Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / src / jalview / javascript / MouseOverStructureListener.java

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 6071933..e79106d 100644 (file)
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -30,7 +30,6 @@ import jalview.ext.jmol.JmolCommands;
 import jalview.structure.AtomSpec;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.HttpUtils;
 
@@ -157,8 +156,8 @@ public class MouseOverStructureListener extends JSFunctionExec
                     "" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
       } catch (Exception ex)
       {
-        System.err.println("Couldn't execute callback with " + _listenerfn
-                + " for atomSpec: " + atom);
+        jalview.bin.Console.errPrintln("Couldn't execute callback with "
+                + _listenerfn + " for atomSpec: " + atom);
         ex.printStackTrace();
       }
     }
@@ -173,7 +172,7 @@ public class MouseOverStructureListener extends JSFunctionExec
 
     if (JalviewLite.debug)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               this.getClass().getName() + " modelSet[0]: " + modelSet[0]);
       ssm.reportMapping();
     }
@@ -198,7 +197,7 @@ public class MouseOverStructureListener extends JSFunctionExec
         }
         // if (jvlite.debug)
         // {
-        // System.err.println("Mapped '" + modelSet[m] + "' to "
+        // jalview.bin.Console.errPrintln("Mapped '" + modelSet[m] + "' to "
         // + sequence[m].length + " sequences.");
         // }
       }
@@ -220,21 +219,21 @@ public class MouseOverStructureListener extends JSFunctionExec
 
       // Form a colour command from the given alignment panel for each distinct
       // structure
-      ArrayList<String[]> ccomands = new ArrayList<String[]>();
-      ArrayList<String> pdbfn = new ArrayList<String>();
-      StructureMappingcommandSet[] colcommands = JmolCommands
-              .getColourBySequenceCommand(ssm, modelSet, sequence, sr,
-                      (AlignmentViewPanel) source);
+      ArrayList<String[]> ccomands = new ArrayList<>();
+      ArrayList<String> pdbfn = new ArrayList<>();
+      String[] colcommands = new JmolCommands().colourBySequence(ssm,
+              modelSet, sequence, sr, (AlignmentViewPanel) source);
       if (colcommands == null)
       {
         return;
       }
       int sz = 0;
-      for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
+      // for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
+      for (String command : colcommands)
       {
-        sz += ccset.commands.length;
-        ccomands.add(ccset.commands);
-        pdbfn.add(ccset.mapping);
+        // sz += ccset.commands.length;
+        // ccomands.add(command); // ccset.commands);
+        // pdbfn.add(ccset.mapping);
       }
 
       String mclass, mhandle;
@@ -261,9 +260,9 @@ public class MouseOverStructureListener extends JSFunctionExec
           executeJavascriptFunction(true, _listenerfn, st);
         } catch (Exception ex)
         {
-          System.err.println("Couldn't execute callback with " + _listenerfn
-                  + " using args { " + st[0] + ", " + st[1] + ", " + st[2]
-                  + "," + st[3] + "}"); // + ","+st[4]+"\n");
+          jalview.bin.Console.errPrintln("Couldn't execute callback with "
+                  + _listenerfn + " using args { " + st[0] + ", " + st[1]
+                  + ", " + st[2] + "," + st[3] + "}"); // + ","+st[4]+"\n");
           ex.printStackTrace();
 
         }
@@ -275,7 +274,7 @@ public class MouseOverStructureListener extends JSFunctionExec
        * executeJavascriptFunction( false, _listenerfn, st = new String[] {
        * "colourstruct", "" + ((jalview.appletgui.AlignmentPanel) source).av
        * .getViewId(), handle, "" }); } catch (Exception ex) {
-       * System.err.println("Couldn't execute callback with " + _listenerfn +
+       * jalview.bin.Console.errPrintln("Couldn't execute callback with " + _listenerfn +
        * " using args { " + st[0] + ", " + st[1] + ", " + st[2] + "," + st[3] +
        * "\n"); ex.printStackTrace();
        *