Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

[jalview.git] / src / jalview / ext / rbvi / chimera / JalviewChimeraBinding.java

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 460b156..0907695 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -36,6 +36,7 @@ import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
 import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
@@ -271,7 +272,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * @param pdbfnum
    * @return
    */
-  protected String getModelSpec(int pdbfnum)
+  @Override
+  public String getModelSpec(int pdbfnum)
   {
     if (pdbfnum < 0 || pdbfnum >= getPdbCount())
     {
@@ -284,9 +286,16 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
      * to the Chimera command 'list models type molecule', see
      * ChimeraManager.getModelList().
      */
-    List<ChimeraModel> maps = chimeraMaps.get(getStructureFiles()[pdbfnum]);
+    String[] structureFiles = getStructureFiles();
+    if (pdbfnum < 0 || pdbfnum >= structureFiles.length)
+    {
+      return "";
+    }
+
+    List<ChimeraModel> maps = chimeraMaps.get(structureFiles[pdbfnum]);
     boolean hasSubModels = maps != null && maps.size() > 1;
-    return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
+    String spec = "#" + String.valueOf(pdbfnum);
+    return hasSubModels ? spec + ".1" : spec;
   }
 
   /**
@@ -577,7 +586,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   public int sendFeaturesToViewer(AlignmentViewPanel avp)
   {
     // TODO refactor as required to pull up to an interface
-
     Map<String, Map<Object, AtomSpecModel>> featureValues = buildFeaturesMap(
             avp);
     List<StructureCommandI> commands = getCommandGenerator()
@@ -822,4 +830,80 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   {
     return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
   }
+
+  @Override
+  public void showStructures(AlignViewportI av, boolean refocus)
+  {
+    StructureCommandI cmd = buildShowStructuresCommand(av, refocus);
+    executeCommand(cmd, false);
+  }
+
+  /**
+   * Builds a command to show parts of the structure, depending on whether
+   * <ul>
+   * <li>all structures or regions mapped to alignment only are shown</li>
+   * <li>all chains or only selected chains are shown</li>
+   * </ul>
+   * 
+   * @param av
+   * @param refocus
+   * @return
+   */
+  protected StructureCommandI buildShowStructuresCommand(
+          AlignViewportI av,
+          boolean refocus)
+  {
+    // TODO refactor using command generator
+    // pull up this method and Jmol variant to base class
+    StringBuilder cmd = new StringBuilder(128);
+    cmd.append("~display");
+
+    if (isShowAlignmentOnly())
+    {
+      AtomSpecModel model = getShownResidues(av);
+      String atomSpec = getCommandGenerator().getAtomSpec(model, false);
+      if (!atomSpec.isEmpty())
+      {
+        cmd.append("; ~ribbon; ribbon ").append(atomSpec);
+      }
+    }
+    else
+    {
+      cmd.append("; ribbon");
+    }
+
+    /*
+     * hide any chains selected not to be shown (whether mapped to
+     * sequence in the alignment or not)
+     */
+    for (String pdbChain : chainsToHide)
+    {
+      String chainId = pdbChain.split(":")[1];
+      String modelNo = getModelIdForFile(getFileForChain(pdbChain));
+      if (!"".equals(modelNo))
+      {
+        cmd.append("; ~ribbon #").append(modelNo).append(":.")
+                .append(chainId);
+      }
+    }
+    if (refocus)
+    {
+      cmd.append("; focus");
+    }
+    return new StructureCommand(cmd.toString());
+  }
+
+  @Override
+  public int getModelForPdbFile(String fileName, int fileIndex)
+  {
+    if (chimeraMaps.containsKey(fileName))
+    {
+      List<ChimeraModel> models = chimeraMaps.get(fileName);
+      if (!models.isEmpty())
+      {
+        return models.get(0).getModelNumber();
+      }
+    }
+    return -1;
+  }
 }