X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimeraManager.java;h=19d6a8b3489b2d29f0e13a438e2007db40f8360a;hb=3efc24bc7b7855ff135fa96e35ab1004eaeb4f5e;hp=375fa4ad0d2e1919c2f38f6f2ccb189d65ddc01a;hpb=81185d3e4c3897e59411bca01808c8f86bb4044e;p=jalview.git diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java index 375fa4a..19d6a8b 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java @@ -38,6 +38,9 @@ import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; +import java.io.UnsupportedEncodingException; +import java.net.URLEncoder; +import java.nio.charset.StandardCharsets; import java.nio.file.Paths; import java.util.ArrayList; import java.util.Collection; @@ -174,10 +177,11 @@ public class ChimeraManager return hasChimeraModel(modelNubmer, 0); } - public boolean hasChimeraModel(Integer modelNubmer, Integer subModelNumber) + public boolean hasChimeraModel(Integer modelNubmer, + Integer subModelNumber) { - return currentModelsMap.containsKey(ChimUtils.makeModelKey(modelNubmer, - subModelNumber)); + return currentModelsMap.containsKey( + ChimUtils.makeModelKey(modelNubmer, subModelNumber)); } public void addChimeraModel(Integer modelNumber, Integer subModelNumber, @@ -187,7 +191,8 @@ public class ChimeraManager ChimUtils.makeModelKey(modelNumber, subModelNumber), model); } - public void removeChimeraModel(Integer modelNumber, Integer subModelNumber) + public void removeChimeraModel(Integer modelNumber, + Integer subModelNumber) { int modelKey = ChimUtils.makeModelKey(modelNumber, subModelNumber); if (currentModelsMap.containsKey(modelKey)) @@ -242,9 +247,8 @@ public class ChimeraManager if (!modelList.contains(newModel)) { newModel.setModelName(modelName); - sendChimeraCommand( - "setattr M name " + modelName + " #" - + newModel.getModelNumber(), false); + sendChimeraCommand("setattr M name " + modelName + " #" + + newModel.getModelNumber(), false); modelList.add(newModel); } } @@ -314,8 +318,8 @@ public class ChimeraManager { sendChimeraCommand("close " + model.toSpec(), false); // currentModelNamesMap.remove(model.getModelName()); - currentModelsMap.remove(ChimUtils.makeModelKey( - model.getModelNumber(), model.getSubModelNumber())); + currentModelsMap.remove(ChimUtils.makeModelKey(model.getModelNumber(), + model.getSubModelNumber())); // selectionList.remove(chimeraModel); } else @@ -328,7 +332,8 @@ public class ChimeraManager public void startListening() { - sendChimeraCommand("listen start models; listen start selection", false); + sendChimeraCommand("listen start models; listen start selection", + false); } public void stopListening() @@ -361,7 +366,7 @@ public class ChimeraManager * Select something in Chimera * * @param command - * the selection command to pass to Chimera + * the selection command to pass to Chimera */ public void select(String command) { @@ -507,8 +512,8 @@ public class ChimeraManager /** * Return the list of depiction presets available from within Chimera. Chimera - * will return the list as a series of lines with the format: Preset type - * number "description" + * will return the list as a series of lines with the format: Preset type number + * "description" * * @return list of presets */ @@ -549,9 +554,9 @@ public class ChimeraManager } /** - * Launch Chimera, unless an instance linked to this object is already - * running. Returns true if chimera is successfully launched, or already - * running, else false. + * 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 @@ -602,8 +607,8 @@ public class ChimeraManager if (error.length() == 0) { this.chimeraRestPort = getPortNumber(); - System.out.println("Chimera REST API started on port " - + chimeraRestPort); + System.out.println( + "Chimera REST API started on port " + chimeraRestPort); // structureManager.initChimTable(); structureManager.setChimeraPathProperty(workingPath); // TODO: [Optional] Check Chimera version and show a warning if below 1.8 @@ -621,6 +626,7 @@ public class ChimeraManager * Adds command-line arguments to start the REST server *
* Method extracted for Jalview to allow override in ChimeraXManager
+ *
* @param args
*/
protected void addLaunchArguments(Listnull
.
*/
public List