+/* 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;
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;
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.
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
{
this.haveGUI = haveGUI;
// Create the Chimera interface
chimeraManager = new ChimeraManager(this);
- chimSelectionList = new ArrayList<ChimeraStructuralObject>();
+ chimSelectionList = new ArrayList<>();
pathProps = new Properties();
}
ModelType type)
{
// new models
- Map<String, List<ChimeraModel>> newModels = new HashMap<String, List<ChimeraModel>>();
+ Map<String, List<ChimeraModel>> newModels = new HashMap<>();
if (chimObjNames.size() > 0)
{
List<String> names = chimObjNames.iterator().next();
for (String chimObjName : names)
{
// get or open the corresponding models if they already exist
- List<ChimeraModel> currentModels = chimeraManager.getChimeraModels(
- chimObjName, type);
+ List<ChimeraModel> currentModels = chimeraManager
+ .getChimeraModels(chimObjName, type);
if (currentModels.size() == 0)
{
// open and return models
// 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);
{
for (ChimeraChain selectedChain : selectedModel.getChains())
{
- ChimeraChain dataChain = dataModel.getChain(selectedChain
- .getChainId());
+ ChimeraChain dataChain = dataModel
+ .getChain(selectedChain.getChainId());
if (selectedChain.getResidueCount() == dataChain
.getResidueCount())
{
// alDialog.dispose();
// }
// System.out.println("launch align dialog");
- List<ChimeraStructuralObject> chimObjectList = new ArrayList<ChimeraStructuralObject>();
+ List<ChimeraStructuralObject> chimObjectList = new ArrayList<>();
for (ChimeraModel model : chimeraManager.getChimeraModels())
{
if (useChains)
public List<String> getAllChimeraResidueAttributes()
{
- List<String> attributes = new ArrayList<String>();
+ List<String> attributes = new ArrayList<>();
// attributes.addAll(rinManager.getResAttrs());
attributes.addAll(chimeraManager.getAttrList());
return attributes;
StructureSettings defaultSettings = null;
// TODO: [Optional] Change priority of Chimera paths
- public List<String> getChimeraPaths()
+ public static List<String> getChimeraPaths(boolean isChimeraX)
{
- List<String> pathList = new ArrayList<String>();
+ List<String> 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;
}
git://source.jalview.org / jalview.git / blobdiff