X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimeraManager.java;h=736e45965d3d56cfe4d9a0d6e3f39e549655f182;hb=36c3f2b9e9081149762bac7b69b5890f34eb53a9;hp=3ed27a3ddac19ea4cd3d65240ad0e094931aabc2;hpb=f2f654875a6eb5f4e90b2c5c545bfed3a70f2b5f;p=jalview.git diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java index 3ed27a3..736e459 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java @@ -1,5 +1,39 @@ +/* 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; + import java.awt.Color; import java.io.BufferedReader; import java.io.File; @@ -20,13 +54,15 @@ import org.slf4j.LoggerFactory; import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType; import ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads; -import jalview.ws.HttpClientUtils; - /** * This object maintains the Chimera communication information. */ 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; @@ -178,6 +214,7 @@ public class ChimeraManager { logger.info("chimera open " + modelPath); // stopListening(); + List modelList = getModelList(); List response = null; // TODO: [Optional] Handle modbase models if (type == ModelType.MODBASE_MODEL) @@ -197,76 +234,29 @@ public class ChimeraManager logger.warn("Could not open " + modelPath); return null; } - List models = new ArrayList(); - int[] modelNumbers = null; - if (type == ModelType.PDB_MODEL) - { - for (String line : response) - { - if (line.startsWith("#")) - { - modelNumbers = ChimUtils.parseOpenedModelNumber(line); - if (modelNumbers != null) - { - int modelNumber = ChimUtils.makeModelKey(modelNumbers[0], - modelNumbers[1]); - if (currentModelsMap.containsKey(modelNumber)) - { - continue; - } - ChimeraModel newModel = new ChimeraModel(modelName, type, - modelNumbers[0], modelNumbers[1]); - currentModelsMap.put(modelNumber, newModel); - models.add(newModel); - - // - // patch for Jalview - set model name in Chimera - // - sendChimeraCommand("setattr M name " + modelName + " #" - + modelNumbers[0], false); - // end patch for Jalview - - modelNumbers = null; - } - } - } - } - else + + // patch for Jalview - set model name in Chimera + // TODO: find a variant that works for sub-models + for (ChimeraModel newModel : getModelList()) { - // TODO: [Optional] Open smiles from file would fail. Do we need it? - // If parsing fails, iterate over all open models to get the right one - List openModels = getModelList(); - for (ChimeraModel openModel : openModels) + if (!modelList.contains(newModel)) { - String openModelName = openModel.getModelName(); - if (openModelName.endsWith("...")) - { - openModelName = openModelName.substring(0, - openModelName.length() - 3); - } - if (modelPath.startsWith(openModelName)) - { - openModel.setModelName(modelPath); - int modelNumber = ChimUtils - .makeModelKey(openModel.getModelNumber(), - openModel.getSubModelNumber()); - if (!currentModelsMap.containsKey(modelNumber)) - { - currentModelsMap.put(modelNumber, openModel); - models.add(openModel); - } - } + newModel.setModelName(modelName); + sendChimeraCommand( + "setattr M name " + modelName + " #" + + newModel.getModelNumber(), false); + modelList.add(newModel); } } // assign color and residues to open models - for (ChimeraModel newModel : models) + for (ChimeraModel chimeraModel : modelList) { // get model color - Color modelColor = getModelColor(newModel); + Color modelColor = getModelColor(chimeraModel); if (modelColor != null) { - newModel.setModelColor(modelColor); + chimeraModel.setModelColor(modelColor); } // Get our properties (default color scheme, etc.) @@ -276,13 +266,13 @@ public class ChimeraManager // Create the information we need for the navigator if (type != ModelType.SMILES) { - addResidues(newModel); + addResidues(chimeraModel); } } sendChimeraCommand("focus", false); // startListening(); // see ChimeraListener - return models; + return modelList; } /** @@ -302,13 +292,12 @@ public class ChimeraManager // TODO: [Optional] Convert path to name in a better way if (modelPath.lastIndexOf(File.separator) > 0) { - modelName = modelPath.substring(modelPath - .lastIndexOf(File.separator) + 1); + modelName = modelPath + .substring(modelPath.lastIndexOf(File.separator) + 1); } else if (modelPath.lastIndexOf("/") > 0) { - modelName = modelPath - .substring(modelPath.lastIndexOf("/") + 1); + modelName = modelPath.substring(modelPath.lastIndexOf("/") + 1); } return modelName; } @@ -344,7 +333,7 @@ public class ChimeraManager public void stopListening() { - sendChimeraCommand("listen stop models; listen stop selection", false); + sendChimeraCommand("listen stop models ; listen stop selection ", false); } /** @@ -354,20 +343,9 @@ public class ChimeraManager */ public void startListening(String uri) { - sendChimeraCommand("listen start models url " + uri, false); - sendChimeraCommand("listen start select prefix SelectionChanged url " - + uri, false); - } - - /** - * Tell Chimera we have stopped listening on the given URI - * - * @param uri - */ - public void stopListening(String uri) - { - sendChimeraCommand("listen stop models url " + uri, false); - sendChimeraCommand("listen stop selection url " + uri, false); + sendChimeraCommand("listen start models url " + uri + + ";listen start select prefix SelectionChanged url " + uri, + false); } /** @@ -391,7 +369,7 @@ public class ChimeraManager { chimera = null; currentModelsMap.clear(); - this.chimeraRestPort = 0; + this.chimeraRestPort = 0; structureManager.clearOnChimeraExit(); } @@ -543,6 +521,14 @@ public class ChimeraManager return launched; } + /** + * Launch Chimera, unless an instance linked to this object is already + * running. Returns true if chimera is successfully launched, or already + * running, else false. + * + * @param chimeraPaths + * @return + */ public boolean launchChimera(List chimeraPaths) { // Do nothing if Chimera is already launched @@ -558,6 +544,8 @@ public class ChimeraManager 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"; @@ -567,6 +555,8 @@ public class ChimeraManager { List args = new ArrayList(); args.add(chimeraPath); + // shows Chimera output window but suppresses REST responses: + // args.add("--debug"); args.add("--start"); args.add("RESTServer"); ProcessBuilder pb = new ProcessBuilder(args); @@ -591,7 +581,7 @@ public class ChimeraManager // TODO: [Optional] Check Chimera version and show a warning if below 1.8 // Ask Chimera to give us updates // startListening(); // later - see ChimeraListener - return true; + return (chimeraRestPort > 0); } // Tell the user that Chimera could not be started because of an error @@ -608,21 +598,29 @@ public class ChimeraManager InputStream readChan = chimera.getInputStream(); BufferedReader lineReader = new BufferedReader(new InputStreamReader( readChan)); - String response = null; + StringBuilder responses = new StringBuilder(); try { - // expect: REST server on host 127.0.0.1 port port_number - response = lineReader.readLine(); - String [] tokens = response.split(" "); - if (tokens.length == 7 && "port".equals(tokens[5])) { - port = Integer.parseInt(tokens[6]); - logger.info("Chimera REST service listening on port " - + chimeraRestPort); + String response = lineReader.readLine(); + while (response != null) + { + responses.append("\n" + response); + // expect: REST server on host 127.0.0.1 port port_number + if (response.startsWith("REST server")) + { + String[] tokens = response.split(" "); + if (tokens.length == 7 && "port".equals(tokens[5])) + { + port = Integer.parseInt(tokens[6]); + break; + } + } + response = lineReader.readLine(); } } catch (Exception e) { - logger.error("Failed to get REST port number from " + response + ": " - + e.getMessage()); + logger.error("Failed to get REST port number from " + responses + + ": " + e.getMessage()); } finally { try @@ -632,6 +630,13 @@ public class ChimeraManager { } } + if (port == 0) + { + System.err + .println("Failed to start Chimera with REST service, response was: " + + responses); + } + logger.info("Chimera REST service listening on port " + chimeraRestPort); return port; } @@ -760,6 +765,7 @@ public class ChimeraManager */ public List sendChimeraCommand(String command, boolean reply) { + // System.out.println("chimeradebug>> " + command); if (!isChimeraLaunched() || command == null || "".equals(command.trim())) { @@ -804,24 +810,24 @@ public class ChimeraManager */ protected List sendRestCommand(String command) { - // System.out.println("Rest: " + command); - // TODO start a separate thread to do this so we don't block? String restUrl = "http://127.0.0.1:" + this.chimeraRestPort + "/run"; List commands = new ArrayList(1); commands.add(new BasicNameValuePair("command", command)); List reply = new ArrayList(); BufferedReader response = null; - try { - response = HttpClientUtils - .doHttpUrlPost(restUrl, commands, 100, 2000); + try + { + response = HttpClientUtils.doHttpUrlPost(restUrl, commands, CONNECTION_TIMEOUT_MS, + REST_REPLY_TIMEOUT_MS); String line = ""; - while ((line = response.readLine()) != null) { + while ((line = response.readLine()) != null) + { reply.add(line); } } catch (Exception e) { - logger.error("REST call " + command + " failed: " + e.getMessage()); + logger.error("REST call '" + command + "' failed: " + e.getMessage()); } finally { if (response != null)