-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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 java.util.*;\r
-\r
-import java.awt.*;\r
-\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
- for (int i = 0; i < maxWidth; i++)\r
- {\r
- cons2[i][j] = 0;\r
- }\r
- }\r
-\r
- int res;\r
- int i;\r
- int j = 0;\r
- char[] 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
- if ( (seq.length - 1) < i)\r
- {\r
- res = 23;\r
- }\r
- else\r
- {\r
- res = ResidueProperties.aaIndex[seq[i]];\r
- }\r
-\r
- cons2[i][res]++;\r
- }\r
-\r
- j++;\r
- }\r
-\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(char c)\r
- {\r
- return Color.pink;\r
- }\r
-\r
- public Color findColour(char c, int j)\r
- {\r
- Color currentColour;\r
-\r
- if (cons2.length <= j || (threshold != 0 && !aboveThreshold(c, j)))\r
- {\r
- return Color.white;\r
- }\r
-\r
- int i = ResidueProperties.aaIndex[c];\r
-\r
- currentColour = Color.white;\r
-\r
- if (i > 19)\r
- {\r
- return currentColour;\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
- currentColour = ResidueColour[i].c;\r
- }\r
- }\r
-\r
- if (i == 4)\r
- {\r
- if (conses[27].isConserved(cons2, j, size))\r
- {\r
- currentColour = (Color) colhash.get("PINK");\r
- }\r
- }\r
-\r
- if (conservationColouring)\r
- {\r
- currentColour = applyConservation(currentColour, j);\r
- }\r
-\r
- return currentColour;\r
- }\r
-}\r
-\r
-class ConsensusColour\r
-{\r
- Consensus[] conses;\r
- Color c;\r
-\r
- public ConsensusColour(Color c, Consensus[] conses)\r
- {\r
- this.conses = conses;\r
-\r
- // this.list = list;\r
- this.c = c;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * 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., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.schemes;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+
+public class ClustalxColourScheme
+ extends ResidueColourScheme // implements IParameterizable
+{
+ public static Hashtable colhash = new Hashtable();
+ Hashtable[] cons;
+ int[][] cons2;
+ ConsensusColour[] colours;
+ ConsensusColour[] ResidueColour;
+ int size;
+ Consensus[] conses = new Consensus[32];
+ Vector colourTable = new Vector();
+ private boolean includeGaps=true;
+
+ {
+ colhash.put("RED", new Color( (float) 0.9, (float) 0.2, (float) 0.1));
+ colhash.put("BLUE", new Color( (float) 0.5, (float) 0.7, (float) 0.9));
+ colhash.put("GREEN", new Color( (float) 0.1, (float) 0.8, (float) 0.1));
+ colhash.put("ORANGE", new Color( (float) 0.9, (float) 0.6, (float) 0.3));
+ colhash.put("CYAN", new Color( (float) 0.1, (float) 0.7, (float) 0.7));
+ colhash.put("PINK", new Color( (float) 0.9, (float) 0.5, (float) 0.5));
+ colhash.put("MAGENTA", new Color( (float) 0.8, (float) 0.3, (float) 0.8));
+ colhash.put("YELLOW", new Color( (float) 0.8, (float) 0.8, (float) 0.0));
+ }
+
+ public ClustalxColourScheme(Vector seqs, int maxWidth)
+ {
+ resetClustalX(seqs, maxWidth);
+ }
+
+ public void resetClustalX(Vector seqs, int maxWidth)
+ {
+ cons2 = new int[maxWidth][24];
+ includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to get the current setting of the includeGaps param.
