/*\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
+ * 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
-\r
-import java.awt.*;\r
-\r
import java.util.*;\r
\r
+import java.awt.*;\r
\r
-public class ClustalxColourScheme extends ResidueColourScheme {\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
- Vector colourTable = new Vector();\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
+ 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
+\r
+ int start = 0;\r
+\r
+ // Initialize the array\r
+ for (int j = 0; j < 24; j++)\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
- resetClustalX(seqs, maxWidth);\r
+ for (int i = 0; i < maxWidth; i++)\r
+ {\r
+ cons2[i][j] = 0;\r
+ }\r
}\r
\r
- public void resetClustalX(Vector seqs, int maxWidth) {\r
- cons2 = new int[maxWidth][24];\r
+ int res;\r
+ int i;\r
+ int j = 0;\r
+ String seq;\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
- cons2[i][j] = 0;\r
-\r
- int res;\r
- int i;\r
- int j = 0;\r
- String seq;\r
-\r
- while (j < seqs.size()) {\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
- if ((seq.length() - 1) < i) {\r
- res = 23;\r
- } else {\r
- res = ((Integer) ResidueProperties.aaHash.get(seq.charAt(i) +\r
- "")).intValue();\r
- }\r
+ while (j < seqs.size())\r
+ {\r
+ seq = ( (SequenceI) seqs.elementAt(j)).getSequence();\r
\r
- cons2[i][res]++;\r
- }\r
+ int end_j = seq.length() - 1;\r
\r
- j++;\r
+ for (i = start; i <= end_j; i++)\r
+ {\r
+ if ( (seq.length() - 1) < i)\r
+ {\r
+ res = 23;\r
+ }\r
+ else\r
+ {\r
+ res = ( (Integer) ResidueProperties.aaHash.get(seq.charAt(i) +\r
+ "")).intValue();\r
}\r
\r
- this.size = seqs.size();\r
- makeColours();\r
- }\r
+ cons2[i][res]++;\r
+ }\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
- // We now construct the colours\r
- colours = new ConsensusColour[11];\r
-\r
- Consensus[] tmp8 = new Consensus[1];\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
-\r
- Consensus[] tmp10 = new Consensus[1];\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[1] = conses[1]; //#\r
- tmp1[2] = conses[26]; //A\r
- tmp1[3] = conses[27]; //C\r
- tmp1[4] = conses[11]; //F\r
- tmp1[5] = conses[13]; //H\r
- tmp1[6] = conses[14]; //I\r
- tmp1[7] = conses[15]; //L\r
- tmp1[8] = conses[16]; //M\r
- tmp1[9] = conses[23]; //V\r
- tmp1[10] = conses[24]; //W\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
-\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[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
-\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
-\r
- Consensus[] tmp4 = new Consensus[6];\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[4] = conses[28]; //K\r
- tmp4[5] = conses[20]; //R\r
- colours[3] = new ConsensusColour((Color) colhash.get("GREEN"), tmp4);\r
-\r
- Consensus[] tmp5 = new Consensus[4];\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
-\r
- Consensus[] tmp6 = new Consensus[5];\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[4] = conses[19]; //Q\r
- colours[5] = new ConsensusColour((Color) colhash.get("MAGENTA"), tmp6);\r
-\r
- Consensus[] tmp7 = new Consensus[5];\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[4] = conses[2]; //DE\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
- ResidueColour[0] = colours[0]; // A\r
- ResidueColour[1] = colours[4]; // R\r
- ResidueColour[2] = colours[2]; // N\r
- ResidueColour[3] = colours[6]; // D\r
- ResidueColour[4] = colours[0]; // C\r
- ResidueColour[5] = colours[3]; // Q\r
- ResidueColour[6] = colours[5]; // E\r
- ResidueColour[7] = colours[7]; // G\r
- ResidueColour[8] = colours[10]; // H\r
- ResidueColour[9] = colours[0]; // I\r
- ResidueColour[10] = colours[0]; // L\r
- ResidueColour[11] = colours[4]; // K\r
- ResidueColour[12] = colours[0]; // M\r
