-/*\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.analysis.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class ResidueColourScheme\r
- implements ColourSchemeI\r
-{\r
-\r
- boolean conservationColouring = 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 = AAFrequency.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
- * 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
- 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
- else\r
- {\r
- currentColour = Color.white;\r
- }\r
-\r
- if (conservationColouring)\r
- {\r
- currentColour = applyConservation(currentColour, j);\r
- }\r
-\r
- return currentColour;\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 threshold;\r
- }\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
- {\r
- this.ignoreGaps = AAFrequency.PID_NOGAPS;\r
- }\r
- else\r
- {\r
- this.ignoreGaps = AAFrequency.PID_GAPS;\r
- }\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(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
- if (consensus == null || consensus[j] == null)\r
- {\r
- return false;\r
- }\r
-\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
- return false;\r
- }\r
-\r
- public boolean conservationApplied()\r
- {\r
- return conservationColouring;\r
- }\r
-\r
- public void setConservationInc(int i)\r
- {\r
- inc = i;\r
- }\r
-\r
- public int getConservationInc()\r
- {\r
- return inc;\r
- }\r
-\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
- 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
- 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
- }\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 ( (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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.schemes;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ResidueColourScheme implements ColourSchemeI
+{
+
+ boolean conservationColouring = false;
+
+ Color[] colors = null;
+
+ int threshold = 0;
+
+ /* Set when threshold colouring to either pid_gaps or pid_nogaps */
+ protected String ignoreGaps = AAFrequency.PID_GAPS;
+
+ /** Consenus as a hashtable array */
+ Hashtable[] consensus;
+
+ /** Conservation string as a char array */
+ char[] conservation;
+
+ int conservationLength = 0;
+
+ /** DOCUMENT ME!! */
+ int inc = 30;
+
+ /**
+ * 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(char c)
+ {
+ return colors == null ? Color.white
+ : colors[ResidueProperties.aaIndex[c]];
+ }
+
+ public Color findColour(char c, int j)
+ {
+ Color currentColour;
+
+ if ((threshold == 0) || aboveThreshold(c, j))
+ {
+ currentColour = colors[ResidueProperties.aaIndex[c]];
+ }
+ else
+ {
+ currentColour = Color.white;
+ }
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, 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 = AAFrequency.PID_NOGAPS;
+ }
+ else
+ {
+ this.ignoreGaps = AAFrequency.PID_GAPS;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean aboveThreshold(char c, int j)
+ {
+ if ('a' <= c && c <= 'z')
+ {
+ // TO UPPERCASE !!!
+ // Faster than toUpperCase
+ c -= ('a' - 'A');
+ }
+
+ if (consensus == null || consensus.length < j || consensus[j] == null)
+ {
+ return false;
+ }
+
+ if ((((Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1)
+ && consensus[j].contains(String.valueOf(c)))
+ {
+ 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(Hashtable[] consensus)
+ {
+ if (consensus == null)
+ {
+ return;
+ }
+
+ this.consensus = consensus;
+ }
+
+ 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);
+ }
+ conservationLength = conservation.length;
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
+ * @param i
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+
+ Color applyConservation(Color currentColour, int i)
+ {
+
+ if ((conservationLength > i) && (conservation[i] != '*')
+ && (conservation[i] != '+'))
+ {
+ if (jalview.util.Comparison.isGap(conservation[i]))
+ {
+ currentColour = Color.white;
+ }
+ else
+ {
+ float t = 11 - (conservation[i] - '0');
+ if (t == 0)
+ {
+ return Color.white;
+ }
+
+ 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);
+ }
+ }
+ }
+ return currentColour;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff