-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\r
+/*\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
*\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.schemes;\r
\r
-import jalview.datamodel.*;\r
import java.util.*;\r
+\r
import java.awt.*;\r
\r
-public class ClustalxColourScheme implements ColourSchemeI\r
+import jalview.datamodel.*;\r
+\r
+public class ClustalxColourScheme\r
+ extends ResidueColourScheme\r
{\r
+ public static Hashtable colhash = new Hashtable();\r
Hashtable[] cons;\r
int[][] cons2;\r
ConsensusColour[] colours;\r
ConsensusColour[] ResidueColour;\r
int size;\r
- Consensus[] conses = new Consensus[32];\r
- public static Hashtable colhash = new Hashtable();\r
-\r
- {\r
- colhash.put("RED",new Color((float)0.9,(float)0.2,(float)0.1));\r
- colhash.put("BLUE",new Color((float)0.5,(float)0.7,(float)0.9));\r
- colhash.put("GREEN",new Color((float)0.1,(float)0.8,(float)0.1));\r
- colhash.put("ORANGE",new Color((float)0.9,(float)0.6,(float)0.3));\r
- colhash.put("CYAN",new Color((float)0.1,(float)0.7,(float)0.7));\r
- colhash.put("PINK",new Color((float)0.9,(float)0.5,(float)0.5));\r
- colhash.put("MAGENTA",new Color((float)0.8,(float)0.3,(float)0.8));\r
- colhash.put("YELLOW",new Color((float)0.8,(float)0.8,(float)0.0));\r
-\r
- }\r
+ Consensus[] conses = new Consensus[32];\r
Vector colourTable = new Vector();\r
\r
+ {\r
+ colhash.put("RED", new Color( (float) 0.9, (float) 0.2, (float) 0.1));\r
+ colhash.put("BLUE", new Color( (float) 0.5, (float) 0.7, (float) 0.9));\r
+ colhash.put("GREEN", new Color( (float) 0.1, (float) 0.8, (float) 0.1));\r
+ colhash.put("ORANGE", new Color( (float) 0.9, (float) 0.6, (float) 0.3));\r
+ colhash.put("CYAN", new Color( (float) 0.1, (float) 0.7, (float) 0.7));\r
+ colhash.put("PINK", new Color( (float) 0.9, (float) 0.5, (float) 0.5));\r
+ colhash.put("MAGENTA", new Color( (float) 0.8, (float) 0.3, (float) 0.8));\r
+ colhash.put("YELLOW", new Color( (float) 0.8, (float) 0.8, (float) 0.0));\r
+ }\r
\r
public ClustalxColourScheme(Vector seqs, int maxWidth)\r
{\r
+ resetClustalX(seqs, maxWidth);\r
+ }\r
+\r
+ public void resetClustalX(Vector seqs, int maxWidth)\r
+ {\r
cons2 = new int[maxWidth][24];\r
- int start = 0, end = maxWidth-1;\r
+\r
+ int start = 0;\r
\r
// Initialize the array\r
- for (int j=0;j<24;j++)\r
- for (int i=0; i < maxWidth;i++)\r
+ for (int j = 0; j < 24; j++)\r
+ {\r
+ for (int i = 0; i < maxWidth; i++)\r
+ {\r
cons2[i][j] = 0;\r
+ }\r
+ }\r
\r
- int res,i, j = 0;\r
- String seq;\r
- while(j < seqs.size())\r
+ int res;\r
+ int i;\r
+ int j = 0;\r
+ String seq;\r
+\r
+ while (j < seqs.size())\r
+ {\r
+ seq = ( (SequenceI) seqs.elementAt(j)).getSequence();\r
+\r
+ int end_j = seq.length() - 1;\r
+\r
+ for (i = start; i <= end_j; i++)\r
{\r
- seq = ( (SequenceI) seqs.get(j)).getSequence();\r
- int end_j = seq.length()-1;\r
- for (i = start; i <= end_j; i++)\r
+ if ( (seq.length() - 1) < i)\r
{\r
- if(seq.length()-1<i)\r
- res = 23;\r
- else\r
- res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) + "")).intValue();\r
- cons2[i][res]++;\r
+ res = 23;\r
}\r
- j++;\r
+ else\r
+ {\r
+ res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) +\r
+ "")).intValue();\r
+ }\r
+\r
+ cons2[i][res]++;\r
}\r
\r
+ j++;\r
+ }\r
+\r
this.size = seqs.size();\r
makeColours();\r
}\r
- public void makeColours() {\r
- conses[0] = new Consensus("WLVIMAFCYHP",60);\r
- conses[1] = new Consensus("WLVIMAFCYHP",80);\r
- conses[2] = new Consensus("ED",50);\r
- conses[3] = new Consensus("KR",60);\r
- conses[4] = new Consensus("G",50);\r
- conses[5] = new Consensus("N",50);\r
- conses[6] = new Consensus("QE",50);\r
- conses[7] = new Consensus("P",50);\r
- conses[8] = new Consensus("TS",50);\r
-\r
