+/* 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;
*/
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;
{
logger.info("chimera open " + modelPath);
// stopListening();
+ List<ChimeraModel> modelList = getModelList();
List<String> response = null;
// TODO: [Optional] Handle modbase models
if (type == ModelType.MODBASE_MODEL)
logger.warn("Could not open " + modelPath);
return null;
}
- List<ChimeraModel> models = new ArrayList<ChimeraModel>();
- 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
- // TODO: find a variant that works for sub-models
- 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<ChimeraModel> 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.)
// 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;
}
/**
*/
public List<String> sendChimeraCommand(String command, boolean reply)
{
- // System.out.println("chimeradebug>> " + command);
+ // System.out.println("chimeradebug>> " + command);
if (!isChimeraLaunched() || command == null
|| "".equals(command.trim()))
{
BufferedReader response = null;
try
{
- response = HttpClientUtils
- .doHttpUrlPost(restUrl, commands, 100, 5000);
+ response = HttpClientUtils.doHttpUrlPost(restUrl, commands, CONNECTION_TIMEOUT_MS,
+ REST_REPLY_TIMEOUT_MS);
String line = "";
while ((line = response.readLine()) != null)
{
git://source.jalview.org / jalview.git / blobdiff