X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FStructureManager.java;h=f7dba792be3cb627bd303cba91e9d7ea431dddc0;hp=12086382b08a108da35911045dff6c821b9b0fa7;hb=14e1f9dbb9c7a4535734fd3be7ddeee2a5ae72dc;hpb=4167762603a83df3e00713307e6522bb027bdd59 diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java index 1208638..f7dba79 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java @@ -1,8 +1,37 @@ +/* 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 java.io.File; import java.io.IOException; import java.util.ArrayList; @@ -10,6 +39,7 @@ import java.util.Arrays; import java.util.Collection; import java.util.HashMap; import java.util.List; +import java.util.Locale; import java.util.Map; import java.util.Properties; import java.util.Set; @@ -17,6 +47,9 @@ import java.util.Set; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import jalview.bin.Cache; +import jalview.gui.Preferences; + /** * This object maintains the relationship between Chimera objects and Cytoscape * objects. @@ -24,15 +57,36 @@ import org.slf4j.LoggerFactory; public class StructureManager { - static final String[] defaultStructureKeys = - { "Structure", "pdb", "pdbFileName", "PDB ID", "structure", - "biopax.xref.PDB", "pdb_ids", "ModelName", "ModelNumber" }; + /* + * Version numbers to build Windows installation paths for + * Chimera https://www.cgl.ucsf.edu/chimera/download.html + * ChimeraX http://www.rbvi.ucsf.edu/chimerax/download.html#release + * https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog + * These are a fallback for Jalview users who don't save path in Preferences; + * these will need to be updated as new versions are released; + * deliberately not 'final' (so modifiable using Groovy). + * + * May 2020: 1.14 is Chimera latest, anticipating a few more... + * 0.93 is ChimeraX latest, 1.0 expected soon + */ + private static String[] CHIMERA_VERSIONS = new String[] { "1.16.2", + "1.16.1", "1.16", "1.15.2", "1.15.1", "1.15", "1.14.2", "1.14.1", + "1.14", "1.13.1", "1.13", "1.12.2", "1.12.1", "1.12", "1.11.2", + "1.11.2", "1.11.1", "1.11" }; + + // Missing 1.1 as this has known bug see JAL-2422 + private static String[] CHIMERAX_VERSIONS = new String[] { "1.3", "1.2.5", + "1.0", "0.93", "0.92", "0.91", "0.9" }; + + 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 +119,7 @@ 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 +132,7 @@ 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 +143,8 @@ 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 +584,11 @@ 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 +598,8 @@ 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 +868,7 @@ 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 +909,7 @@ public class StructureManager public List getAllChimeraResidueAttributes() { - List attributes = new ArrayList(); + List attributes = new ArrayList<>(); // attributes.addAll(rinManager.getResAttrs()); attributes.addAll(chimeraManager.getAttrList()); return attributes; @@ -864,48 +918,144 @@ public class StructureManager StructureSettings defaultSettings = null; // TODO: [Optional] Change priority of Chimera paths - public List getChimeraPaths() + public static List getChimeraPaths(boolean isChimeraX) { - 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; + // } + // } + + String os = System.getProperty("os.name"); + String userPath = Cache + .getDefault(isChimeraX ? Preferences.CHIMERAX_PATH + : Preferences.CHIMERA_PATH, null); + + /* + * paths are based on getChimeraPaths() in + * Chimera: + * https://github.com/RBVI/structureViz2/blob/master/src/main/java/edu/ucsf/rbvi/structureViz2/internal/model/StructureManager.java + * ChimeraX: + * https://github.com/RBVI/structureVizX/blob/master/src/main/java/edu/ucsf/rbvi/structureVizX/internal/model/StructureManager.java + */ + String chimera = isChimeraX ? "ChimeraX" : "Chimera"; + String chimeraExe = isChimeraX ? "ChimeraX" : "chimera"; /* - * Jalview