X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=503413429adca6ca9c4a814777a634ca7a863a70;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=bc5e8ea4f3dbe6f385a673a957b3d8df14254305;hpb=85867b5d46751cfce6500002e098a431fec0950e;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index bc5e8ea..5034134 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,29 +1,238 @@
-/* Jalview - a java multiple alignment editor
- * Copyright (C) 1998  Michele Clamp
- *
- * 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., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
- */
-
-package jalview.schemes;
-
-import java.awt.*;
-
-public class UserColourScheme extends ResidueColourScheme
-{
-  public void setColourScheme(Color [] newColors)
-  {
-    colors = newColors;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.util.*;
+
+import java.awt.*;
+
+public class UserColourScheme extends ResidueColourScheme
+{
+  Color[] lowerCaseColours;
+
+  protected String schemeName;
+
+  public UserColourScheme()
+  {
+  }
+
+  public UserColourScheme(Color[] newColors)
+  {
+    colors = newColors;
+  }
+
+  public UserColourScheme(String colour)
+  {
+    Color col = getColourFromString(colour);
+
+    if (col == null)
+    {
+      System.out.println("Unknown colour!! " + colour);
+      col = createColourFromName(colour);
+    }
+
+    colors = new Color[24];
+    for (int i = 0; i < 24; i++)
+    {
+      colors[i] = col;
+    }
+    schemeName = colour;
+  }
+
+  public Color[] getColours()
+  {
+    return colors;
+  }
+
+  public Color[] getLowerCaseColours()
+  {
+    return lowerCaseColours;
+  }
+
+  public void setName(String name)
+  {
+    schemeName = name;
+  }
+
+  public String getName()
+  {
+    return schemeName;
+  }
+
+  public Color getColourFromString(String colour)
+  {
+    colour = colour.trim();
+
+    Color col = null;
+    try
+    {
+      int value = Integer.parseInt(colour, 16);
+      col = new Color(value);
+    } catch (NumberFormatException ex)
+    {
+    }
+
+    if (col == null)
+    {
+      col = ColourSchemeProperty.getAWTColorFromName(colour);
+    }
+
+    if (col == null)
+    {
+      try
+      {
+        java.util.StringTokenizer st = new java.util.StringTokenizer(
+                colour, ",");
+        int r = Integer.parseInt(st.nextToken());
+        int g = Integer.parseInt(st.nextToken());
+        int b = Integer.parseInt(st.nextToken());
+        col = new Color(r, g, b);
+      } catch (Exception ex)
+      {
+      }
+    }
+
+    return col;
+
+  }
+
+  public Color createColourFromName(String name)
+  {
+    int r, g, b;
+
+    int lsize = name.length();
+    int start = 0, end = lsize / 3;
+
+    int rgbOffset = Math.abs(name.hashCode() % 10) * 15;
+
+    r = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
+    start = end;
+    end += lsize / 3;
+    if (end > lsize)
+    {
+      end = lsize;
+    }
+
+    g = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
+
+    b = Math.abs(name.substring(end).hashCode() + rgbOffset) % 210 + 20;
+
+    Color color = new Color(r, g, b);
+
+    return color;
+  }
+
+  public void parseAppletParameter(String paramValue)
+  {
+    StringTokenizer st = new StringTokenizer(paramValue, ";");
+    StringTokenizer st2;
+    String token = null, colour, residues;
+    try
+    {
+      while (st.hasMoreElements())
+      {
+        token = st.nextToken().trim();
+        residues = token.substring(0, token.indexOf("="));
+        colour = token.substring(token.indexOf("=") + 1);
+
+        st2 = new StringTokenizer(residues, " ,");
+        while (st2.hasMoreTokens())
+        {
+          token = st2.nextToken();
+
+          if (ResidueProperties.aaIndex[token.charAt(0)] == -1)
+          {
+            continue;
+          }
+
+          int colIndex = ResidueProperties.aaIndex[token.charAt(0)];
+
+          if (token.equalsIgnoreCase("lowerCase"))
+          {
+            if (lowerCaseColours == null)
+            {
+              lowerCaseColours = new Color[23];
+            }
+            for (int i = 0; i < 23; i++)
+            {
+              if (lowerCaseColours[i] == null)
+              {
+                lowerCaseColours[i] = getColourFromString(colour);
+              }
+            }
+
+            continue;
+          }
+
+          if (token.equals(token.toLowerCase()))
+          {
+            if (lowerCaseColours == null)
+            {
+              lowerCaseColours = new Color[23];
+            }
+            lowerCaseColours[colIndex] = getColourFromString(colour);
+          }
+          else
+          {
+            colors[colIndex] = getColourFromString(colour);
+          }
+        }
+      }
+    } catch (Exception ex)
+    {
+      System.out.println("Error parsing userDefinedColours:\n" + token
+              + "\n" + ex);
+    }
+
+  }
+
+  public Color findColour(char c, int j)
+  {
+    Color currentColour;
+    int index = ResidueProperties.aaIndex[c];
+
+    if ((threshold == 0) || aboveThreshold(c, j))
+    {
+      if (lowerCaseColours != null && 'a' <= c && c <= 'z')
+      {
+        currentColour = lowerCaseColours[index];
+      }
+      else
+      {
+        currentColour = colors[index];
+      }
+    }
+    else
+    {
+      currentColour = Color.white;
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+
+  public void setLowerCaseColours(Color[] lcolours)
+  {
+    lowerCaseColours = lcolours;
+  }
+
+}