+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+*/\r
package jalview.schemes;\r
\r
-import jalview.datamodel.*;\r
-import java.util.*;\r
import java.awt.*;\r
\r
-public class ResidueColourScheme implements ColourSchemeI{\r
- Color [] colors;\r
- int threshold = 0;\r
- public Vector consensus;\r
+import java.util.*;\r
+\r
\r
- public ResidueColourScheme(Color[] colors, int threshold) {\r
- this.colors = colors;\r
- this.threshold = threshold;\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class ResidueColourScheme implements ColourSchemeI\r
+{\r
+ Color[] colors;\r
+ int threshold = 0;\r
+\r
+ /* Set when threshold colouring to either pid_gaps or pid_nogaps*/\r
+ protected String ignoreGaps = "pid_gaps";\r
+\r
+ /** DOCUMENT ME!! */\r
+ public Hashtable [] consensus;\r
+\r
+ /**\r
+ * Creates a new ResidueColourScheme object.\r
+ *\r
+ * @param colors DOCUMENT ME!\r
+ * @param threshold DOCUMENT ME!\r
+ */\r
+ public ResidueColourScheme(Color[] colors, int threshold)\r
+ {\r
+ this.colors = colors;\r
+ this.threshold = threshold;\r
}\r
\r
+ /**\r
+ * Creates a new ResidueColourScheme object.\r
+ */\r
public ResidueColourScheme()\r
- { }\r
+ {\r
+ }\r
\r
- public void setConsensus(Vector consensus)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param consensus DOCUMENT ME!\r
+ */\r
+ public void setConsensus(Vector vconsensus)\r
{\r
- this.consensus = consensus;\r
+ int i, iSize=vconsensus.size();\r
+ consensus = new Hashtable[iSize];\r
+ for(i=0; i<iSize; i++)\r
+ consensus[i] = (Hashtable)vconsensus.elementAt(i);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param aa DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public Color findColour(String aa)\r
{\r
- return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];\r
+ return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];\r
}\r
\r
- public Color findColour(String s, int j) {\r
-\r
- if( threshold==0 || aboveThreshold(s,j))\r
- return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];\r
- else\r
- return Color.white;\r
-\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param j DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Color findColour(String s, int j)\r
+ {\r
+ if ((threshold == 0) || aboveThreshold(s, j))\r
+ {\r
+ return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];\r
+ }\r
+ else\r
+ {\r
+ return Color.white;\r
+ }\r
}\r
\r
- public int getThreshold() {\r
- return threshold;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getThreshold()\r
+ {\r
+ return threshold;\r
}\r
\r
- public void setThreshold(int ct) {\r
- threshold = ct;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param ct DOCUMENT ME!\r
+ */\r
+ public void setThreshold(int ct, boolean ignoreGaps)\r
+ {\r
+ threshold = ct;\r
+ if(ignoreGaps)\r
+ this.ignoreGaps = "pid_nogaps";\r
+ else\r
+ this.ignoreGaps = "pid_gaps";\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param j DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public boolean aboveThreshold(String s, int j)\r
{\r
- Hashtable hash = (Hashtable)consensus.elementAt(j);\r
-\r
- if ( ( (Integer) hash.get("maxCount")).intValue() != -1 && hash.contains(s))\r
+ if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&\r
+ consensus[j].contains(s))\r
{\r
- //// resCount//////////////////// ///////////////seq count////////////\r
- double sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ( (Integer) hash.get("size")).intValue();\r
-\r
- if (sc >= threshold)\r
- return true;\r
+ float ratio = ((Float)consensus[j].get(ignoreGaps)).floatValue();\r
\r
+ if (ratio >= threshold)\r
+ {\r
+ return true;\r
+ }\r
}\r
\r
- return false;\r
- }\r
-\r
- public boolean canThreshold() {\r
- return true;\r
- }\r
- public boolean isUserDefinable() {\r
- return false;\r
+ return false;\r
}\r
}\r