formatting

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

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 662145e..f1fa3d4 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -71,8 +71,8 @@ public class AlignmentView
 \r
   /**\r
    * Construct an alignmentView from a live jalview alignment view. Note -\r
-   * hidden rows will be excluded from alignmentView\r
-   * Note: JAL-1179\r
+   * hidden rows will be excluded from alignmentView Note: JAL-1179\r
+   * \r
    * @param alignment\r
    *          - alignment as referenced by an AlignViewport\r
    * @param columnSelection\r
@@ -104,11 +104,12 @@ public class AlignmentView
     // and record non-empty groups in group list.\r
     // record / sub-select selected region on the alignment view\r
     SequenceI[] selseqs;\r
-    if (selection != null && selection.getSize()>0)\r
+    if (selection != null && selection.getSize() > 0)\r
     {\r
       List<SequenceI> sel = selection.getSequences(null);\r
       this.selected = new Vector();\r
-      selseqs = selection.getSequencesInOrder(alignment, selectedRegionOnly);\r
+      selseqs = selection\r
+              .getSequencesInOrder(alignment, selectedRegionOnly);\r
     }\r
     else\r
     {\r
@@ -147,9 +148,9 @@ public class AlignmentView
             {\r
               sg.setEndRes(esel);\r
             }\r
-            sg.setStartRes(sg.getStartRes()-ssel+1);\r
-            sg.setEndRes(sg.getEndRes()-ssel+1);\r
-            \r
+            sg.setStartRes(sg.getStartRes() - ssel + 1);\r
+            sg.setEndRes(sg.getEndRes() - ssel + 1);\r
+\r
             isg.addElement(sg);\r
           }\r
         }\r
@@ -174,7 +175,8 @@ public class AlignmentView
     {\r
       if (selseqs[i] != null)\r
       {\r
-        if (selection != null && selection.getSize()>0 && !selectedRegionOnly)\r
+        if (selection != null && selection.getSize() > 0\r
+                && !selectedRegionOnly)\r
         {\r
           sequences[csi].setGroupMembership(selected);\r
           selected.addElement(sequences[csi]);\r
@@ -355,7 +357,8 @@ public class AlignmentView
             // may need to shift/trim start and end ?\r
             if (r && !viscontigs)\r
             {\r
-              // Not fully tested code - routine not yet called with viscontigs==false\r
+              // Not fully tested code - routine not yet called with\r
+              // viscontigs==false\r
               if (nsg[g].getStartRes() < gstart)\r
               {\r
                 nsg[g].setStartRes(0);\r
@@ -365,9 +368,9 @@ public class AlignmentView
                 nsg[g].setStartRes(nsg[g].getStartRes() - gstart);\r
                 nsg[g].setEndRes(nsg[g].getEndRes() - gstart);\r
               }\r
-              if (nsg[g].getEndRes() > (gend-gstart))\r
+              if (nsg[g].getEndRes() > (gend - gstart))\r
               {\r
-                nsg[g].setEndRes(gend-gstart);\r
+                nsg[g].setEndRes(gend - gstart);\r
               }\r
             }\r
           }\r
@@ -486,15 +489,15 @@ public class AlignmentView
     for (nvc = 0; nvc < contigviews.length; nvc++)\r
     {\r
       vcals[nvc] = new Alignment(contigviews[nvc]);\r
-      if (scGroups!=null && scGroups.size()>0)\r
+      if (scGroups != null && scGroups.size() > 0)\r
       {\r
-        addPrunedGroupsInOrder(vcals[nvc], vcontigs[nvc*2],vcontigs[nvc*2+1], true);\r
+        addPrunedGroupsInOrder(vcals[nvc], vcontigs[nvc * 2],\r
+                vcontigs[nvc * 2 + 1], true);\r
       }\r
     }\r
     return vcals;\r
   }\r
 \r
-\r
   /**\r
    * get an array of visible sequence strings for a view on an alignment using\r
    * the given gap character\r
@@ -992,10 +995,13 @@ public class AlignmentView
           PrintStream os)\r
   {\r
     os.print("View has " + view.sequences.length + " of which ");\r
-    if (view.selected == null) {\r
+    if (view.selected == null)\r
+    {\r
       os.print("None");\r
-    } else {\r
-      os.print(" "+view.selected.size());\r
+    }\r
+    else\r
+    {\r
+      os.print(" " + view.selected.size());\r
     }\r
     os.println(" are selected.");\r
     os.print("View is " + view.getWidth() + " columns wide");\r
@@ -1044,9 +1050,9 @@ public class AlignmentView
                 + " wide and has " + visal.getHeight() + " seqs.");\r
         if (visal.getGroups() != null && visal.getGroups().size() > 0)\r
         {\r
-          \r
+\r
           int i = 1;\r
-          for (SequenceGroup sg:visal.getGroups())\r
+          for (SequenceGroup sg : visal.getGroups())\r
           {\r
             os.println("Group " + (i++) + " begins at column "\r
                     + sg.getStartRes() + " and ends at " + sg.getEndRes());\r