X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimeraManager.java;h=1a8bd76f4cf8c0a9def087082473900e96ce2166;hb=34567bb79dfa8f163f44c3f3448083fcd145f308;hp=c0c7c467cfb728c3535864d2151c78465264f2d9;hpb=cf91582565215c6d51b902a343300ba95aab1cd3;p=jalview.git diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java index c0c7c46..1a8bd76 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java @@ -1,3 +1,35 @@ +/* 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.ws.HttpClientUtils; @@ -8,6 +40,7 @@ import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; +import java.nio.file.Paths; import java.util.ArrayList; import java.util.Collection; import java.util.HashMap; @@ -27,6 +60,10 @@ import ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads; */ public class ChimeraManager { + private static final int REST_REPLY_TIMEOUT_MS = 15000; + + private static final int CONNECTION_TIMEOUT_MS = 100; + private static final boolean debug = false; private int chimeraRestPort; @@ -47,7 +84,7 @@ public class ChimeraManager this.structureManager = structureManager; chimera = null; chimeraListenerThread = null; - currentModelsMap = new HashMap(); + currentModelsMap = new HashMap<>(); } @@ -62,7 +99,7 @@ public class ChimeraManager public List getChimeraModels(String modelName, ModelType modelType) { - List models = new ArrayList(); + List models = new ArrayList<>(); for (ChimeraModel model : currentModelsMap.values()) { if (modelName.equals(model.getModelName()) @@ -76,7 +113,7 @@ public class ChimeraManager public Map> getChimeraModelsMap() { - Map> models = new HashMap>(); + Map> models = new HashMap<>(); for (ChimeraModel model : currentModelsMap.values()) { String modelName = model.getModelName(); @@ -217,7 +254,7 @@ public class ChimeraManager for (ChimeraModel chimeraModel : modelList) { // get model color - Color modelColor = getModelColor(chimeraModel); + Color modelColor = isChimeraX() ? null : getModelColor(chimeraModel); if (modelColor != null) { chimeraModel.setModelColor(modelColor); @@ -228,7 +265,7 @@ public class ChimeraManager // chimeraSend("repr stick "+newModel.toSpec()); // Create the information we need for the navigator - if (type != ModelType.SMILES) + if (type != ModelType.SMILES && !isChimeraX()) { addResidues(chimeraModel); } @@ -297,7 +334,11 @@ public class ChimeraManager public void stopListening() { - sendChimeraCommand("listen stop models ; listen stop selection ", false); + // TODO send this command when viewer connection is closed in Jalview + String command = isChimeraX + ? "info notify stop models jalview; info notify stop selection jalview" + : "listen stop models ; listen stop selection "; + sendChimeraCommand(command, false); } /** @@ -307,9 +348,15 @@ public class ChimeraManager */ public void startListening(String uri) { - sendChimeraCommand("listen start models url " + uri - + ";listen start select prefix SelectionChanged url " + uri, - false); + String command = isChimeraX + ? ("info notify start models prefix ModelChanged jalview url " + + uri + + "; info notify start selection jalview prefix SelectionChanged url " + + uri) + : ("listen start models url " + uri + + ";listen start select prefix SelectionChanged url " + + uri); + sendChimeraCommand(command, false); } /** @@ -344,6 +391,8 @@ public class ChimeraManager sendChimeraCommand("stop really", false); try { + // TODO is this too violent? could it force close the process + // before it has done an orderly shutdown? chimera.destroy(); } catch (Exception ex) { @@ -355,7 +404,7 @@ public class ChimeraManager public Map getSelectedModels() { - Map selectedModelsMap = new HashMap(); + Map selectedModelsMap = new HashMap<>(); List chimeraReply = sendChimeraCommand( "list selection level molecule", true); if (chimeraReply != null) @@ -380,15 +429,34 @@ public class ChimeraManager */ public List getSelectedResidueSpecs() { - List selectedResidues = new ArrayList(); - List chimeraReply = sendChimeraCommand( - "list selection level residue", true); + List selectedResidues = new ArrayList<>(); + + /* + * skip for now if ChimeraX - times out + */ + if (isChimeraX) + { + return selectedResidues; + } + + // in fact 'listinfo' (undocumented) works in ChimeraX + String command = (isChimeraX ? "info" : "list") + + " selection level residue"; + List chimeraReply = sendChimeraCommand(command, true); if (chimeraReply != null) { + /* + * expect 0, 1 or more lines of the format either + * Chimera: + * residue id #0:43.A type GLY + * ChimeraX: + * residue id /A:89 name THR index 88 + * We are only interested in the atomspec (third token of the reply) + */ for (String inputLine : chimeraReply) { String[] inputLineParts = inputLine.split("\\s+"); - if (inputLineParts.length == 5) + if (inputLineParts.length >= 5) { selectedResidues.add(inputLineParts[2]); } @@ -428,18 +496,20 @@ public class ChimeraManager // TODO: [Optional] Handle smiles names in a better way in Chimera? public List getModelList() { - List modelList = new ArrayList(); - List list = sendChimeraCommand("list models type molecule", - true); - if (list != null) - { - for (String modelLine : list) - { - ChimeraModel chimeraModel = new