Merge branch 'develop' into features/JAL-250_hideredundantseqs

[jalview.git] / src / jalview / renderer / ResidueShaderI.java

diff --git a/src/jalview/renderer/ResidueShaderI.java b/src/jalview/renderer/ResidueShaderI.java
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+++ b/src/jalview/renderer/ResidueShaderI.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.renderer;
+
+import jalview.analysis.Conservation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
+
+import java.awt.Color;
+import java.util.Map;
+
+public interface ResidueShaderI
+{
+
+  public abstract void setConsensus(ProfilesI cons);
+
+  public abstract boolean conservationApplied();
+
+  public abstract void setConservationApplied(boolean conservationApplied);
+
+  public abstract void setConservation(Conservation cons);
+
+  public abstract void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps);
+
+  /**
+   * Sets the percentage consensus threshold value, and whether gaps are ignored
+   * in percentage identity calculation
+   * 
+   * @param consensusThreshold
+   * @param ignoreGaps
+   */
+  public abstract void setThreshold(int consensusThreshold,
+          boolean ignoreGaps);
+
+  public abstract void setConservationInc(int i);
+
+  public abstract int getConservationInc();
+
+  /**
+   * Get the percentage threshold for this colour scheme
+   * 
+   * @return Returns the percentage threshold
+   */
+  public abstract int getThreshold();
+
+  /**
+   * Returns the possibly context dependent colour for the given symbol at the
+   * aligned position in the given sequence. For example, the colour may depend
+   * on the symbol's relationship to the consensus residue for the column.
+   * 
+   * @param symbol
+   * @param position
+   * @param seq
+   * @return
+   */
+  public abstract Color findColour(char symbol, int position,
+          SequenceI seq);
+
+  public abstract ColourSchemeI getColourScheme();
+
+  public abstract void setColourScheme(ColourSchemeI cs);
+
+}
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