Merge branch 'feature/JAL-3187linkedFeatures' into feature/JAL-3251biotypedMappings

[jalview.git] / src / jalview / schemes / IdColourScheme.java

diff --git a/src/jalview/schemes/IdColourScheme.java b/src/jalview/schemes/IdColourScheme.java
new file mode 100644 (file)
index 0000000..5add470
--- /dev/null
+++ b/src/jalview/schemes/IdColourScheme.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Map;
+
+/**
+ * shade sequences using the colour shown in the ID panel. Useful to map
+ * sequence groupings onto residue data (eg tree subgroups visualised on
+ * structures or overview window)
+ * 
+ * @author jprocter
+ */
+public class IdColourScheme implements ColourSchemeI
+{
+  AlignViewportI view = null;
+
+  public IdColourScheme()
+  {
+
+  }
+  public IdColourScheme(AlignViewportI view, AnnotatedCollectionI coll)
+  {
+    this.view = view;
+  }
+
+
+  @Override
+  public String getSchemeName()
+  {
+    return JalviewColourScheme.IdColour.toString();
+  }
+
+  /**
+   * Returns a new instance of this colour scheme with which the given data may
+   * be coloured
+   */
+  @Override
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI coll)
+  {
+    return new IdColourScheme(view, coll);
+  }
+
+  @Override
+  public void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+  }
+
+  @Override
+  public Color findColour(char symbol, int position, SequenceI seq,
+          String consensusResidue, float pid)
+  {
+    // rather than testing if coll is a sequence group, and if so looking at
+    // ((SequenceGroup)coll).idColour
+    // we always return the sequence ID colour, in case the user has customised
+    // the displayed Id colour by right-clicking an internal node in the tree.
+    if (view == null)
+    {
+      return Color.WHITE;
+    }
+    Color col = view.getSequenceColour(seq);
+    return Color.WHITE.equals(col) ? Color.WHITE : col.darker();
+  }
+
+  @Override
+  public boolean hasGapColour()
+  {
+    return false;
+  }
+
+  @Override
+  public boolean isApplicableTo(AnnotatedCollectionI ac)
+  {
+    return true;
+  }
+
+  @Override
+  public boolean isSimple()
+  {
+    return false;
+  }
+}