JAL-3438 spotless for 2.11.2.0

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

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index d992e4e..2fb9cdd 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -35,6 +35,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.FeaturesFile;
+import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
@@ -97,19 +98,22 @@ public class AlignViewController implements AlignViewControllerI
       viewport.getAlignment().deleteAllGroups();
       viewport.clearSequenceColours();
       viewport.setSelectionGroup(null);
+      ColourSchemeI colours = viewport.getGlobalColourScheme();
       // set view properties for each group
       for (int g = 0; g < gps.length; g++)
       {
         // gps[g].setShowunconserved(viewport.getShowUnconserved());
         gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
         viewport.getAlignment().addGroup(gps[g]);
-        Color col = new Color((int) (Math.random() * 255),
-                (int) (Math.random() * 255), (int) (Math.random() * 255));
-        col = col.brighter();
-        for (SequenceI sq : gps[g].getSequences(null))
+        if (colours != null)
         {
-          viewport.setSequenceColour(sq, col);
+          gps[g].setColourScheme(colours.getInstance(viewport, gps[g]));
         }
+        Color col = new Color((int) (Math.random() * 255),
+                (int) (Math.random() * 255), (int) (Math.random() * 255));
+        gps[g].idColour = col;
+        viewport.setUpdateStructures(true);
+        viewport.addSequenceGroup(gps[g]);
       }
       return true;
     }
@@ -162,9 +166,11 @@ 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();
+    boolean searchSelection = viewport.getSelectionGroup() != null
+            && !extendCurrent;
+    SequenceCollectionI sqcol = searchSelection
+            ? viewport.getSelectionGroup()
+            : viewport.getAlignment();
 
     int nseq = findColumnsWithFeature(featureType, sqcol, bs);
 
@@ -200,8 +206,10 @@ public class AlignViewController implements AlignViewControllerI
     }
     else
     {
-      avcg.setStatus(MessageManager
-              .formatMessage("label.no_feature_of_type_found", new String[]
+      String key = searchSelection ? "label.no_feature_found_selection"
+              : "label.no_feature_of_type_found";
+      avcg.setStatus(
+              MessageManager.formatMessage(key, new String[]
               { featureType }));
       if (!extendCurrent)
       {
@@ -223,11 +231,11 @@ public class AlignViewController implements AlignViewControllerI
    * @param bs
    * @return
    */
-  int findColumnsWithFeature(String featureType,
-          SequenceCollectionI sqcol, BitSet bs)
+  int findColumnsWithFeature(String featureType, SequenceCollectionI sqcol,
+          BitSet bs)
   {
-    FeatureRenderer fr = alignPanel == null ? null : alignPanel
-            .getFeatureRenderer();
+    FeatureRenderer fr = alignPanel == null ? null
+            : alignPanel.getFeatureRenderer();
 
     final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
     final int endColumn = sqcol.getEndRes() + 1;
@@ -238,8 +246,8 @@ public class AlignViewController implements AlignViewControllerI
       if (sq != null)
       {
         // int ist = sq.findPosition(sqcol.getStartRes());
-        List<SequenceFeature> sfs = sq.findFeatures(startColumn,
-                endColumn, featureType);
+        List<SequenceFeature> sfs = sq.findFeatures(startColumn, endColumn,
+                featureType);
 
         boolean found = false;
         for (SequenceFeature sf : sfs)
@@ -304,16 +312,33 @@ public class AlignViewController implements AlignViewControllerI
   @Override
   public void sortAlignmentByFeatureDensity(List<String> typ)
   {
-    sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+    String methodText = MessageManager.getString("label.sort_by_density");
+    sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_DENSITY);
   }
 
-  protected void sortBy(List<String> typ, String methodText,
+  /**
+   * Sorts the alignment (or current selection) by either average score or
+   * density of the specified feature types, and adds to the command history. If
+   * {@code types} is null, all visible feature types are used for the sort. If
+   * no feature types apply, does nothing.
+   * 
+   * @param types
+   * @param methodText
+   *          - text shown in Undo/Redo command
+   * @param method
+   *          - passed to jalview.analysis.AlignmentSorter.sortByFeatures()
+   */
+  protected void sortByFeatures(List<String> types, String methodText,
           final String method)
   {
     FeatureRenderer fr = alignPanel.getFeatureRenderer();
-    if (typ == null && fr != null)
+    if (types == null && fr != null)
+    {
+      types = fr.getDisplayedFeatureTypes();
+    }
+    if (types.isEmpty())
     {
-      typ = fr.getDisplayedFeatureTypes();
+      return; // nothing to do
     }
     List<String> gps = null;
     if (fr != null)
@@ -335,7 +360,7 @@ public class AlignViewController implements AlignViewControllerI
       stop = al.getWidth();
     }
     SequenceI[] oldOrder = al.getSequencesArray();
-    AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
+    AlignmentSorter.sortByFeature(types, gps, start, stop, al, method);
     avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
             viewport.getAlignment()));
     alignPanel.paintAlignment(true, false);
@@ -345,11 +370,12 @@ public class AlignViewController implements AlignViewControllerI
   @Override
   public void sortAlignmentByFeatureScore(List<String> typ)
   {
-    sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+    String methodText = MessageManager.getString("label.sort_by_score");
+    sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_SCORE);
   }
 
   @Override
-  public boolean parseFeaturesFile(String file, DataSourceType protocol,
+  public boolean parseFeaturesFile(Object file, DataSourceType protocol,
           boolean relaxedIdMatching)
   {
     boolean featuresAdded = false;
@@ -435,7 +461,7 @@ public class AlignViewController implements AlignViewControllerI
     else
     {
       avcg.setStatus(MessageManager
-              .formatMessage("No highlighted regions marked"));
+              .getString("label.no_highlighted_regions_marked"));
       if (!extendCurrent)
       {
         cs.clear();