+ int start = 0;
+
+ // Initialize the array
+ for (int j = 0; j < 24; j++)
+ {
+ for (int i = 0; i < maxWidth; i++)
+ {
+ cons2[i][j] = 0;
+ }
+ }
+
+ int res;
+ int i;
+ int j = 0;
+ char[] seq;
+
+ while (j < seqs.size())
+ {
+ seq = ( (SequenceI) seqs.elementAt(j)).getSequence();
+
+ int end_j = seq.length - 1;
+
+ for (i = start; i <= end_j; i++)
+ {
+ if ( (seq.length - 1) < i)
+ {
+ res = 23;
+ }
+ else
+ {
+ res = ResidueProperties.aaIndex[seq[i]];
+ }
+
+ cons2[i][res]++;
+ }
+
+ j++;
+ }
+
+ this.size = seqs.size();
+ makeColours();
+ }
+
+ public void makeColours()
+ {
+ conses[0] = new Consensus("WLVIMAFCYHP", 60);
+ conses[1] = new Consensus("WLVIMAFCYHP", 80);
+ conses[2] = new Consensus("ED", 50);
+ conses[3] = new Consensus("KR", 60);
+ conses[4] = new Consensus("G", 50);
+ conses[5] = new Consensus("N", 50);
+ conses[6] = new Consensus("QE", 50);
+ conses[7] = new Consensus("P", 50);
+ conses[8] = new Consensus("TS", 50);
+
+ conses[26] = new Consensus("A", 85);
+ conses[27] = new Consensus("C", 85);
+ conses[10] = new Consensus("E", 85);
+ conses[11] = new Consensus("F", 85);
+ conses[12] = new Consensus("G", 85);
+ conses[13] = new Consensus("H", 85);
+ conses[14] = new Consensus("I", 85);
+ conses[15] = new Consensus("L", 85);
+ conses[16] = new Consensus("M", 85);
+ conses[17] = new Consensus("N", 85);
+ conses[18] = new Consensus("P", 85);
+ conses[19] = new Consensus("Q", 85);
+ conses[20] = new Consensus("R", 85);
+ conses[21] = new Consensus("S", 85);
+ conses[22] = new Consensus("T", 85);
+ conses[23] = new Consensus("V", 85);
+ conses[24] = new Consensus("W", 85);
+ conses[25] = new Consensus("Y", 85);
+ conses[28] = new Consensus("K", 85);
+ conses[29] = new Consensus("D", 85);
+
+ conses[30] = new Consensus("G", 0);
+ conses[31] = new Consensus("P", 0);
+
+ // We now construct the colours
+ colours = new ConsensusColour[11];
+
+ Consensus[] tmp8 = new Consensus[1];
+ tmp8[0] = conses[30]; //G
+ colours[7] = new ConsensusColour( (Color) colhash.get("ORANGE"), tmp8);
+
+ Consensus[] tmp9 = new Consensus[1];
+ tmp9[0] = conses[31]; //P
+ colours[8] = new ConsensusColour( (Color) colhash.get("YELLOW"), tmp9);
+
+ Consensus[] tmp10 = new Consensus[1];
+ tmp10[0] = conses[27]; //C
+ colours[9] = new ConsensusColour( (Color) colhash.get("PINK"), tmp8);
+
+ Consensus[] tmp1 = new Consensus[14];
+ tmp1[0] = conses[0]; //%
+ tmp1[1] = conses[1]; //#
+ tmp1[2] = conses[26]; //A
+ tmp1[3] = conses[27]; //C
+ tmp1[4] = conses[11]; //F
+ tmp1[5] = conses[13]; //H
+ tmp1[6] = conses[14]; //I
+ tmp1[7] = conses[15]; //L
+ tmp1[8] = conses[16]; //M
+ tmp1[9] = conses[23]; //V
+ tmp1[10] = conses[24]; //W
+ tmp1[11] = conses[25]; //Y
+ tmp1[12] = conses[18]; //P
+ tmp1[13] = conses[19]; //p
+ colours[0] = new ConsensusColour( (Color) colhash.get("BLUE"), tmp1);
+
+ colours[10] = new ConsensusColour( (Color) colhash.get("CYAN"), tmp1);
+
+ Consensus[] tmp2 = new Consensus[5];
+ tmp2[0] = conses[8]; //t
+ tmp2[1] = conses[21]; //S
+ tmp2[2] = conses[22]; //T
+ tmp2[3] = conses[0]; //%
+ tmp2[4] = conses[1]; //#
+ colours[1] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp2);
+
+ Consensus[] tmp3 = new Consensus[3];
+
+ tmp3[0] = conses[17]; //N
+ tmp3[1] = conses[29]; //D
+ tmp3[2] = conses[5]; //n