- ResidueColour[13] = colours[0]; // F\r
- ResidueColour[14] = colours[8]; // P\r
- ResidueColour[15] = colours[1]; // S\r
- ResidueColour[16] = colours[1]; // T\r
- ResidueColour[17] = colours[0]; // W\r
- ResidueColour[18] = colours[10]; // Y\r
- ResidueColour[19] = colours[0]; // V\r
+ j++;\r
}\r
\r
- public Color findColour(String s) {\r
- return Color.pink;\r
+ this.size = seqs.size();\r
+ makeColours();\r
+ }\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
+ Consensus[] tmp8 = new Consensus[1];\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
+\r
+ Consensus[] tmp10 = new Consensus[1];\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[1] = conses[1]; //#\r
+ tmp1[2] = conses[26]; //A\r
+ tmp1[3] = conses[27]; //C\r
+ tmp1[4] = conses[11]; //F\r
+ tmp1[5] = conses[13]; //H\r
+ tmp1[6] = conses[14]; //I\r
+ tmp1[7] = conses[15]; //L\r
+ tmp1[8] = conses[16]; //M\r
+ tmp1[9] = conses[23]; //V\r
+ tmp1[10] = conses[24]; //W\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
+\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[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
+\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
+\r
+ Consensus[] tmp4 = new Consensus[6];\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[4] = conses[28]; //K\r
+ tmp4[5] = conses[20]; //R\r
+ colours[3] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp4);\r
+\r
+ Consensus[] tmp5 = new Consensus[4];\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
+\r
+ Consensus[] tmp6 = new Consensus[5];\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[4] = conses[19]; //Q\r
+ colours[5] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp6);\r
+\r
+ Consensus[] tmp7 = new Consensus[5];\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[4] = conses[2]; //DE\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
+ ResidueColour[0] = colours[0]; // A\r
+ ResidueColour[1] = colours[4]; // R\r
+ ResidueColour[2] = colours[2]; // N\r
+ ResidueColour[3] = colours[6]; // D\r
+ ResidueColour[4] = colours[0]; // C\r
+ ResidueColour[5] = colours[3]; // Q\r
+ ResidueColour[6] = colours[5]; // E\r
+ ResidueColour[7] = colours[7]; // G\r
+ ResidueColour[8] = colours[10]; // H\r
+ ResidueColour[9] = colours[0]; // I\r
+ ResidueColour[10] = colours[0]; // L\r
+ ResidueColour[11] = colours[4]; // K\r
+ ResidueColour[12] = colours[0]; // M\r
+ ResidueColour[13] = colours[0]; // F\r
+ ResidueColour[14] = colours[8]; // P\r
+ ResidueColour[15] = colours[1]; // S\r
+ ResidueColour[16] = colours[1]; // T\r
+ ResidueColour[17] = colours[0]; // W\r
+ ResidueColour[18] = colours[10]; // Y\r
+ ResidueColour[19] = colours[0]; // V\r
+ }\r
+\r
+ public Color findColour(String s)\r
+ {\r
+ return Color.pink;\r
+ }\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) {\r
- if ((threshold != 0) && !aboveThreshold(s, j)) {\r
- return Color.white;\r
- }\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
- }\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
- }\r
+ if (i > 19)\r
+ {\r
+ return c;\r
+ }\r
\r
- if (i == 4) {\r
- if (conses[27].isConserved(cons2, j, size)) {\r
- c = (Color) colhash.get("PINK");\r
- }\r
- }\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
- return c;\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
-class ConsensusColour {\r
- Consensus[] conses;\r
- Color c;\r
+class ConsensusColour\r
+{\r
+ Consensus[] conses;\r
+ Color c;\r
\r
- public ConsensusColour(Color c, Consensus[] conses) {\r
- this.conses = conses;\r
+ public ConsensusColour(Color c, Consensus[] conses)\r
+ {\r
+ this.conses = conses;\r
\r
- // this.list = list;\r
- this.c = c;\r
- }\r
+ // this.list = list;\r
+ this.c = c;\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff