+/*\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 jalview.datamodel.*;\r
-import jalview.jbgui.*;\r
-\r
import java.util.*;\r
+\r
import java.awt.*;\r
\r
-public class ResidueColourScheme implements ColourSchemeI {\r
- Color [] colors;\r
- int threshold = 90;\r
+import jalview.analysis.*;\r
\r
- public ResidueColourScheme(Color[] colors, int threshold) {\r
- this.colors = colors;\r
- this.threshold = threshold;\r
- }\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class ResidueColourScheme\r
+ implements ColourSchemeI\r
+{\r
\r
- public ResidueColourScheme() {\r
- }\r
+ boolean conservationColouring = false;\r
\r
- public Color findColour(String aa)\r
- {\r
- return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];\r
- }\r
+ Color[] colors;\r
+ int threshold = 0;\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
- }\r
+ /* Set when threshold colouring to either pid_gaps or pid_nogaps*/\r
+ protected String ignoreGaps = AAFrequency.PID_GAPS;\r
\r
- // aa should maybe be a class\r
- public Color getColour(SequenceI seq, int j,Vector aa) {\r
+ /** Consenus as a hashtable array */\r
+ Hashtable[] consensus;\r
\r
- Color c = Color.white;\r
- String s = seq.getSequence(j,j+1);\r
+ /** Conservation string as a char array */\r
+ char[] conservation;\r
+ int conservationLength=0;\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
+ /** DOCUMENT ME!! */\r
+ int inc = 30;\r
+\r
+ /**\r
+ * Creates a new ResidueColourScheme object.\r
+ *\r
+ * @param colors DOCUMENT ME!\r
+ * @param threshold DOCUMENT ME!\r
+ */\r
+ public ResidueColourScheme(Color[] colours, int threshold)\r
+ {\r
+ this.colors = colours;\r
+ this.threshold = threshold;\r
+ }\r
+\r
+ /**\r
+ * Creates a new ResidueColourScheme object.\r
+ */\r
+ public ResidueColourScheme()\r
+ {\r
+ }\r
\r
+ /**\r
+ * Find a colour without an index in a sequence\r
+ */\r
+ public Color findColour(char c)\r
+ {\r
+ return colors[ResidueProperties.aaIndex[c]];\r
+ }\r
\r
- return c;\r
+ public Color findColour(char c, int j)\r
+ {\r
+ Color currentColour;\r
+\r
+ if ( (threshold == 0) || aboveThreshold(c, j))\r
+ {\r
+ currentColour = colors[ResidueProperties.aaIndex[c]];\r
}\r
- public int getThreshold() {\r
- return threshold;\r
+ else\r
+ {\r
+ currentColour = Color.white;\r
}\r
\r
- public void setThreshold(int ct) {\r
- threshold = ct;\r
+ if (conservationColouring)\r
+ {\r
+ currentColour = applyConservation(currentColour, j);\r
}\r
\r
- public Vector getColours(SequenceI s, Vector aa) {\r
- Vector colours = new Vector();\r
+ return currentColour;\r
+ }\r
\r
- for (int j = 0; j < s.getLength(); j++)\r
- colours.addElement(getColour(s,j,aa));\r
+ /**\r
+ * Get the percentage threshold for this colour scheme\r
+ *\r
+ * @return Returns the percentage threshold\r
+ */\r
+ public int getThreshold()\r
+ {\r
+ return threshold;\r
+ }\r
\r
- return colours;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param ct DOCUMENT ME!\r
+ */\r
+ public void setThreshold(int ct, boolean ignoreGaps)\r
+ {\r
+ threshold = ct;\r
+ if (ignoreGaps)\r
+ {\r
+ this.ignoreGaps = AAFrequency.PID_NOGAPS;\r
}\r
+ else\r
+ {\r
+ this.ignoreGaps = AAFrequency.PID_GAPS;\r
+ }\r
+ }\r
\r
- public Vector getColours(SequenceGroup sg, Vector aa) {\r