- conses[26] = new Consensus("A",85);\r
- conses[27] = new Consensus("C",85);\r
- conses[10] = new Consensus("E",85);\r
- conses[11] = new Consensus("F",85);\r
- conses[12] = new Consensus("G",85);\r
- conses[13] = new Consensus("H",85);\r
- conses[14] = new Consensus("I",85);\r
- conses[15] = new Consensus("L",85);\r
- conses[16] = new Consensus("M",85);\r
- conses[17] = new Consensus("N",85);\r
- conses[18] = new Consensus("P",85);\r
- conses[19] = new Consensus("Q",85);\r
- conses[20] = new Consensus("R",85);\r
- conses[21] = new Consensus("S",85);\r
- conses[22] = new Consensus("T",85);\r
- conses[23] = new Consensus("V",85);\r
- conses[24] = new Consensus("W",85);\r
- conses[25] = new Consensus("Y",85);\r
- conses[28] = new Consensus("K",85);\r
- conses[29] = new Consensus("D",85);\r
-\r
- conses[30] = new Consensus("G",0);\r
- conses[31] = new Consensus("P",0);\r
+\r
+ public void makeColours()\r
+ {\r
+ conses[0] = new Consensus("WLVIMAFCYHP", 60);\r
+ conses[1] = new Consensus("WLVIMAFCYHP", 80);\r
+ conses[2] = new Consensus("ED", 50);\r
+ conses[3] = new Consensus("KR", 60);\r
+ conses[4] = new Consensus("G", 50);\r
+ conses[5] = new Consensus("N", 50);\r
+ conses[6] = new Consensus("QE", 50);\r
+ conses[7] = new Consensus("P", 50);\r
+ conses[8] = new Consensus("TS", 50);\r
+\r
+ conses[26] = new Consensus("A", 85);\r
+ conses[27] = new Consensus("C", 85);\r
+ conses[10] = new Consensus("E", 85);\r
+ conses[11] = new Consensus("F", 85);\r
+ conses[12] = new Consensus("G", 85);\r
+ conses[13] = new Consensus("H", 85);\r
+ conses[14] = new Consensus("I", 85);\r
+ conses[15] = new Consensus("L", 85);\r
+ conses[16] = new Consensus("M", 85);\r
+ conses[17] = new Consensus("N", 85);\r
+ conses[18] = new Consensus("P", 85);\r
+ conses[19] = new Consensus("Q", 85);\r
+ conses[20] = new Consensus("R", 85);\r
+ conses[21] = new Consensus("S", 85);\r
+ conses[22] = new Consensus("T", 85);\r
+ conses[23] = new Consensus("V", 85);\r
+ conses[24] = new Consensus("W", 85);\r
+ conses[25] = new Consensus("Y", 85);\r
+ conses[28] = new Consensus("K", 85);\r
+ conses[29] = new Consensus("D", 85);\r
+\r
+ conses[30] = new Consensus("G", 0);\r
+ conses[31] = new Consensus("P", 0);\r
\r
// We now construct the colours\r
colours = new ConsensusColour[11];\r
\r
-\r
Consensus[] tmp8 = new Consensus[1];\r
- tmp8[0] = conses[30];//G\r
- colours[7] =new ConsensusColour((Color)colhash.get("ORANGE"),tmp8);\r
+ tmp8[0] = conses[30]; //G\r
+ colours[7] = new ConsensusColour( (Color) colhash.get("ORANGE"), tmp8);\r
\r
Consensus[] tmp9 = new Consensus[1];\r
- tmp9[0] = conses[31];//P\r
- colours[8] =new ConsensusColour((Color)colhash.get("YELLOW"),tmp9);\r
+ tmp9[0] = conses[31]; //P\r
+ colours[8] = new ConsensusColour( (Color) colhash.get("YELLOW"), tmp9);\r
\r
Consensus[] tmp10 = new Consensus[1];\r
- tmp10[0] = conses[27];//C\r
- colours[9] =new ConsensusColour((Color)colhash.get("PINK"),tmp8);\r
+ tmp10[0] = conses[27]; //C\r
+ colours[9] = new ConsensusColour( (Color) colhash.get("PINK"), tmp8);\r
\r
Consensus[] tmp1 = new Consensus[14];\r
tmp1[0] = conses[0]; //%\r
tmp1[11] = conses[25]; //Y\r
tmp1[12] = conses[18]; //P\r
tmp1[13] = conses[19]; //p\r
- colours[0] = new ConsensusColour((Color)colhash.get("BLUE"),tmp1);\r
+ colours[0] = new ConsensusColour( (Color) colhash.get("BLUE"), tmp1);\r
\r
- colours[10] = new ConsensusColour((Color)colhash.get("CYAN"),tmp1);\r
+ colours[10] = new ConsensusColour( (Color) colhash.get("CYAN"), tmp1);\r
\r
Consensus[] tmp2 = new Consensus[5];\r
- tmp2[0] = conses[8]; //t\r
+ tmp2[0] = conses[8]; //t\r
tmp2[1] = conses[21]; //S\r
tmp2[2] = conses[22]; //T\r
- tmp2[3] = conses[0]; //%\r
- tmp2[4] = conses[1]; //#\r
- colours[1] = new ConsensusColour((Color)colhash.get("GREEN"),tmp2);\r
