JAL-4090 JAL-4160 JAL-4274 image export dimensions and scale factor configurable...

[jalview.git] / src / jalview / datamodel / AlignmentView.java

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index d3d1b2b..6ab71c7 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -74,7 +74,7 @@ public class AlignmentView
 
     ScGroup()
     {
-      seqs = new ArrayList<SeqCigar>();
+      seqs = new ArrayList<>();
     }
 
     /**
@@ -160,7 +160,6 @@ public class AlignmentView
     SequenceI[] selseqs;
     if (selection != null && selection.getSize() > 0)
     {
-      List<SequenceI> sel = selection.getSequences(null);
       this.selected = new ScGroup();
       selseqs = selection.getSequencesInOrder(alignment,
               selectedRegionOnly);
@@ -170,9 +169,9 @@ public class AlignmentView
       selseqs = alignment.getSequencesArray();
     }
 
-    List<List<SequenceI>> seqsets = new ArrayList<List<SequenceI>>();
+    List<List<SequenceI>> seqsets = new ArrayList<>();
     // get the alignment's group list and make a copy
-    List<SequenceGroup> grps = new ArrayList<SequenceGroup>();
+    List<SequenceGroup> grps = new ArrayList<>();
     List<SequenceGroup> gg = alignment.getGroups();
     grps.addAll(gg);
     ScGroup[] sgrps = null;
@@ -185,7 +184,7 @@ public class AlignmentView
         // strip out any groups that do not actually intersect with the
         // visible and selected region
         int ssel = selection.getStartRes(), esel = selection.getEndRes();
-        List<SequenceGroup> isg = new ArrayList<SequenceGroup>();
+        List<SequenceGroup> isg = new ArrayList<>();
         for (SequenceGroup sg : grps)
         {
           if (!(sg.getStartRes() > esel || sg.getEndRes() < ssel))
@@ -245,7 +244,7 @@ public class AlignmentView
               {
                 if (scGroups == null)
                 {
-                  scGroups = new ArrayList<ScGroup>();
+                  scGroups = new ArrayList<>();
                 }
                 addedgps[sg] = true;
                 scGroups.add(sgrps[sg]);
@@ -1129,11 +1128,11 @@ public class AlignmentView
   public static void testSelectionViews(AlignmentI alignment,
           HiddenColumns hidden, SequenceGroup selection)
   {
-    System.out.println("Testing standard view creation:\n");
+    jalview.bin.Console.outPrintln("Testing standard view creation:\n");
     AlignmentView view = null;
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View with no hidden columns, no limit to selection, no groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, false, false,
               false);
@@ -1142,12 +1141,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View with no hidden columns, no limit to selection, and all groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, false, false,
               true);
@@ -1155,12 +1154,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection marked but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View with no hidden columns, limited to selection and no groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, false, true,
               false);
@@ -1168,12 +1167,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection restricted but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View with no hidden columns, limited to selection, and all groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, false, true,
               true);
@@ -1181,12 +1180,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection restricted and groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View *with* hidden columns, no limit to selection, no groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, true, false,
               false);
@@ -1194,12 +1193,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View *with* hidden columns, no limit to selection, and all groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, true, false,
               true);
@@ -1207,12 +1206,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection marked but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View *with* hidden columns, limited to selection and no groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, true, true,
               false);
@@ -1220,12 +1219,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection restricted but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View *with* hidden columns, limited to selection, and all groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, true, true,
               true);
@@ -1233,7 +1232,7 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection restricted and groups marked.");
     }