-/*\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 java.awt.*;\r
-\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
- Color[] colors;\r
- int threshold = 0;\r
-\r
- /** DOCUMENT ME!! */\r
- public Vector consensus;\r
-\r
- /**\r
- * Creates a new ResidueColourScheme object.\r
- *\r
- * @param colors DOCUMENT ME!\r
- * @param threshold DOCUMENT ME!\r
- */\r
- public ResidueColourScheme(Color[] colors, int threshold)\r
- {\r
- this.colors = colors;\r
- this.threshold = threshold;\r
- }\r
-\r
- /**\r
- * Creates a new ResidueColourScheme object.\r
- */\r
- public ResidueColourScheme()\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param consensus DOCUMENT ME!\r
- */\r
- public void setConsensus(Vector consensus)\r
- {\r
- this.consensus = consensus;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param aa DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color findColour(String aa)\r
- {\r
- return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param j DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color findColour(String s, int j)\r
- {\r
- if ((threshold == 0) || aboveThreshold(s, j))\r
- {\r
- return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];\r
- }\r
- else\r
- {\r
- return Color.white;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getThreshold()\r
- {\r
- return threshold;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param ct DOCUMENT ME!\r
- */\r
- public void setThreshold(int ct)\r
- {\r
- threshold = ct;\r
- }\r
-\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
- Hashtable hash = (Hashtable) consensus.elementAt(j);\r
-\r
- if ((((Integer) hash.get("maxCount")).intValue() != -1) &&\r
- hash.contains(s))\r
- {\r
- //// resCount//////////////////// ///////////////seq count////////////\r
- double sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(\r
- "size")).intValue();\r
-\r
- if (sc >= threshold)\r
- {\r
- return true;\r
- }\r
- }\r
-\r
- return false;\r
- }\r
-}\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 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 jalview.analysis.*;
+
+import java.awt.*;
+
+import java.util.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ResidueColourScheme implements ColourSchemeI
+{
+
+ boolean conservationColouring = false;
+ boolean consensusColouring = false;
+
+ Color[] colors;
+ int threshold = 0;
+
+ /* Set when threshold colouring to either pid_gaps or pid_nogaps*/
+ protected String ignoreGaps = "pid_gaps";
+
+ /** Consenus as a hashtable array */
+ Hashtable [] consensus;
+
+ /** Conservation string as a char array */
+ char [] conservation;
+
+ /** DOCUMENT ME!! */
+ int inc = 30;
+
+ /**
+ * The colour to be calculated, manipulated and returned
+ */
+ Color currentColour = null;
+
+
+
+ /**
+ * Creates a new ResidueColourScheme object.
+ *
+ * @param colors DOCUMENT ME!
+ * @param threshold DOCUMENT ME!
+ */
+ public ResidueColourScheme(Color[] colours, int threshold)
+ {
+ this.colors = colours;
+ this.threshold = threshold;
+ }
+
+ /**
+ * Creates a new ResidueColourScheme object.
+ */
+ public ResidueColourScheme()
+ {
+ }
+
+ /**
+ * Find a colour without an index in a sequence
+ */
+ public Color findColour(String aa)
+ {
+ return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];
+ }
+
+
+
+ public Color findColour(String s, int j)
+ {
+
+ int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();
+
+ if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
+ {
+ currentColour = colors[index];
+ }
+ else
+ {
+ currentColour = Color.white;
+ }
+
+ if(conservationColouring)
+ applyConservation(j);
+
+
+ return currentColour;
+ }
+
+
+ /**
+ * Get the percentage threshold for this colour scheme
+ *
+ * @return Returns the percentage threshold
+ */
+ public int getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ct DOCUMENT ME!
+ */
+ public void setThreshold(int ct, boolean ignoreGaps)
+ {
+ threshold = ct;
+ if(ignoreGaps)
+ this.ignoreGaps = "pid_nogaps";
+ else
+ this.ignoreGaps = "pid_gaps";
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s DOCUMENT ME!
+ * @param j DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean aboveThreshold(String s, int j)
+ {
+ if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&
+ consensus[j].contains(s))
+ {
+ if (((Float)consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+ {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+
+ public boolean conservationApplied()
+ {
+ return conservationColouring;
+ }
+
+ public void setConservationInc(int i)
+ {
+ inc = i;
+ }
+
+ public int getConservationInc()
+ {
+ return inc;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param consensus DOCUMENT ME!
+ */
+ public void setConsensus(Vector vconsensus)
+ {
+ if(vconsensus==null)
+ return;
+
+ int i, iSize=vconsensus.size();
+ consensus = new Hashtable[iSize];
+ for(i=0; i<iSize; i++)
+ consensus[i] = (Hashtable)vconsensus.elementAt(i);
+ }
+
+
+ public void setConservation(Conservation cons)
+ {
+ if(cons==null)
+ {
+ conservationColouring = false;
+ conservation = null;
+ }
+ else
+ {
+ conservationColouring = true;
+ int i, iSize = cons.getConsSequence().getLength();
+ conservation = new char[iSize];
+ for (i = 0; i < iSize; i++)
+ conservation[i] = cons.getConsSequence().getCharAt(i);
+ }
+
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s DOCUMENT ME!
+ * @param i DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+
+ void applyConservation(int i)
+ {
+
+ if ((conservation[i] != '*') && (conservation[i] != '+'))
+ {
+ if(jalview.util.Comparison.isGap(conservation[i]))
+ {
+ currentColour = Color.white;
+ }
+ else
+ {
+ float t = 11 - (conservation[i] - '0');
+ if(t==0)
+ {
+ currentColour = Color.white;
+ return;
+ }
+
+ int red = currentColour.getRed();
+ int green = currentColour.getGreen();
+ int blue = currentColour.getBlue();
+
+ int dr = 255 - red;
+ int dg = 255 - green;
+ int db = 255 - blue;
+
+ dr *= t / 10f;
+ dg *= t / 10f;
+ db *= t / 10f;
+
+ red += (inc / 20f) * dr;
+ green += (inc / 20f) * dg;
+ blue += (inc / 20f) * db;
+
+ if (red > 255 || green > 255 || blue > 255)
+ currentColour = Color.white;
+ else
+ currentColour = new Color(red, green, blue);
+ }
+ }
+ }
+
+
+}
git://source.jalview.org / jalview.git / blobdiff