X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=add76a0f883aaba155fe21c16c311929646eadda;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=b83244d61ea9d2a8857ff451c5e46076a4db6e81;hpb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;p=jalview.git

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index b83244d..add76a0 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,263 +1,263 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-package jalview.schemes;
-
-import jalview.analysis.*;
-
-import java.awt.*;
-
-import java.util.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class ResidueColourScheme implements ColourSchemeI
-{
-
-    boolean conservationColouring = false;
-    boolean consensusColouring = false;
-
-    Color[] colors;
-    int threshold = 0;
-
-    /* Set when threshold colouring to either pid_gaps or pid_nogaps*/
-    protected String ignoreGaps = "pid_gaps";
-
-    /** Consenus as a hashtable array */
-    Hashtable [] consensus;
-
-    /** Conservation string as a char array */
-   char [] conservation;
-
-   /** DOCUMENT ME!! */
-   int inc = 30;
-
-   /**
-    * The colour to be calculated, manipulated and returned
-    */
-   Color currentColour = null;
-
-
-
-    /**
-     * Creates a new ResidueColourScheme object.
-     *
-     * @param colors DOCUMENT ME!
-     * @param threshold DOCUMENT ME!
-     */
-    public ResidueColourScheme(Color[] colours, int threshold)
-    {
-        this.colors = colours;
-        this.threshold = threshold;
-    }
-
-    /**
-     * Creates a new ResidueColourScheme object.
-     */
-    public ResidueColourScheme()
-    {
-    }
-
-    /**
-    * Find a colour without an index in a sequence
-    */
-   public Color findColour(String aa)
-   {
-       return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];
-   }
-
-
-
-   public Color findColour(String s, int j)
-   {
-
-       int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();
-
-       if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
-       {
-           currentColour = colors[index];
-       }
-       else
-       {
-           currentColour = Color.white;
-       }
-
-       if(conservationColouring)
-         applyConservation(j);
-
-
-       return currentColour;
-   }
-
-
-    /**
-     * Get the percentage threshold for this colour scheme
-     *
-     * @return Returns the percentage threshold
-     */
-    public int getThreshold()
-    {
-        return threshold;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param ct DOCUMENT ME!
-     */
-    public void setThreshold(int ct, boolean ignoreGaps)
-    {
-        threshold = ct;
-        if(ignoreGaps)
-          this.ignoreGaps = "pid_nogaps";
-        else
-          this.ignoreGaps = "pid_gaps";
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean aboveThreshold(String s, int j)
-    {
-        if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&
-                consensus[j].contains(s))
-        {
-            if (((Float)consensus[j].get(ignoreGaps)).floatValue() >= threshold)
-            {
-                return true;
-            }
-        }
-
-        return false;
-    }
-
-
-    public boolean conservationApplied()
-    {
-      return conservationColouring;
-    }
-
-    public void setConservationInc(int i)
-    {
-      inc = i;
-    }
-
-    public int getConservationInc()
-    {
-      return inc;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param consensus DOCUMENT ME!
-     */
-    public void setConsensus(Vector vconsensus)
-    {
-      if(vconsensus==null)
-        return;
-
-       int i, iSize=vconsensus.size();
-       consensus = new Hashtable[iSize];
-       for(i=0; i<iSize; i++)
-        consensus[i] = (Hashtable)vconsensus.elementAt(i);
-    }
-
-
-    public void setConservation(Conservation cons)
-    {
-      if(cons==null)
-      {
-        conservationColouring = false;
-        conservation = null;
-      }
-      else
-      {
-        conservationColouring = true;
-        int i, iSize = cons.getConsSequence().getLength();
-        conservation = new char[iSize];
-        for (i = 0; i < iSize; i++)
-          conservation[i] = cons.getConsSequence().getCharAt(i);
-      }
-
-    }
-
-
-    /**
-    * DOCUMENT ME!
-    *
-    * @param s DOCUMENT ME!
-    * @param i DOCUMENT ME!
-    *
-    * @return DOCUMENT ME!