+ tmp2[3] = conses[0]; //%\r
+ tmp2[4] = conses[1]; //#\r
+ colours[1] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp2);\r
\r
Consensus[] tmp3 = new Consensus[3];\r
\r
tmp3[0] = conses[17]; //N\r
tmp3[1] = conses[29]; //D\r
- tmp3[2] = conses[5]; //n\r
- colours[2] = new ConsensusColour((Color)colhash.get("GREEN"),tmp3);\r
+ tmp3[2] = conses[5]; //n\r
+ colours[2] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp3);\r
\r
Consensus[] tmp4 = new Consensus[6];\r
- tmp4[0] = conses[6]; // q = QE\r
+ tmp4[0] = conses[6]; // q = QE\r
tmp4[1] = conses[19]; //Q\r
tmp4[2] = conses[22]; //E\r
- tmp4[3] = conses[3]; //+\r
+ tmp4[3] = conses[3]; //+\r
tmp4[4] = conses[28]; //K\r
tmp4[5] = conses[20]; //R\r
- colours[3] = new ConsensusColour((Color)colhash.get("GREEN"),tmp4);\r
+ colours[3] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp4);\r
+\r
Consensus[] tmp5 = new Consensus[4];\r
- tmp5[0] = conses[3]; //+\r
+ tmp5[0] = conses[3]; //+\r
tmp5[1] = conses[28]; //K\r
tmp5[2] = conses[20]; //R\r
tmp5[3] = conses[19]; //Q\r
- colours[4] = new ConsensusColour((Color)colhash.get("RED"),tmp5);\r
+ colours[4] = new ConsensusColour( (Color) colhash.get("RED"), tmp5);\r
+\r
Consensus[] tmp6 = new Consensus[5];\r
- tmp6[0] = conses[3]; //-\r
+ tmp6[0] = conses[3]; //-\r
tmp6[1] = conses[29]; //D\r
tmp6[2] = conses[10]; //E\r
- tmp6[3] = conses[6]; //q\r
+ tmp6[3] = conses[6]; //q\r
tmp6[4] = conses[19]; //Q\r
- colours[5] = new ConsensusColour((Color)colhash.get("MAGENTA"),tmp6);\r
+ colours[5] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp6);\r
\r
Consensus[] tmp7 = new Consensus[5];\r
- tmp7[0] = conses[3]; //-\r
+ tmp7[0] = conses[3]; //-\r
tmp7[1] = conses[29]; //D\r
tmp7[2] = conses[10]; //E\r
- tmp7[3] = conses[17]; //N\r
+ tmp7[3] = conses[17]; //N\r
tmp7[4] = conses[2]; //DE\r
- colours[6] = new ConsensusColour((Color)colhash.get("MAGENTA"),tmp7);\r
+ colours[6] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp7);\r
\r
// Now attach the ConsensusColours to the residue letters\r
ResidueColour = new ConsensusColour[20];\r
return Color.pink;\r
}\r
\r
- public void setGroupSizeChanged(int i)\r
- {\r
- size = i;\r
- }\r
+ public Color findColour(String s, int j)\r
+ {\r
+ if ( (threshold != 0) && !aboveThreshold(s, j))\r
+ {\r
+ return Color.white;\r
+ }\r
\r
- public Color findColour(String s, int j, Vector seqs)\r
- {\r
- int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();\r
+ int i = ( (Integer) ResidueProperties.aaHash.get(s)).intValue();\r
\r
- Color c = Color.white;\r
+ Color c = Color.white;\r
\r
- if(i>19)\r
- return c;\r
+ if (i > 19)\r
+ {\r
+ return c;\r
+ }\r
\r
- for (int k=0; k < ResidueColour[i].conses.length ; k++)\r
- if (ResidueColour[i].conses[k].isConserved(cons2,j,size))\r
- c = ResidueColour[i].c;\r
+ for (int k = 0; k < ResidueColour[i].conses.length; k++)\r
+ {\r
+ if (ResidueColour[i].conses[k].isConserved(cons2, j, size))\r
+ {\r
+ c = ResidueColour[i].c;\r
+ }\r
+ }\r
\r
- if (i == 4)\r
+ if (i == 4)\r
{\r
if (conses[27].isConserved(cons2, j, size))\r
+ {\r
c = (Color) colhash.get("PINK");\r
+ }\r
}\r
\r
-\r
- return c;\r
-\r
- }\r
-\r
-\r
- public boolean canThreshold()\r
- {\r
- return false;\r
+ return c;\r
}\r
-\r
- public boolean isUserDefinable()\r
- {\r
- return false;\r
- }\r
-\r
-\r
}\r
\r
-class ConsensusColour {\r
-\r
+class ConsensusColour\r
+{\r
Consensus[] conses;\r
Color c;\r
\r
- public ConsensusColour(Color c,Consensus[] conses) {\r
+ public ConsensusColour(Color c, Consensus[] conses)\r
+ {\r
this.conses = conses;\r
+\r
// this.list = list;\r
this.c = c;\r
}\r
}\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
git://source.jalview.org / jalview.git / blobdiff