JAL-3244 renamed Platform method for clarity

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

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index cf5974c..0d2ec68 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -4187,10 +4187,8 @@ public class Jalview2XML
           // TODO: verify 'associate with all views' works still
           tp.getTreeCanvas().setViewport(av); // af.viewport;
           tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
-          // FIXME: should we use safeBoolean here ?
-          tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
-
         }
+        tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
         if (tp == null)
         {
           warn("There was a problem recovering stored Newick tree: \n"
@@ -4522,7 +4520,7 @@ public class Jalview2XML
           String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
           filedat = oldFiles.get(new File(reformatedOldFilename));
         }
-        newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
+        newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath()));
         pdbfilenames.add(filedat.getFilePath());
         pdbids.add(filedat.getPdbId());
         seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
@@ -5115,7 +5113,7 @@ public class Jalview2XML
         }
         else
         {
-          featureOrder.put(featureType, new Float(
+          featureOrder.put(featureType, Float.valueOf(
                   fs / jm.getFeatureSettings().getSetting().size()));
         }
         if (safeBoolean(setting.isDisplay()))
@@ -5127,7 +5125,7 @@ public class Jalview2XML
       for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
       {
         Group grp = jm.getFeatureSettings().getGroup().get(gs);
-        fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
+        fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
       }
       // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
       // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?