+ colours[2] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp3);
+
+ Consensus[] tmp4 = new Consensus[6];
+ tmp4[0] = conses[6]; // q = QE
+ tmp4[1] = conses[19]; //Q
+ tmp4[2] = conses[22]; //E
+ tmp4[3] = conses[3]; //+
+ tmp4[4] = conses[28]; //K
+ tmp4[5] = conses[20]; //R
+ colours[3] = new ConsensusColour( (Color) colhash.get("GREEN"), tmp4);
+
+ Consensus[] tmp5 = new Consensus[4];
+ tmp5[0] = conses[3]; //+
+ tmp5[1] = conses[28]; //K
+ tmp5[2] = conses[20]; //R
+ tmp5[3] = conses[19]; //Q
+ colours[4] = new ConsensusColour( (Color) colhash.get("RED"), tmp5);
+
+ Consensus[] tmp6 = new Consensus[5];
+ tmp6[0] = conses[3]; //-
+ tmp6[1] = conses[29]; //D
+ tmp6[2] = conses[10]; //E
+ tmp6[3] = conses[6]; //q
+ tmp6[4] = conses[19]; //Q
+ colours[5] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp6);
+
+ Consensus[] tmp7 = new Consensus[5];
+ tmp7[0] = conses[3]; //-
+ tmp7[1] = conses[29]; //D
+ tmp7[2] = conses[10]; //E
+ tmp7[3] = conses[17]; //N
+ tmp7[4] = conses[2]; //DE
+ colours[6] = new ConsensusColour( (Color) colhash.get("MAGENTA"), tmp7);
+
+ // Now attach the ConsensusColours to the residue letters
+ ResidueColour = new ConsensusColour[20];
+ ResidueColour[0] = colours[0]; // A
+ ResidueColour[1] = colours[4]; // R
+ ResidueColour[2] = colours[2]; // N
+ ResidueColour[3] = colours[6]; // D
+ ResidueColour[4] = colours[0]; // C
+ ResidueColour[5] = colours[3]; // Q
+ ResidueColour[6] = colours[5]; // E
+ ResidueColour[7] = colours[7]; // G
+ ResidueColour[8] = colours[10]; // H
+ ResidueColour[9] = colours[0]; // I
+ ResidueColour[10] = colours[0]; // L
+ ResidueColour[11] = colours[4]; // K
+ ResidueColour[12] = colours[0]; // M
+ ResidueColour[13] = colours[0]; // F
+ ResidueColour[14] = colours[8]; // P
+ ResidueColour[15] = colours[1]; // S
+ ResidueColour[16] = colours[1]; // T
+ ResidueColour[17] = colours[0]; // W
+ ResidueColour[18] = colours[10]; // Y
+ ResidueColour[19] = colours[0]; // V
+ }
+
+ public Color findColour(char c)
+ {
+ return Color.pink;
+ }
+
+ public Color findColour(char c, int j)
+ {
+ Color currentColour;
+
+ if (cons2.length <= j || (includeGaps && threshold != 0 && !aboveThreshold(c, j)))
+ {
+ return Color.white;
+ }
+
+ int i = ResidueProperties.aaIndex[c];
+
+ currentColour = Color.white;
+
+ if (i > 19)
+ {
+ return currentColour;
+ }
+
+ for (int k = 0; k < ResidueColour[i].conses.length; k++)
+ {
+ if (ResidueColour[i].conses[k].isConserved(cons2, j, size, includeGaps))
+ {
+ currentColour = ResidueColour[i].c;
+ }
+ }
+
+ if (i == 4)
+ {
+ if (conses[27].isConserved(cons2, j, size, includeGaps))
+ {
+ currentColour = (Color) colhash.get("PINK");
+ }
+ }
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+
+ return currentColour;
+ }
+
+ /**
+ * @return the includeGaps
+ */
+ protected boolean isIncludeGaps()
+ {
+ return includeGaps;
+ }
+
+ /**
+ * @param includeGaps the includeGaps to set
+ */
+ protected void setIncludeGaps(boolean includeGaps)
+ {
+ this.includeGaps = includeGaps;
+ }
+}
+
+class ConsensusColour
+{
+ Consensus[] conses;
+ Color c;
+
+ public ConsensusColour(Color c, Consensus[] conses)
+ {
+ this.conses = conses;
+
+ // this.list = list;
+ this.c = c;
+ }
+}
git://source.jalview.org / jalview.git / commitdiff