JAL-2418 source formatting

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 806e9a5..24fc181 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -33,6 +33,7 @@ import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
 import jalview.io.FeaturesFile;
 import jalview.util.MessageManager;
 
@@ -84,10 +85,11 @@ public class AlignViewController implements AlignViewControllerI
     SequenceGroup[] gps = null;
     if (sg != null && (cs == null || cs.isEmpty()))
     {
-      gps = jalview.analysis.Grouping.makeGroupsFrom(viewport
-              .getSequenceSelection(), viewport.getAlignmentView(true)
-              .getSequenceStrings(viewport.getGapCharacter()), viewport
-              .getAlignment().getGroups());
+      gps = jalview.analysis.Grouping.makeGroupsFrom(
+              viewport.getSequenceSelection(),
+              viewport.getAlignmentView(true)
+                      .getSequenceStrings(viewport.getGapCharacter()),
+              viewport.getAlignment().getGroups());
     }
     else
     {
@@ -95,8 +97,8 @@ public class AlignViewController implements AlignViewControllerI
       {
         gps = jalview.analysis.Grouping.makeGroupsFromCols(
                 (sg == null) ? viewport.getAlignment().getSequencesArray()
-                        : sg.getSequences().toArray(new SequenceI[0]), cs,
-                viewport.getAlignment().getGroups());
+                        : sg.getSequences().toArray(new SequenceI[0]),
+                cs, viewport.getAlignment().getGroups());
       }
     }
     if (gps != null)
@@ -169,8 +171,9 @@ public class AlignViewController implements AlignViewControllerI
     // JBPNote this routine could also mark rows, not just columns.
     // need a decent query structure to allow all types of feature searches
     BitSet bs = new BitSet();
-    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
-            .getAlignment() : viewport.getSelectionGroup();
+    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
+            || extendCurrent) ? viewport.getAlignment()
+                    : viewport.getSelectionGroup();
 
     int nseq = findColumnsWithFeature(featureType, sqcol, bs);
 
@@ -188,14 +191,14 @@ public class AlignViewController implements AlignViewControllerI
       {
         viewport.setColumnSelection(cs);
         alignPanel.paintAlignment(true);
-        int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
-                - bs.cardinality()
+        int columnCount = invert
+                ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+                        - bs.cardinality()
                 : bs.cardinality();
         avcg.setStatus(MessageManager.formatMessage(
-                "label.view_controller_toggled_marked",
-                new String[] {
-                    toggle ? MessageManager.getString("label.toggled")
-                            : MessageManager.getString("label.marked"),
+                "label.view_controller_toggled_marked", new String[]
+                { toggle ? MessageManager.getString("label.toggled")
+                        : MessageManager.getString("label.marked"),
                     String.valueOf(columnCount),
                     invert ? MessageManager
                             .getString("label.not_containing")
@@ -206,9 +209,9 @@ public class AlignViewController implements AlignViewControllerI
     }
     else
     {
-      avcg.setStatus(MessageManager.formatMessage(
-              "label.no_feature_of_type_found",
-              new String[] { featureType }));
+      avcg.setStatus(MessageManager
+              .formatMessage("label.no_feature_of_type_found", new String[]
+              { featureType }));
       if (!extendCurrent)
       {
         cs.clear();
@@ -357,8 +360,8 @@ public class AlignViewController implements AlignViewControllerI
     }
     SequenceI[] oldOrder = al.getSequencesArray();
     AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
-    avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport
-            .getAlignment()));
+    avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
+            viewport.getAlignment()));
     alignPanel.paintAlignment(true);
 
   }
@@ -370,15 +373,16 @@ public class AlignViewController implements AlignViewControllerI
   }
 
   @Override
-  public boolean parseFeaturesFile(String file, String protocol,
+  public boolean parseFeaturesFile(String file, DataSourceType protocol,
           boolean relaxedIdMatching)
   {
     boolean featuresFile = false;
     try
     {
-      featuresFile = new FeaturesFile(false, file, protocol).parse(viewport
-              .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
-              .getFeatureColours(), false, relaxedIdMatching);
+      featuresFile = new FeaturesFile(false, file, protocol).parse(
+              viewport.getAlignment().getDataset(),
+              alignPanel.getFeatureRenderer().getFeatureColours(), false,
+              relaxedIdMatching);
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -402,4 +406,67 @@ public class AlignViewController implements AlignViewControllerI
     return featuresFile;
 
   }
+
+  @Override
+  public boolean markHighlightedColumns(boolean invert,
+          boolean extendCurrent, boolean toggle)
+  {
+    if (!viewport.hasSearchResults())
+    {
+      // do nothing if no selection exists
+      return false;
+    }
+    // JBPNote this routine could also mark rows, not just columns.
+    BitSet bs = new BitSet();
+    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
+            || extendCurrent) ? viewport.getAlignment()
+                    : viewport.getSelectionGroup();
+
+    // this could be a lambda... - the remains of the method is boilerplate,
+    // except for the different messages for reporting selection.
+    int nseq = viewport.getSearchResults().markColumns(sqcol, bs);
+
+    ColumnSelection cs = viewport.getColumnSelection();
+    if (cs == null)
+    {
+      cs = new ColumnSelection();
+    }
+
+    if (bs.cardinality() > 0 || invert)
+    {
+      boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+              sqcol.getEndRes(), invert, extendCurrent, toggle);
+      if (changed)
+      {
+        viewport.setColumnSelection(cs);
+        alignPanel.paintAlignment(true);
+        int columnCount = invert
+                ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+                        - bs.cardinality()
+                : bs.cardinality();
+        avcg.setStatus(MessageManager.formatMessage(
+                "label.view_controller_toggled_marked", new String[]
+                { toggle ? MessageManager.getString("label.toggled")
+                        : MessageManager.getString("label.marked"),
+                    String.valueOf(columnCount),
+                    invert ? MessageManager
+                            .getString("label.not_containing")
+                            : MessageManager.getString("label.containing"),
+                    "Highlight", Integer.valueOf(nseq).toString() }));
+        return true;
+      }
+    }
+    else
+    {
+      avcg.setStatus(MessageManager
+              .formatMessage("No highlighted regions marked"));
+      if (!extendCurrent)
+      {
+        cs.clear();
+        alignPanel.paintAlignment(true);
+      }
+    }
+    return false;
+  }
+
 }