addition: check if path set in user preferences. + * Jalview addition: check if path set in user preferences */ - String userPath = Cache.getDefault(Preferences.CHIMERA_PATH, null); if (userPath != null) { - pathList.add(userPath); + // in macos, deal with the user selecting the .app folder + boolean adjusted = false; + if (os.startsWith("Mac") && userPath.endsWith((".app"))) + { + String possiblePath = String.format("%s/Contents/MacOS/%s", + userPath, chimeraExe); + if (new File(possiblePath).exists()) + { + pathList.add(possiblePath); + adjusted = true; + } + } + if (!adjusted) + { + pathList.add(userPath); + } } // Add default installation paths - String os = System.getProperty("os.name"); if (os.startsWith("Linux")) { - pathList.add("/usr/local/chimera/bin/chimera"); - pathList.add("/usr/local/bin/chimera"); - pathList.add("/usr/bin/chimera"); + // ChimeraX .deb and .rpm packages put symbolic link from + // /usr/bin/chimerax + pathList.add(String.format("/usr/bin/%s", + chimeraExe.toLowerCase(Locale.ROOT))); + pathList.add(String.format("/usr/bin/%s", chimeraExe)); + + pathList.add(String.format("/usr/local/bin/%s", + chimeraExe.toLowerCase(Locale.ROOT))); + pathList.add(String.format("/usr/local/bin/%s", chimeraExe)); + + // these paths also used by .deb and .rpm + pathList.add(String.format("/usr/lib/ucsf-%s/bin/%s", + chimera.toLowerCase(Locale.ROOT), chimeraExe)); + pathList.add(String.format("/usr/libexec/UCSF-%s/bin/%s", chimera, + chimeraExe)); + + pathList.add(String.format("/usr/local/chimera/bin/%s", chimeraExe)); + + // user home paths + pathList.add( + String.format("%s/bin/%s", System.getProperty("user.home"), + chimeraExe.toLowerCase(Locale.ROOT))); + pathList.add(String.format("%s/bin/%s", + System.getProperty("user.home"), chimeraExe)); + pathList.add(String.format("%s/opt/bin/%s", + System.getProperty("user.home"), + chimeraExe.toLowerCase(Locale.ROOT))); + pathList.add(String.format("%s/opt/bin/%s", + System.getProperty("user.home"), chimeraExe)); + pathList.add(String.format("%s/local/bin/%s", + System.getProperty("user.home"), + chimeraExe.toLowerCase(Locale.ROOT))); + pathList.add(String.format("%s/local/bin/%s", + System.getProperty("user.home"), chimeraExe)); } else if (os.startsWith("Windows")) { - pathList.add("\\Program Files\\Chimera\\bin\\chimera"); - pathList.add("C:\\Program Files\\Chimera\\bin\\chimera.exe"); + for (String root : new String[] { "\\Program Files", + "C:\\Program Files", "\\Program Files (x86)", + "C:\\Program Files (x86)", String.format("%s\\AppData\\Local", + System.getProperty("user.home")) }) + { + String[] candidates = isChimeraX ? CHIMERAX_VERSIONS + : CHIMERA_VERSIONS; + for (String version : candidates) + { + // TODO original code doesn't include version in path; which is right? + String path = String.format("%s\\%s %s\\bin\\%s", root, chimera, + version, chimeraExe); + pathList.add(path); + pathList.add(path + ".exe"); + } + // try without a version number too + String path = String.format("%s\\%s\\bin\\%s", root, chimera, + chimeraExe); + pathList.add(path); + pathList.add(path + ".exe"); + } } else if (os.startsWith("Mac")) { - pathList.add("/Applications/Chimera.app/Contents/MacOS/chimera"); + // check for installations with version numbers first + String[] candidates = isChimeraX ? CHIMERAX_VERSIONS + : CHIMERA_VERSIONS; + for (String version : candidates) + { + pathList.add( + String.format("/Applications/%s-%s.app/Contents/MacOS/%s", + chimera, version, chimeraExe)); + pathList.add( + String.format("%s/Applications/%s-%s.app/Contents/MacOS/%s", + System.getProperty("user.home"), chimera, version, + chimeraExe)); + } + pathList.add(String.format("/Applications/%s.app/Contents/MacOS/%s", + chimera, chimeraExe)); + pathList.add(String.format("%s/Applications/%s.app/Contents/MacOS/%s", + System.getProperty("user.home"), chimera, chimeraExe)); } return pathList; }