HashMap>(); + Map> newModels = new HashMap<>(); if (chimObjNames.size() > 0) { List names = chimObjNames.iterator().next(); @@ -89,8 +123,8 @@ public class StructureManager for (String chimObjName : names) { // get or open the corresponding models if they already exist - List currentModels = chimeraManager.getChimeraModels( - chimObjName, type); + List currentModels = chimeraManager + .getChimeraModels(chimObjName, type); if (currentModels.size() == 0) { // open and return models @@ -530,11 +564,11 @@ public class StructureManager // Get the corresponding "real" model if (chimeraManager.hasChimeraModel(modelNumber, subModelNumber)) { - ChimeraModel dataModel = chimeraManager.getChimeraModel( - modelNumber, subModelNumber); - if (dataModel.getResidueCount() == selectedModel - .getResidueCount() - || dataModel.getModelType() == StructureManager.ModelType.SMILES) + ChimeraModel dataModel = chimeraManager + .getChimeraModel(modelNumber, subModelNumber); + if (dataModel.getResidueCount() == selectedModel.getResidueCount() + || dataModel + .getModelType() == StructureManager.ModelType.SMILES) { // Select the entire model addChimSelection(dataModel); @@ -544,8 +578,8 @@ public class StructureManager { for (ChimeraChain selectedChain : selectedModel.getChains()) { - ChimeraChain dataChain = dataModel.getChain(selectedChain - .getChainId()); + ChimeraChain dataChain = dataModel + .getChain(selectedChain.getChainId()); if (selectedChain.getResidueCount() == dataChain .getResidueCount()) { @@ -814,7 +848,7 @@ public class StructureManager // alDialog.dispose(); // } // System.out.println("launch align dialog"); - List chimObjectList = new ArrayList(); + List chimObjectList = new ArrayList<>(); for (ChimeraModel model : chimeraManager.getChimeraModels()) { if (useChains) @@ -855,7 +889,7 @@ public class StructureManager public List getAllChimeraResidueAttributes() { - List attributes = new ArrayList(); + List attributes = new ArrayList<>(); // attributes.addAll(rinManager.getResAttrs()); attributes.addAll(chimeraManager.getAttrList()); return attributes; @@ -864,22 +898,24 @@ public class StructureManager StructureSettings defaultSettings = null; // TODO: [Optional] Change priority of Chimera paths - public List getChimeraPaths() + public static List getChimeraPaths() { - List pathList = new ArrayList(); + List pathList = new ArrayList<>(); // if no network is available and the settings have been modified by the // user, check for a // path to chimera - if (defaultSettings != null) - { - String defaultPath = defaultSettings.getChimeraPath(); - if (defaultPath != null && !defaultPath.equals("")) - { - pathList.add(defaultPath); - return pathList; - } - } + // + // For Jalview, Preferences/Cache plays this role instead + // if (defaultSettings != null) + // { + // String defaultPath = defaultSettings.getChimeraPath(); + // if (defaultPath != null && !defaultPath.equals("")) + // { + // pathList.add(defaultPath); + // return pathList; + // } + // } /* * Jalview addition: check if path set in user preferences. @@ -887,7 +923,7 @@ public class StructureManager String userPath = Cache.getDefault(Preferences.CHIMERA_PATH, null); if (userPath != null) { - pathList.add(userPath); + pathList.add(0, userPath); } // Add default installation paths @@ -897,11 +933,20 @@ public class StructureManager pathList.add("/usr/local/chimera/bin/chimera"); pathList.add("/usr/local/bin/chimera"); pathList.add("/usr/bin/chimera"); + pathList.add(Platform.getUserPath("opt/bin/chimera")); } else if (os.startsWith("Windows")) { - pathList.add("\\Program Files\\Chimera\\bin\\chimera"); - pathList.add("C:\\Program Files\\Chimera\\bin\\chimera.exe"); + /* + * typical Windows installation path is + * C:\Program Files\Chimera 1.12\bin\chimera.exe + */ + // current drive: + pathList.addAll(FileUtils.findMatches("\\", + "Program Files*/Chimera*/bin/{chimera,chimera.exe}")); + // C: drive (note may add as duplicates) + pathList.addAll(FileUtils.findMatches("C:\\", + "Program Files*/Chimera*/bin/{chimera,chimera.exe}")); } else if (os.startsWith("Mac")) {