From d787bb9555e6ad57ae4e10a89f842345ff05ec77 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Tue, 9 Feb 2016 10:25:14 +0000 Subject: [PATCH] JAL-1957 enabled multi-chain mapping and highlight for Chimera viewer --- src/jalview/ext/rbvi/chimera/ChimeraCommands.java | 2 +- src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java | 10 +++++++--- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index 5342dc8..a551ca2 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java @@ -232,7 +232,7 @@ public class ChimeraCommands addColourRange(colourMap, lastColour, pdbfnum, startPos, lastPos, lastChain); } - break; + // break; } } } diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 368918b..cae2457 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -831,6 +831,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } StringBuilder atomSpecs = new StringBuilder(); boolean first = true; + for (AtomSpec atom : atoms) { int pdbResNum = atom.getPdbResNum(); @@ -843,9 +844,9 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * Formatting as #0:34.A,#1:33.A doesn't work as desired, so instead we * concatenate multiple 'show' commands */ - atomSpecs.append(first ? "" : ";show "); + atomSpecs.append(first ? "" : ","); first = false; - atomSpecs.append("#" + cms.get(0).getModelNumber()); + atomSpecs.append(cms.get(0).getModelNumber()); atomSpecs.append(":" + pdbResNum); if (!chain.equals(" ")) { @@ -867,7 +868,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel viewerCommandHistory(false); if (atomSpec.length() > 0) { - command.append("show ").append(atomSpec); + command.append("show #").append(atomSpec); viewer.sendChimeraCommand(command.toString(), false); } viewerCommandHistory(true); @@ -994,6 +995,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ public abstract void refreshGUI(); + @Override public void setLoadingFromArchive(boolean loadingFromArchive) { this.loadingFromArchive = loadingFromArchive; @@ -1004,6 +1006,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @return true if Chimeral is still restoring state or loading is still going * on (see setFinsihedLoadingFromArchive) */ + @Override public boolean isLoadingFromArchive() { return loadingFromArchive && !loadingFinished; @@ -1015,6 +1018,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * * @param finishedLoading */ + @Override public void setFinishedLoadingFromArchive(boolean finishedLoading) { loadingFinished = finishedLoading; -- 1.7.10.2