JAL-244 JAL-4091 FIXME for JAL-3362 patch testCalculateIdWidth_withMaxWidth test...

[jalview.git] / src / jalview / project / Jalview2XML.java

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index bc2046e..af3b2c8 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -26,7 +26,6 @@ import static jalview.math.RotatableMatrix.Axis.Z;
 
 import java.awt.Color;
 import java.awt.Font;
-import java.awt.FontMetrics;
 import java.awt.Rectangle;
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
@@ -87,6 +86,7 @@ import jalview.api.analysis.SimilarityParamsI;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.bin.Console;
+import jalview.bin.Jalview;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -534,7 +534,8 @@ public class Jalview2XML
     }
     if (unresolved > 0)
     {
-      jalview.bin.Console.errPrintln("Jalview Project Import: There were " + unresolved
+      jalview.bin.Console.errPrintln("Jalview Project Import: There were "
+              + unresolved
               + " forward references left unresolved on the stack.");
     }
     if (failedtoresolve > 0)
@@ -1139,38 +1140,55 @@ public class Jalview2XML
            * only view *should* be coped with sensibly.
            */
           // This must have been loaded, is it still visible?
-          JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-          String matchedFile = null;
-          for (int f = frames.length - 1; f > -1; f--)
+          List<JalviewStructureDisplayI> viewFrames = new ArrayList<>();
+          if (Desktop.desktop != null)
           {
-            if (frames[f] instanceof StructureViewerBase)
+            JInternalFrame[] jifs = Desktop.desktop.getAllFrames();
+            if (jifs != null)
             {
-              StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
-              matchedFile = saveStructureViewer(ap, jds, pdb, entry,
-                      viewIds, matchedFile, viewFrame);
-              /*
-               * Only store each structure viewer's state once in the project
-               * jar. First time through only (storeDS==false)
-               */
-              String viewId = viewFrame.getViewId();
-              String viewerType = viewFrame.getViewerType().toString();
-              if (!storeDS && !viewIds.contains(viewId))
+              for (JInternalFrame jif : jifs)
               {
-                viewIds.add(viewId);
-                File viewerState = viewFrame.saveSession();
-                if (viewerState != null)
-                {
-                  copyFileToJar(jout, viewerState.getPath(),
-                          getViewerJarEntryName(viewId), viewerType);
-                }
-                else
+                if (jif instanceof JalviewStructureDisplayI)
                 {
-                  Console.error(
-                          "Failed to save viewer state for " + viewerType);
+                  viewFrames.add((JalviewStructureDisplayI) jif);
                 }
               }
             }
           }
+          else if (Jalview.isHeadlessMode()
+                  && Jalview.getInstance().getCommands() != null)
+          {
+            viewFrames.addAll(
+                    StructureViewerBase.getAllStructureViewerBases());
+          }
+
+          String matchedFile = null;
+          for (JalviewStructureDisplayI viewFrame : viewFrames)
+          {
+            matchedFile = saveStructureViewer(ap, jds, pdb, entry, viewIds,
+                    matchedFile, viewFrame);
+            /*
+             * Only store each structure viewer's state once in the project
+             * jar. First time through only (storeDS==false)
+             */
+            String viewId = viewFrame.getViewId();
+            String viewerType = viewFrame.getViewerType().toString();
+            if (!storeDS && !viewIds.contains(viewId))
+            {
+              viewIds.add(viewId);
+              File viewerState = viewFrame.saveSession();
+              if (viewerState != null)
+              {
+                copyFileToJar(jout, viewerState.getPath(),
+                        getViewerJarEntryName(viewId), viewerType);
+              }
+              else
+              {
+                Console.error(
+                        "Failed to save viewer state for " + viewerType);
+              }
+            }
+          }
 
           if (matchedFile != null || entry.getFile() != null)
           {
@@ -2147,7 +2165,7 @@ public class Jalview2XML
    */
   protected String saveStructureViewer(AlignmentPanel ap, SequenceI jds,
           Pdbids pdb, PDBEntry entry, List<String> viewIds,
-          String matchedFile, StructureViewerBase viewFrame)
+          String matchedFile, JalviewStructureDisplayI viewFrame)
   {
     final AAStructureBindingModel bindingModel = viewFrame.getBinding();
 