- Vector colours = new Vector();\r
-\r
- for (int j = 0; j < sg.getSize(); j++) {\r
- SequenceI s = sg.getSequenceAt(j);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param j DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean aboveThreshold(char c, int j)\r
+ {\r
+ if ('a' <= c && c <= 'z')\r
+ {\r
+ // TO UPPERCASE !!!\r
+ //Faster than toUpperCase\r
+ c -= ('a' - 'A');\r
+ }\r
\r
- for (int i = 0; i < s.getLength();i++) {\r
- colours.addElement(getColour(s,i,aa));\r
- }\r
- }\r
- return colours;\r
+ if (consensus == null || consensus.length<j || consensus[j] == null)\r
+ {\r
+ return false;\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
+ if ( ( ( (Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1) &&\r
+ consensus[j].contains(String.valueOf(c)))\r
+ {\r
+ if ( ( (Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)\r
+ {\r
+ return true;\r
+ }\r
+ }\r
\r
- if (j < aa.size()) {\r
- String maxRes = (String)hash.get("maxResidue");\r
+ return false;\r
+ }\r
\r
- double sc = 0;\r
+ public boolean conservationApplied()\r
+ {\r
+ return conservationColouring;\r
+ }\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
+ public void setConservationInc(int i)\r
+ {\r
+ inc = i;\r
+ }\r
\r
- sc = resCount * 100.0 / resCount;\r
+ public int getConservationInc()\r
+ {\r
+ return inc;\r
+ }\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
+ * DOCUMENT ME!\r
+ *\r
+ * @param consensus DOCUMENT ME!\r
+ */\r
+ public void setConsensus(Hashtable[] consensus)\r
+ {\r
+ if (consensus == null)\r
+ {\r
+ return;\r
}\r
\r
- public boolean canThreshold() {\r
- return true;\r
+ this.consensus = consensus;\r
+ }\r
+\r
+ public void setConservation(Conservation cons)\r
+ {\r
+ if (cons == null)\r
+ {\r
+ conservationColouring = false;\r
+ conservation = null;\r
}\r
- public boolean isUserDefinable() {\r
- return false;\r
+ else\r
+ {\r
+ conservationColouring = true;\r
+ int i, iSize = cons.getConsSequence().getLength();\r
+ conservation = new char[iSize];\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ conservation[i] = cons.getConsSequence().getCharAt(i);\r
+ }\r
+ conservationLength = conservation.length;\r
+ }\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param i DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+\r
+ Color applyConservation(Color currentColour, int i)\r
+ {\r
+\r
+ if ((conservationLength>i) && (conservation[i] != '*') && (conservation[i] != '+'))\r
+ {\r
+ if ( jalview.util.Comparison.isGap(conservation[i]))\r
+ {\r
+ currentColour = Color.white;\r
+ }\r
+ else\r
+ {\r
+ float t = 11 - (conservation[i] - '0');\r
+ if (t == 0)\r
+ {\r
+ return Color.white;\r
+ }\r
+\r
+ int red = currentColour.getRed();\r
+ int green = currentColour.getGreen();\r
+ int blue = currentColour.getBlue();\r
+\r
+ int dr = 255 - red;\r
+ int dg = 255 - green;\r
+ int db = 255 - blue;\r
+\r
+ dr *= t / 10f;\r
+ dg *= t / 10f;\r
+ db *= t / 10f;\r
+\r
+ red += (inc / 20f) * dr;\r
+ green += (inc / 20f) * dg;\r
+ blue += (inc / 20f) * db;\r
+\r
+ if (red > 255 || green > 255 || blue > 255)\r
+ {\r
+ currentColour = Color.white;\r
+ }\r
+ else\r
+ {\r
+ currentColour = new Color(red, green, blue);\r
+ }\r
+ }\r
}\r
+ return currentColour;\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff