+/*\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
-import java.util.*;\r
+import jalview.analysis.*;\r
+\r
import java.awt.*;\r
\r
-public class ResidueColourScheme implements ColourSchemeI {\r
- Color [] colors;\r
- int threshold = 90;\r
+import java.util.*;\r
+\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class ResidueColourScheme implements ColourSchemeI\r
+{\r
+\r
+ boolean conservationColouring = false;\r
+ boolean consensusColouring = false;\r
+\r
+ Color[] colors;\r
+ int threshold = 0;\r
+\r
+ /* Set when threshold colouring to either pid_gaps or pid_nogaps*/\r
+ protected String ignoreGaps = "pid_gaps";\r
+\r
+ /** Consenus as a hashtable array */\r
+ Hashtable [] consensus;\r
+\r
+ /** Conservation string as a char array */\r
+ char [] conservation;\r
+\r
+ /** DOCUMENT ME!! */\r
+ int inc = 30;\r
+\r
+ /**\r
+ * The colour to be calculated, manipulated and returned\r
+ */\r
+ Color currentColour = null;\r
\r
- public ResidueColourScheme(Color[] colors, int threshold) {\r
- this.colors = colors;\r
- this.threshold = threshold;\r
+\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
- public ResidueColourScheme() {\r
+ /**\r
+ * Creates a new ResidueColourScheme object.\r
+ */\r
+ public ResidueColourScheme()\r
+ {\r
}\r
\r
- public Color findColour(String aa)\r
+ /**\r
+ * Find a colour without an index in a sequence\r
+ */\r
+ public Color findColour(String aa)\r
+ {\r
+ return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];\r
+ }\r
+\r
+\r
+\r
+ public Color findColour(String s, int j)\r
+ {\r
+\r
+ int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();\r
+\r
+ if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))\r
+ {\r
+ currentColour = colors[index];\r
+ }\r
+ else\r
+ {\r
+ currentColour = Color.white;\r
+ }\r
+\r
+ if(conservationColouring)\r
+ applyConservation(j);\r
+\r
+\r
+ return currentColour;\r
+ }\r
+\r
+\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 colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];\r
+ return threshold;\r
}\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
+ * 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
+ this.ignoreGaps = "pid_nogaps";\r
+ else\r
+ this.ignoreGaps = "pid_gaps";\r
}\r
\r
- // aa should maybe be a class\r
- public Color getColour(SequenceI seq, int j,Vector aa) {\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(String s, int j)\r
+ {\r
+ if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&\r
+ consensus[j].contains(s))\r
+ {\r
+ if (((Float)consensus[j].get(ignoreGaps)).floatValue() >= threshold)\r
+ {\r
+ return true;\r
+ }\r
+ }\r
\r
- Color c = Color.white;\r
- String s = seq.getSequence(j,j+1);\r
+ return false;\r
+ }\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
\r
+ public boolean conservationApplied()\r
+ {\r
+ return conservationColouring;\r
+ }\r
\r
- return c;\r
+ public void setConservationInc(int i)\r
+ {\r
+ inc = i;\r
}\r
- public int getThreshold() {\r
- return threshold;\r
+\r
+ public int getConservationInc()\r
+ {\r
+ return inc;\r
}\r
\r
- public void setThreshold(int ct) {\r
- threshold = ct;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param consensus DOCUMENT ME!\r
+ */\r
+ public void setConsensus(Vector vconsensus)\r
+ {\r
+ int i, iSize=vconsensus.size();\r
+ consensus = new Hashtable[iSize];\r
+ for(i=0; i<iSize; i++)\r
+ consensus[i] = (Hashtable)vconsensus.elementAt(i);\r
}\r
\r
- public Vector getColours(SequenceI s, Vector aa) {\r
- Vector colours = new Vector();\r
\r
- for (int j = 0; j < s.getLength(); j++)\r
- colours.addElement(getColour(s,j,aa));\r
+ public void setConservation(Conservation cons)\r
+ {\r
+ if(cons==null)\r
+ {\r
+ conservationColouring = false;\r
+ conservation = null;\r
+ }\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
+ conservation[i] = cons.getConsSequence().getCharAt(i);\r
+ }\r
\r
- return colours;\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 i DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ void applyConservation(int i)\r
+ {\r
+ if ((conservation[i] != '*') && (conservation[i] != '+'))\r
+ {\r
+ int tmp = 10;\r
+ int t = 0;\r
\r
- for (int i = 0; i < s.getLength();i++) {\r
- colours.addElement(getColour(s,i,aa));\r
- }\r
- }\r
- return colours;\r
- }\r
+ if (!jalview.util.Comparison.isGap(conservation[i]))\r
+ {\r
+ t = conservation[i]-'0';\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
+ while (tmp >= t)\r
+ {\r
+ lighter(inc);\r
+ tmp--;\r
+ }\r
+ }\r
\r
- if (j < aa.size()) {\r
- String maxRes = (String)hash.get("maxResidue");\r
+ }\r
\r
- double sc = 0;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param c DOCUMENT ME!\r
+ * @param inc DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ void lighter(int inc)\r
+ {\r
+ int red = currentColour.getRed();\r
+ int blue = currentColour.getBlue();\r
+ int green = currentColour.getGreen();\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
+ if (red < (255 - inc))\r
+ {\r
+ red = red + inc;\r
+ }\r
+ else\r
+ {\r
+ red = 255;\r
+ }\r
\r
- sc = resCount * 100.0 / resCount;\r
+ if (blue < (255 - inc))\r
+ {\r
+ blue = blue + inc;\r
+ }\r
+ else\r
+ {\r
+ blue = 255;\r
+ }\r
+\r
+ if (green < (255 - inc))\r
+ {\r
+ green = green + inc;\r
+ }\r
+ else\r
+ {\r
+ green = 255;\r
+ }\r
+\r
+ currentColour = new Color(red, green, blue);\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
\r
- public boolean canThreshold() {\r
- return true;\r
- }\r
- public boolean isUserDefinable() {\r
- return false;\r
- }\r
}\r
git://source.jalview.org / jalview.git / blobdiff