X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimeraManager.java;h=c0c7c467cfb728c3535864d2151c78465264f2d9;hb=dddd6b7545b9b75f1d387f838b66867d4c19c1f8;hp=80c8df537dff7179326c6739cbefb73a0bf05288;hpb=a97a5c93ecd4b0ecd0c55ae2c58c6174c05190f0;p=jalview.git diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java index 80c8df5..c0c7c46 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java @@ -1,5 +1,7 @@ package ext.edu.ucsf.rbvi.strucviz2; +import jalview.ws.HttpClientUtils; + import java.awt.Color; import java.io.BufferedReader; import java.io.File; @@ -20,8 +22,6 @@ 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. */ @@ -178,6 +178,7 @@ 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 +198,29 @@ public class ChimeraManager logger.warn("Could not open " + modelPath); return null; } - List models = new ArrayList(); - int[] modelNumbers = null; - if (type == ModelType.PDB_MODEL) + + // patch for Jalview - set model name in Chimera + // TODO: find a variant that works for sub-models + for (ChimeraModel newModel : getModelList()) { - for (String line : response) + if (!modelList.contains(newModel)) { - 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 - // TODO: find a variant that works for sub-models - sendChimeraCommand("setattr M name " + modelName + " #" - + modelNumbers[0], false); - // end patch for Jalview - - modelNumbers = null; - } - } - } - } - else - { - // 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) - { - 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 +230,13 @@ 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 +256,12 @@ 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; } @@ -355,7 +308,8 @@ public class ChimeraManager public void startListening(String uri) { sendChimeraCommand("listen start models url " + uri - + ";listen start select prefix SelectionChanged url " + uri, false); + + ";listen start select prefix SelectionChanged url " + uri, + false); } /** @@ -379,7 +333,7 @@ public class ChimeraManager { chimera = null; currentModelsMap.clear(); - this.chimeraRestPort = 0; + this.chimeraRestPort = 0; structureManager.clearOnChimeraExit(); } @@ -554,6 +508,8 @@ 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"; @@ -563,6 +519,8 @@ 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); @@ -587,7 +545,7 @@ 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 @@ -604,21 +562,29 @@ 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 @@ -628,6 +594,13 @@ 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; } @@ -756,7 +729,7 @@ 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())) { @@ -807,16 +780,18 @@ public class ChimeraManager List reply = new ArrayList(); BufferedReader response = null; - try { + try + { response = HttpClientUtils .doHttpUrlPost(restUrl, commands, 100, 5000); 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)