Start merging of Laurens Code

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

diff --git a/src/jalview/schemes/CovariationColourScheme.java b/src/jalview/schemes/CovariationColourScheme.java
new file mode 100644 (file)
index 0000000..fe533ed
--- /dev/null
+++ b/src/jalview/schemes/CovariationColourScheme.java
@@ -0,0 +1,121 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+package jalview.schemes;
+
+import java.awt.*;
+import java.util.Hashtable;
+
+import jalview.datamodel.AlignmentAnnotation;
+
+/**
+ * Became RNAHelicesColour.java. Placeholder for true covariation color scheme
+ * 
+ * @author Lauren Michelle Lui
+ * @version 2.5
+ */
+public class CovariationColourScheme extends ResidueColourScheme
+{
+  public Hashtable helixcolorhash = new Hashtable();
+
+  public Hashtable positionsToHelix = new Hashtable();
+
+  int numHelix = 0;
+
+  public AlignmentAnnotation annotation;
+
+  /**
+   * Creates a new CovariationColourScheme object.
+   */
+  public CovariationColourScheme(AlignmentAnnotation annotation)
+  {
+    this.annotation = annotation;
+
+    for (int x = 0; x < this.annotation._rnasecstr.length; x++)
+    {
+      // System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+      // this.annotation._rnasecstr[x].getBegin());
+      // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+      // pairs.put(this.annotation._rnasecstr[x].getBegin(),
+      // this.annotation._rnasecstr[x].getEnd());
+
+      positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(),
+              this.annotation._rnasecstr[x].getFeatureGroup());
+      positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
+              this.annotation._rnasecstr[x].getFeatureGroup());
+
+      if (Integer.parseInt(this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
+      {
+        numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
+                .getFeatureGroup());
+      }
+
+    }
+
+    for (int j = 0; j <= numHelix; j++)
+    {
+      helixcolorhash.put(Integer.toString(j), jalview.util.ColorUtils
+              .generateRandomColor(Color.white));
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c)
+  {
+    // System.out.println("called"); log.debug
+    // Generate a random pastel color
+
+    return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];// jalview.util.ColorUtils.generateRandomColor(Color.white);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *          DOCUMENT ME!
+   * @param j
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Color findColour(char c, int j)
+  {
+    Color currentColour = Color.white;
+    String currentHelix = null;
+    // System.out.println(c + " " + j);
+    currentHelix = (String) positionsToHelix.get(j);
+    // System.out.println(positionsToHelix.get(j));
+
+    if (currentHelix != null)
+    {
+      currentColour = (Color) helixcolorhash.get(currentHelix);
+    }
+
+    // System.out.println(c + " " + j + " helix " + currentHelix + " " +
+    // currentColour);
+    return currentColour;
+  }
+
+}