-/*\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
-\r
-package jalview.schemes;\r
-\r
-import jalview.datamodel.*;\r
-import java.util.*;\r
-import java.awt.*;\r
-\r
-public class ClustalxColourScheme extends ResidueColourScheme\r
-{\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
- Vector colourTable = new Vector();\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;\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,i, j = 0;\r
- String seq;\r
- while(j < seqs.size())\r
- {\r
- seq = ( (SequenceI) seqs.elementAt(j)).getSequence();\r
- int end_j = seq.length()-1;\r
- for (i = start; i <= end_j; 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
- }\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
- // 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
-\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
- 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
- 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
- return Color.white;\r
-\r
-\r
- int i = ((Integer)ResidueProperties.aaHash.get(s)).intValue();\r
-\r
- Color c = Color.white;\r
-\r
- if(i>19)\r
- return c;\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 == 4)\r
- {\r
- if (conses[27].isConserved(cons2, j, size))\r
- c = (Color) colhash.get("PINK");\r
- }\r
-\r
-\r
- return c;\r
-\r
- }\r
-}\r
-\r
-class ConsensusColour {\r
-\r
- Consensus[] conses;\r
- Color c;\r
-\r
- public ConsensusColour(Color c,Consensus[] conses) {\r
- this.conses = conses;\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class ClustalxColourScheme extends ResidueColourScheme
+{
+ private static final int EIGHTY_FIVE = 85;
+
+ private static final int FIFTY = 50;
+
+ private static final int EIGHTY = 80;
+
+ private static final int SIXTY = 60;
+
+ /*
+ * Map from conventional colour names to Clustal version of the same
+ */
+ private static Map<Color, Color> colhash = new HashMap<Color, Color>();
+
+ private int[][] cons2;
+
+ private ConsensusColour[] colours;
+
+ private ConsensusColour[] residueColour;
+
+ private int size;
+
+ private Consensus[] conses = new Consensus[32];
+
+ private boolean includeGaps = true;
+
+ static
+ {
+ colhash.put(Color.RED, new Color(0.9f, 0.2f, 0.1f));
+ colhash.put(Color.BLUE, new Color(0.5f, 0.7f, 0.9f));
+ colhash.put(Color.GREEN, new Color(0.1f, 0.8f, 0.1f));
+ colhash.put(Color.ORANGE, new Color(0.9f, 0.6f, 0.3f));
+ colhash.put(Color.CYAN, new Color(0.1f, 0.7f, 0.7f));
+ colhash.put(Color.PINK, new Color(0.9f, 0.5f, 0.5f));
+ colhash.put(Color.MAGENTA, new Color(0.8f, 0.3f, 0.8f));
+ colhash.put(Color.YELLOW, new Color(0.8f, 0.8f, 0.0f));
+ }
+
+ public ClustalxColourScheme(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ alignmentChanged(alignment, hiddenReps);
+ }
+
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ int maxWidth = alignment.getWidth();
+ List<SequenceI> seqs = alignment.getSequences(hiddenReps);
+ 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;
+
+ for (SequenceI sq : seqs)
+ {
+ seq = sq.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", SIXTY);
+ conses[1] = new Consensus("WLVIMAFCYHP", EIGHTY);
+ conses[2] = new Consensus("ED", FIFTY);
+ conses[3] = new Consensus("KR", SIXTY);
+ conses[4] = new Consensus("G", FIFTY);
+ conses[5] = new Consensus("N", FIFTY);
+ conses[6] = new Consensus("QE", FIFTY);
+ conses[7] = new Consensus("P", FIFTY);
+ conses[8] = new Consensus("TS", FIFTY);
+
+ conses[26] = new Consensus("A", EIGHTY_FIVE);
+ conses[27] = new Consensus("C", EIGHTY_FIVE);
+ conses[10] = new Consensus("E", EIGHTY_FIVE);
+ conses[11] = new Consensus("F", EIGHTY_FIVE);
+ conses[12] = new Consensus("G", EIGHTY_FIVE);
+ conses[13] = new Consensus("H", EIGHTY_FIVE);
+ conses[14] = new Consensus("I", EIGHTY_FIVE);
+ conses[15] = new Consensus("L", EIGHTY_FIVE);
+ conses[16] = new Consensus("M", EIGHTY_FIVE);
+ conses[17] = new Consensus("N", EIGHTY_FIVE);
+ conses[18] = new Consensus("P", EIGHTY_FIVE);
+ conses[19] = new Consensus("Q", EIGHTY_FIVE);
+ conses[20] = new Consensus("R", EIGHTY_FIVE);
+ conses[21] = new Consensus("S", EIGHTY_FIVE);
+ conses[22] = new Consensus("T", EIGHTY_FIVE);
+ conses[23] = new Consensus("V", EIGHTY_FIVE);
+ conses[24] = new Consensus("W", EIGHTY_FIVE);
+ conses[25] = new Consensus("Y", EIGHTY_FIVE);
+ conses[28] = new Consensus("K", EIGHTY_FIVE);
+ conses[29] = new Consensus("D", EIGHTY_FIVE);
+
+ 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(colhash.get(Color.ORANGE), tmp8);
+
+ Consensus[] tmp9 = new Consensus[1];
+ tmp9[0] = conses[31]; // P
+ colours[8] = new ConsensusColour(colhash.get(Color.YELLOW), tmp9);
+
+ Consensus[] tmp10 = new Consensus[1];
+ tmp10[0] = conses[27]; // C
+ colours[9] = new ConsensusColour(colhash.get(Color.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(colhash.get(Color.BLUE), tmp1);
+
+ colours[10] = new ConsensusColour(colhash.get(Color.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(colhash.get(Color.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(colhash.get(Color.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(colhash.get(Color.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(colhash.get(Color.RED), tmp5);
+
+ Consensus[] tmp6 = new Consensus[6];
+ tmp6[0] = conses[3]; // -
+ tmp6[1] = conses[29]; // D
+ tmp6[2] = conses[10]; // E
+ tmp6[3] = conses[6]; // QE
+ tmp6[4] = conses[19]; // Q
+ tmp6[5] = conses[2]; // DE
+ colours[5] = new ConsensusColour(colhash.get(Color.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(colhash.get(Color.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
+ }
+
+ @Override
+ public Color findColour(char c)
+ {
+ return Color.pink;
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ 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 = colhash.get(Color.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;
+ }
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ ClustalxColourScheme css = new ClustalxColourScheme(sg,
+ hiddenRepSequences);
+ css.includeGaps = includeGaps;
+ return css;
+ }
+}
+
+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 / blobdiff