@@ -2192,7 +2210,7 @@ public class Jalview2XML
         {
           StructureState state = new StructureState();
           state.setVisible(true);
-          state.setXpos(viewFrame.getX());
+          state.setXpos(viewFrame.getY());
           state.setYpos(viewFrame.getY());
           state.setWidth(viewFrame.getWidth());
           state.setHeight(viewFrame.getHeight());
@@ -2516,6 +2534,7 @@ public class Jalview2XML
     return BitSet.valueOf(newlongvals);
 
   }
+
   private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
   {
     AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
@@ -2959,7 +2978,8 @@ public class Jalview2XML
         });
       } catch (Exception x)
       {
-        jalview.bin.Console.errPrintln("Error loading alignment: " + x.getMessage());
+        jalview.bin.Console
+                .errPrintln("Error loading alignment: " + x.getMessage());
       }
     }
     return af;
@@ -2998,19 +3018,22 @@ public class Jalview2XML
         {
           if (bytes != null)
           {
-            // jalview.bin.Console.outPrintln("Jalview2XML: opening byte jarInputStream for
+            // jalview.bin.Console.outPrintln("Jalview2XML: opening byte
+            // jarInputStream for
             // bytes.length=" + bytes.length);
             return new JarInputStream(new ByteArrayInputStream(bytes));
           }
           if (_url != null)
           {
-            // jalview.bin.Console.outPrintln("Jalview2XML: opening url jarInputStream for "
+            // jalview.bin.Console.outPrintln("Jalview2XML: opening url
+            // jarInputStream for "
             // + _url);
             return new JarInputStream(_url.openStream());
           }
           else
           {
-            // jalview.bin.Console.outPrintln("Jalview2XML: opening file jarInputStream for
+            // jalview.bin.Console.outPrintln("Jalview2XML: opening file
+            // jarInputStream for
             // " + file);
             return new JarInputStream(new FileInputStream(file));
           }
@@ -3121,7 +3144,8 @@ public class Jalview2XML
               "Exception whilst loading jalview XML file : " + ex + "\n");
     } catch (Exception ex)
     {
-      jalview.bin.Console.errPrintln("Parsing as Jalview Version 2 file failed.");
+      jalview.bin.Console
+              .errPrintln("Parsing as Jalview Version 2 file failed.");
       ex.printStackTrace(System.err);
       if (attemptversion1parse)
       {
@@ -3144,7 +3168,8 @@ public class Jalview2XML
     {
       // Don't use the OOM Window here
       errorMessage = "Out of memory loading jalview XML file";
-      jalview.bin.Console.errPrintln("Out of memory whilst loading jalview XML file");
+      jalview.bin.Console
+              .errPrintln("Out of memory whilst loading jalview XML file");
       e.printStackTrace();
     }
 
@@ -3248,8 +3273,8 @@ public class Jalview2XML
         Desktop.addInternalFrame(af, view.getTitle(),
                 safeInt(view.getWidth()), safeInt(view.getHeight()));
         af.setMenusForViewport();
-        jalview.bin.Console.errPrintln("Failed to restore view " + view.getTitle()
-                + " to split frame");
+        jalview.bin.Console.errPrintln("Failed to restore view "
+                + view.getTitle() + " to split frame");
       }
     }
 
@@ -3327,7 +3352,8 @@ public class Jalview2XML
       }
       else
       {
-        jalview.bin.Console.errPrintln("Problem loading Jalview file: " + errorMessage);
+        jalview.bin.Console.errPrintln(
+                "Problem loading Jalview file: " + errorMessage);
       }
     }
     errorMessage = null;
@@ -4491,7 +4517,7 @@ public class Jalview2XML
         {
           if (tree.isColumnWise())
           {
-            AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds
+            AlignmentAnnotation aa = annotationIds
                     .get(tree.getColumnReference());
             if (aa == null)
             {
@@ -5377,8 +5403,9 @@ public class Jalview2XML
     }
     if (matchedAnnotation == null)
     {
-      jalview.bin.Console.errPrintln("Failed to match annotation colour scheme for "
-              + annotationId);
+      jalview.bin.Console
+              .errPrintln("Failed to match annotation colour scheme for "
+                      + annotationId);
       return null;
     }
     // belt-and-braces create a threshold line if the
@@ -6791,7 +6818,8 @@ public class Jalview2XML
       }
       else
       {
-        jalview.bin.Console.errPrintln("Malformed compound filter condition");
+        jalview.bin.Console
+                .errPrintln("Malformed compound filter condition");
       }
     }
   }