+/*\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 jalview.jbgui.*;\r
+import java.awt.*;\r
\r
import java.util.*;\r
-import java.awt.*;\r
+\r
\r
public class ResidueColourScheme implements ColourSchemeI {\r
- Color [] colors;\r
- int threshold = 90;\r
+ Color[] colors;\r
+ int threshold = 0;\r
+ public Vector consensus;\r
\r
public ResidueColourScheme(Color[] colors, int threshold) {\r
- this.colors = colors;\r
- this.threshold = threshold;\r
+ this.colors = colors;\r
+ this.threshold = threshold;\r
}\r
\r
public ResidueColourScheme() {\r
}\r
\r
- public Color findColour(String aa)\r
- {\r
- return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];\r
+ public void setConsensus(Vector consensus) {\r
+ this.consensus = consensus;\r
}\r
\r
- public Color findColour(SequenceI seq,String s, int j, Vector aa) {\r
- try {\r
- return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];\r
- } catch (Exception e) {\r
- return Color.white;\r
- }\r
+ public Color findColour(String aa) {\r
+ return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];\r
}\r
\r
- // aa should maybe be a class\r
- public Color getColour(SequenceI seq, int j,Vector aa) {\r
-\r
- Color c = Color.white;\r
- String s = seq.getSequence(j,j+1);\r
-\r
- if (threshold > 0 && aa != null)\r
- {\r
- if (aboveThreshold(aa,seq,j,threshold))\r
- c = findColour(seq,s,j,aa);\r
- }\r
- else\r
- c = findColour(seq,s,j,aa);\r
-\r
-\r
- return c;\r
+ public Color findColour(String s, int j) {\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
+\r
public int getThreshold() {\r
- return threshold;\r
+ return threshold;\r
}\r
\r
public void setThreshold(int ct) {\r
- threshold = ct;\r
+ threshold = ct;\r
}\r
\r
- public Vector getColours(SequenceI s, Vector aa) {\r
- Vector colours = new Vector();\r
-\r
- for (int j = 0; j < s.getLength(); j++)\r
- colours.addElement(getColour(s,j,aa));\r
-\r
- return colours;\r
- }\r
+ public boolean aboveThreshold(String s, int j) {\r
+ Hashtable hash = (Hashtable) consensus.elementAt(j);\r
\r
- public Vector getColours(SequenceGroup sg, Vector aa) {\r
- Vector colours = new Vector();\r
+ if ((((Integer) hash.get("maxCount")).intValue() != -1) &&\r
+ hash.contains(s)) {\r
+ //// resCount//////////////////// ///////////////seq count////////////\r
+ double sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(\r
+ "size")).intValue();\r
\r
- for (int j = 0; j < sg.getSize(); j++) {\r
- SequenceI s = sg.getSequenceAt(j);\r
+ if (sc >= threshold) {\r
+ return true;\r
+ }\r
+ }\r
\r
- for (int i = 0; i < s.getLength();i++) {\r
- colours.addElement(getColour(s,i,aa));\r
- }\r
- }\r
- return colours;\r
- }\r
-\r
- public boolean aboveThreshold(Vector aa,SequenceI seq, int j, int threshold) {\r
- String s = seq.getSequence(j,j+1);\r
- Hashtable hash = (Hashtable)aa.elementAt(j);\r
-\r
- if (j < aa.size()) {\r
- String maxRes = (String)hash.get("maxResidue");\r
-\r
- double sc = 0;\r
-\r
- if (((Integer)hash.get("maxCount")).intValue() != -1 && hash.contains(s)) {\r
- int maxCount = ((Integer)hash.get("maxCount")).intValue();\r
- int resCount = ((Integer)hash.get(s)).intValue();\r
-\r
- sc = resCount * 100.0 / resCount;\r
-\r
- // This should be isGap somewhere\r
- if ( !s.equals("-") && !s.equals(".") && !s.equals(" ")) {\r
- if (sc >= (double)threshold) {\r
- return true;\r
- }\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
git://source.jalview.org / jalview.git / blobdiff