ChimeraModel(modelLine); - modelList.add(chimeraModel); - } - } - return modelList; + List modelList = new ArrayList<>(); + modelList.add(new ChimeraModel("4zhp", ModelType.PDB_MODEL, 1, 0)); + return modelList; // ChimeraX doesn't have 'list models' command + // List list = sendChimeraCommand("list models type molecule", + // true); + // if (list != null) + // { + // for (String modelLine : list) + // { + // ChimeraModel chimeraModel = new ChimeraModel(modelLine); + // modelList.add(chimeraModel); + // } + // } + // return modelList; } /** @@ -451,7 +521,7 @@ public class ChimeraManager */ public List getPresets() { - ArrayList presetList = new ArrayList(); + ArrayList presetList = new ArrayList<>(); List output = sendChimeraCommand("preset list", true); if (output != null) { @@ -507,22 +577,33 @@ public class ChimeraManager // iterate over possible paths for starting Chimera for (String chimeraPath : chimeraPaths) { - File path = new File(chimeraPath); - // uncomment the next line to simulate Chimera not installed - // path = new File(chimeraPath + "x"); - if (!path.canExecute()) - { - error += "File '" + path + "' does not exist.\n"; - continue; - } try { - List args = new ArrayList(); + // ensure symbolic links are resolved + chimeraPath = Paths.get(chimeraPath).toRealPath().toString(); + isChimeraX = chimeraPath.toLowerCase().contains("chimerax"); + File path = new File(chimeraPath); + // uncomment the next line to simulate Chimera not installed + // path = new File(chimeraPath + "x"); + if (!path.canExecute()) + { + error += "File '" + path + "' does not exist.\n"; + continue; + } + List args = new ArrayList<>(); args.add(chimeraPath); // shows Chimera output window but suppresses REST responses: // args.add("--debug"); - args.add("--start"); - args.add("RESTServer"); + if (isChimeraX()) + { + args.add("--cmd"); + args.add("remote rest start"); + } + else + { + args.add("--start"); + args.add("RESTServer"); + } ProcessBuilder pb = new ProcessBuilder(args); chimera = pb.start(); error = ""; @@ -530,7 +611,7 @@ public class ChimeraManager break; } catch (Exception e) { - // Chimera could not be started + // Chimera could not be started using this path error += e.getMessage(); } } @@ -570,15 +651,23 @@ public class ChimeraManager { responses.append("\n" + response); // expect: REST server on host 127.0.0.1 port port_number + // ChimeraX is the same except "REST server started on host..." if (response.startsWith("REST server")) { String[] tokens = response.split(" "); - if (tokens.length == 7 && "port".equals(tokens[5])) + for (int i = 0; i < tokens.length - 1; i++) { - port = Integer.parseInt(tokens[6]); - break; + if ("port".equals(tokens[i])) + { + port = Integer.parseInt(tokens[i + 1]); + break; + } } } + if (port > 0) + { + break; // hack for hanging readLine() + } response = lineReader.readLine(); } } catch (Exception e) @@ -656,8 +745,9 @@ public class ChimeraManager public List getAttrList() { - List attributes = new ArrayList(); - final List reply = sendChimeraCommand("list resattr", true); + List attributes = new ArrayList<>(); + String command = (isChimeraX ? "info " : "list") + "resattr"; + final List reply = sendChimeraCommand(command, true); if (reply != null) { for (String inputLine : reply) @@ -675,7 +765,7 @@ public class ChimeraManager public Map getAttrValues(String aCommand, ChimeraModel model) { - Map values = new HashMap(); + Map values = new HashMap<>(); final List reply = sendChimeraCommand("list residue spec " + model.toSpec() + " attribute " + aCommand, true); if (reply != null) @@ -716,6 +806,8 @@ public class ChimeraManager private volatile boolean busy = false; + private boolean isChimeraX; + /** * Send a command to Chimera. * @@ -729,7 +821,7 @@ public class ChimeraManager */ public List sendChimeraCommand(String command, boolean reply) { - // System.out.println("chimeradebug>> " + command); + System.out.println("chimeradebug>> " + command); if (!isChimeraLaunched() || command == null || "".equals(command.trim())) { @@ -775,15 +867,25 @@ public class ChimeraManager protected List sendRestCommand(String command) { String restUrl = "http://127.0.0.1:" + this.chimeraRestPort + "/run"; - List commands = new ArrayList(1); - commands.add(new BasicNameValuePair("command", command)); + List commands = new ArrayList<>(1); + String encoded = command.replace(" ", "+").replace("#", "%23") + .replace("|", "%7C").replace(";", "%3B"); + commands.add(new BasicNameValuePair("command", encoded)); - List reply = new ArrayList(); + List reply = new ArrayList<>(); BufferedReader response = null; try { - response = HttpClientUtils - .doHttpUrlPost(restUrl, commands, 100, 5000); + if (isChimeraX()) + { + response = HttpClientUtils.doHttpGet(restUrl, commands, + CONNECTION_TIMEOUT_MS, REST_REPLY_TIMEOUT_MS); + } + else + { + response = HttpClientUtils.doHttpUrlPost(restUrl, commands, + CONNECTION_TIMEOUT_MS, REST_REPLY_TIMEOUT_MS); + } String line = ""; while ((line = response.readLine()) != null) { @@ -850,4 +952,14 @@ public class ChimeraManager { return busy; } + + public Process getChimeraProcess() + { + return chimera; + } + + public boolean isChimeraX() + { + return isChimeraX; + } }