-    */
-
-   void applyConservation(int i)
-   {
-
-     if ((conservation[i] != '*') && (conservation[i] != '+'))
-     {
-       if(jalview.util.Comparison.isGap(conservation[i]))
-       {
-         currentColour = Color.white;
-       }
-       else
-       {
-         float t = 11 - (conservation[i] - '0');
-         if(t==0)
-         {
-           currentColour = Color.white;
-           return;
-         }
-
-         int red = currentColour.getRed();
-         int green = currentColour.getGreen();
-         int blue = currentColour.getBlue();
-
-         int dr = 255 - red;
-         int dg = 255 - green;
-         int db = 255 - blue;
-
-         dr *= t / 10f;
-         dg *= t / 10f;
-         db *= t / 10f;
-
-         red += (inc / 20f) * dr;
-         green += (inc / 20f) * dg;
-         blue += (inc / 20f) * db;
-
-         if (red > 255 || green > 255 || blue > 255)
-           currentColour = Color.white;
-         else
-           currentColour = new Color(red, green, blue);
-       }
-       }
-   }
-
-
-}
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program 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 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
+package jalview.schemes;
+
+import jalview.analysis.*;
+
+import java.awt.*;
+
+import java.util.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ResidueColourScheme implements ColourSchemeI
+{
+
+    boolean conservationColouring = false;
+    boolean consensusColouring = false;
+
+    Color[] colors;
+    int threshold = 0;
+
+    /* Set when threshold colouring to either pid_gaps or pid_nogaps*/
+    protected String ignoreGaps = "pid_gaps";
+
+    /** Consenus as a hashtable array */
+    Hashtable [] consensus;
+
+    /** Conservation string as a char array */
+   char [] conservation;
+
+   /** DOCUMENT ME!! */
+   int inc = 30;
+
+   /**
+    * The colour to be calculated, manipulated and returned
+    */
+   Color currentColour = null;
+
+
+
+    /**
+     * Creates a new ResidueColourScheme object.
+     *
+     * @param colors DOCUMENT ME!
+     * @param threshold DOCUMENT ME!
+     */
+    public ResidueColourScheme(Color[] colours, int threshold)
+    {
+        this.colors = colours;
+        this.threshold = threshold;
+    }
+
+    /**
+     * Creates a new ResidueColourScheme object.
+     */
+    public ResidueColourScheme()
+    {
+    }
+
+    /**
+    * Find a colour without an index in a sequence
+    */
+   public Color findColour(String aa)
+   {
+       return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];
+   }
+
+
+
+   public Color findColour(String s, int j)
+   {
+
+       int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();
+
+       if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
+       {
+           currentColour = colors[index];
+       }
+       else
+       {
+           currentColour = Color.white;
+       }
+
+       if(conservationColouring)
+         applyConservation(j);
+
+
+       return currentColour;
+   }
+
+
+    /**
+     * Get the percentage threshold for this colour scheme
+     *
+     * @return Returns the percentage threshold
+     */
+    public int getThreshold()
+    {
+        return threshold;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param ct DOCUMENT ME!
+     */
+    public void setThreshold(int ct, boolean ignoreGaps)
+    {
+        threshold = ct;
+        if(ignoreGaps)
+          this.ignoreGaps = "pid_nogaps";
+        else
+          this.ignoreGaps = "pid_gaps";
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean aboveThreshold(String s, int j)
+    {
+        if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&
+                consensus[j].contains(s))
+        {
+            if (((Float)consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+            {
+                return true;
+            }
+        }
+
+        return false;
+    }
+
+
+    public boolean conservationApplied()
+    {
+      return conservationColouring;
+    }
+
+    public void setConservationInc(int i)
+    {
+      inc = i;
+    }
+
+    public int getConservationInc()
+    {
+      return inc;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param consensus DOCUMENT ME!
+     */
+    public void setConsensus(Vector vconsensus)
+    {
+      if(vconsensus==null)
+        return;
+
+       int i, iSize=vconsensus.size();
+       consensus = new Hashtable[iSize];
+       for(i=0; i<iSize; i++)
+        consensus[i] = (Hashtable)vconsensus.elementAt(i);
+    }
+
+
+    public void setConservation(Conservation cons)
+    {
+      if(cons==null)
+      {
+        conservationColouring = false;
+        conservation = null;
+      }
+      else
+      {
+        conservationColouring = true;
+        int i, iSize = cons.getConsSequence().getLength();
+        conservation = new char[iSize];
+        for (i = 0; i < iSize; i++)
+          conservation[i] = cons.getConsSequence().getCharAt(i);
+      }
+
+    }
+
+
+    /**
+    * DOCUMENT ME!
+    *
+    * @param s DOCUMENT ME!
+    * @param i DOCUMENT ME!
+    *
+    * @return DOCUMENT ME!
+    */
+
+   void applyConservation(int i)
+   {
+
+     if ((conservation[i] != '*') && (conservation[i] != '+'))
+     {
+       if(jalview.util.Comparison.isGap(conservation[i]))
+       {
+         currentColour = Color.white;
+       }
+       else
+       {
+         float t = 11 - (conservation[i] - '0');
+         if(t==0)
+         {
+           currentColour = Color.white;
+           return;
+         }
+
+         int red = currentColour.getRed();
+         int green = currentColour.getGreen();
+         int blue = currentColour.getBlue();
+
+         int dr = 255 - red;
+         int dg = 255 - green;
+         int db = 255 - blue;
+
+         dr *= t / 10f;
+         dg *= t / 10f;
+         db *= t / 10f;
+
+         red += (inc / 20f) * dr;
+         green += (inc / 20f) * dg;
+         blue += (inc / 20f) * db;
+
+         if (red > 255 || green > 255 || blue > 255)
+           currentColour = Color.white;
+         else
+           currentColour = new Color(red, green, blue);
+       }
+       }
+   }
+
+
+}