JAL-629 Some refactoring to allow more flexible use of PAE files. Not working as...

[jalview.git] / src / jalview / bin / Commands.java

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index af8bf65..a98069a 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -335,7 +335,7 @@ public class Commands
                     .getStructureSelectionManager(Desktop.instance);
             SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
             ssm.computeMapping(false, new SequenceI[] { seq }, null,
-                    openFile, DataSourceType.FILE, null);
+                    openFile, DataSourceType.FILE, null, null, null);
           }
         }
         else
@@ -479,25 +479,24 @@ public class Commands
           {
             Console.info("***** Attaching paeFile '" + paePath + "' to "
                     + "structfile=" + subVals.get("structfile"));
-            EBIAlfaFold.addAlphaFoldPAEToStructure(
-                    af.getCurrentView().getAlignment(), paeFile,
-                    subVals.getIndex(), subVals.get("structfile"), false);
+            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+                    paeFile, subVals.getIndex(), subVals.get("structfile"),
+                    true, false);
           }
           else if (subVals.has("structid"))
           {
             Console.info("***** Attaching paeFile '" + paePath + "' to "
                     + "structid=" + subVals.get("structid"));
-            EBIAlfaFold.addAlphaFoldPAEToStructure(
-                    af.getCurrentView().getAlignment(), paeFile,
-                    subVals.getIndex(), subVals.get("structid"), true);
+            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+                    paeFile, subVals.getIndex(), subVals.get("structid"),
+                    true, true);
           }
           else
           {
             Console.debug("***** Attaching paeFile '" + paePath
                     + "' to sequence index " + subVals.getIndex());
-            EBIAlfaFold.addAlphaFoldPAEToSequence(
-                    af.getCurrentView().getAlignment(), paeFile,
-                    subVals.getIndex(), null);
+            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+                    paeFile, subVals.getIndex(), null, false, false);
             // required to readjust the height and position of the pAE
             // annotation
           }