Merge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch'

[jalview.git] / src / jalview / gui / Jalview2XML_V1.java

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 8d71ccf..e94ee0e 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -93,8 +93,8 @@ public class Jalview2XML_V1
 
     for (int i = 0; i < csize; i++)
     {
-      newColours[i] = new java.awt.Color(Integer.parseInt(colours
-              .getUserColourScheme().getColour(i).getRGB(), 16));
+      newColours[i] = new java.awt.Color(Integer.parseInt(
+              colours.getUserColourScheme().getColour(i).getRGB(), 16));
     }
 
     return new jalview.schemes.UserColourScheme(newColours);
@@ -152,12 +152,13 @@ public class Jalview2XML_V1
           public void run()
           {
 
-            System.err.println("Couldn't locate Jalview XML file : " + ex
-                    + "\n");
+            System.err.println(
+                    "Couldn't locate Jalview XML file : " + ex + "\n");
             JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                     MessageManager.formatMessage("label.couldnt_locate",
-                            new String[] { file }), MessageManager
-                            .getString("label.url_not_found"),
+                            new String[]
+                            { file }),
+                    MessageManager.getString("label.url_not_found"),
                     JvOptionPane.WARNING_MESSAGE);
           }
         });
@@ -178,7 +179,8 @@ public class Jalview2XML_V1
             JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                     MessageManager.formatMessage(
                             "label.error_loading_file_params", new String[]
-                            { file }), MessageManager
+                            { file }),
+                    MessageManager
                             .getString("label.error_loading_jalview_file"),
                     JvOptionPane.WARNING_MESSAGE);
           }
@@ -251,8 +253,9 @@ public class Jalview2XML_V1
             }
           }
           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
-          StructureSelectionManager.getStructureSelectionManager(
-                  Desktop.instance).registerPDBEntry(entry);
+          StructureSelectionManager
+                  .getStructureSelectionManager(Desktop.instance)
+                  .registerPDBEntry(entry);
         }
 
       }
@@ -308,8 +311,9 @@ public class Jalview2XML_V1
 
     for (int i = 0; i < JSEQ.length; i++)
     {
-      af.viewport.setSequenceColour(af.viewport.getAlignment()
-              .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
+      af.viewport.setSequenceColour(
+              af.viewport.getAlignment().getSequenceAt(i),
+              new java.awt.Color(JSEQ[i].getColour()));
     }
 
     // af.changeColour() );
@@ -331,7 +335,8 @@ public class Jalview2XML_V1
           }
           else
           {
-            cs = ColourSchemeProperty.getColourScheme(al, groups[i].getColour());
+            cs = ColourSchemeProperty.getColourScheme(al,
+                    groups[i].getColour());
           }
         }
         int pidThreshold = groups[i].getPidThreshold();
@@ -350,12 +355,13 @@ public class Jalview2XML_V1
                 groups[i].getStart(), groups[i].getEnd());
         sg.getGroupColourScheme().setThreshold(pidThreshold, true);
 
-        sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
+        sg.setOutlineColour(
+                new java.awt.Color(groups[i].getOutlineColour()));
 
         if (groups[i].getConsThreshold() != 0)
         {
-          Conservation c = new Conservation("All", sg.getSequences(null),
-                  0, sg.getWidth() - 1);
+          Conservation c = new Conservation("All", sg.getSequences(null), 0,
+                  sg.getWidth() - 1);
           c.calculate();
           c.verdict(false, 25);
           sg.cs.setConservation(c);
@@ -374,9 +380,8 @@ public class Jalview2XML_V1
     af.viewport.setColourText(view.getShowColourText());
     af.viewport.setConservationSelected(view.getConservationSelected());
     af.viewport.setShowJVSuffix(view.getShowFullId());
-    af.viewport.setFont(
-            new java.awt.Font(view.getFontName(), view.getFontStyle(), view
-                    .getFontSize()), true);
+    af.viewport.setFont(new java.awt.Font(view.getFontName(),
+            view.getFontStyle(), view.getFontSize()), true);
 
     af.viewport.setRenderGaps(view.getRenderGaps());
     af.viewport.setWrapAlignment(view.getWrapAlignment());
@@ -405,17 +410,17 @@ public class Jalview2XML_V1
       // }
     }
 
-    af.viewport.getResidueShading().setThreshold(
-            view.getPidThreshold(), true);
-    af.viewport.getResidueShading().setConsensus(
-            af.viewport.getSequenceConsensusHash());
+    af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
+            true);
+    af.viewport.getResidueShading()
+            .setConsensus(af.viewport.getSequenceConsensusHash());
     af.viewport.setColourAppliesToAllGroups(false);
     af.alignPanel.updateLayout();
     af.changeColour(cs);
     if (view.getConservationSelected() && cs != null)
     {
-      af.viewport.getResidueShading().setConservationInc(
-              view.getConsThreshold());
+      af.viewport.getResidueShading()
+              .setConservationInc(view.getConsThreshold());
     }
 
     af.viewport.setColourAppliesToAllGroups(true);
@@ -427,7 +432,8 @@ public class Jalview2XML_V1
       Hashtable featureColours = new Hashtable();
       String[] renderOrder = new String[jms.getFeatureSettings()
               .getSettingCount()];
-      for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
+      for (int fs = 0; fs < jms.getFeatureSettings()
+              .getSettingCount(); fs++)
       {
         Setting setting = jms.getFeatureSettings().getSetting(fs);
 
@@ -442,8 +448,8 @@ public class Jalview2XML_V1
                   new Integer(setting.getColour()));
         }
       }
-      FeatureRendererSettings frs = new FeatureRendererSettings(
-              renderOrder, new Hashtable(), featureColours, 1.0f, null);
+      FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
+              new Hashtable(), featureColours, 1.0f, null);
       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
               .transferSettings(frs);
     }
@@ -474,13 +480,13 @@ public class Jalview2XML_V1
 
           if (tree.getFontName() != null)
           {
-            tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
-                    .getFontStyle(), tree.getFontSize()));
+            tp.setTreeFont(new java.awt.Font(tree.getFontName(),
+                    tree.getFontStyle(), tree.getFontSize()));
           }
           else
           {
-            tp.setTreeFont(new java.awt.Font(view.getFontName(), view
-                    .getFontStyle(), tree.getFontSize()));
+            tp.setTreeFont(new java.awt.Font(view.getFontName(),
+                    view.getFontStyle(), tree.getFontSize()));
           }
 
           tp.showPlaceholders(tree.getMarkUnlinked());