-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 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.analysis.*;\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
-\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 = 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
- /**\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(String aa)\r
- {\r
- return colors[ResidueProperties.aaIndex[aa.charAt(0)]];\r
- }\r
-\r
-\r
-\r
- public Color findColour(String s, int j)\r
- {\r
- Color currentColour;\r
- int index = ResidueProperties.aaIndex[s.charAt(0)];\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
- currentColour = applyConservation(currentColour, 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 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
- this.ignoreGaps = AAFrequency.PID_NOGAPS;\r
- else\r
- this.ignoreGaps = AAFrequency.PID_GAPS;\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
- char c = s.charAt(0);\r
- if ('a' <= c && c <= 'z')\r
- {\r
- // TO UPPERCASE !!!\r
- //Faster than toUpperCase\r
- c -= ('a' - 'A');\r
- s = String.valueOf(c);\r
- }\r
-\r
- if (consensus == null || consensus[j] == null)\r
- return false;\r
-\r
- if ( ( ( (Integer) consensus[j].get(AAFrequency.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
- return false;\r
- }\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
- return;\r
-\r
- this.consensus = consensus;\r
- }\r
-\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
- 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
- currentColour = Color.white;\r
- else\r
- currentColour = new Color(red, green, blue);\r
- }\r
- }\r
- return currentColour;\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.analysis.Conservation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ProfileI;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.util.Map;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ResidueColourScheme implements ColourSchemeI
+{
+ final int[] symbolIndex;
+
+ boolean conservationColouring = false;
+
+ Color[] colors = null;
+
+ int threshold = 0;
+
+ /* Set when threshold colouring to either pid_gaps or pid_nogaps */
+ protected boolean ignoreGaps = false;
+
+ /*
+ * Consensus data indexed by column
+ */
+ ProfilesI consensus;
+
+ /*
+ * Conservation string as a char array
+ */
+ char[] conservation;
+
+ /*
+ * The conservation slider percentage setting
+ */
+ int inc = 30;
+
+ /**
+ * Creates a new ResidueColourScheme object.
+ *
+ * @param final int[] index table into colors (ResidueProperties.naIndex or
+ * ResidueProperties.aaIndex)
+ * @param colors
+ * colours for symbols in sequences
+ * @param threshold
+ * threshold for conservation shading
+ */
+ public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours,
+ int threshold)
+ {
+ symbolIndex = aaOrnaIndex;
+ this.colors = colours;
+ this.threshold = threshold;
+ }
+
+ /**
+ * Creates a new ResidueColourScheme object with a lookup table for indexing
+ * the colour map
+ */
+ public ResidueColourScheme(int[] aaOrNaIndex)
+ {
+ symbolIndex = aaOrNaIndex;
+ }
+
+ /**
+ * Creates a new ResidueColourScheme object - default constructor for
+ * non-sequence dependent colourschemes
+ */
+ public ResidueColourScheme()
+ {
+ symbolIndex = null;
+ }
+
+ /**
+ * Find a colour without an index in a sequence
+ */
+ @Override
+ public Color findColour(char c)
+ {
+ return colors == null ? Color.white : colors[symbolIndex[c]];
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ Color currentColour;
+
+ if (colors != null && symbolIndex != null && (threshold == 0)
+ || aboveThreshold(c, j))
+ {
+ currentColour = colors[symbolIndex[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
+ */
+ @Override
+ public int getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * Sets the percentage consensus threshold value, and whether gaps are ignored
+ * in percentage identity calculation
+ *
+ * @param consensusThreshold
+ * @param ignoreGaps
+ */
+ @Override
+ public void setThreshold(int consensusThreshold, boolean ignoreGaps)
+ {
+ threshold = consensusThreshold;
+ this.ignoreGaps = ignoreGaps;
+ }
+
+ /**
+ * Answers true if there is a consensus profile for the specified column, and
+ * the given residue matches the consensus (or joint consensus) residue for
+ * the column, and the percentage identity for the profile is equal to or
+ * greater than the current threshold; else answers false. The percentage
+ * calculation depends on whether or not we are ignoring gapped sequences.
+ *
+ * @param residue
+ * @param column
+ * (index into consensus profiles)
+ *
+ * @return
+ * @see #setThreshold(int, boolean)
+ */
+ public boolean aboveThreshold(char residue, int column)
+ {
+ if ('a' <= residue && residue <= 'z')
+ {
+ // TO UPPERCASE !!!
+ // Faster than toUpperCase
+ residue -= ('a' - 'A');
+ }
+
+ if (consensus == null)
+ {
+ return false;
+ }
+
+ ProfileI profile = consensus.get(column);
+
+ /*
+ * test whether this is the consensus (or joint consensus) residue
+ */
+ if (profile != null
+ && profile.getModalResidue().contains(String.valueOf(residue)))
+ {
+ if (profile.getPercentageIdentity(ignoreGaps) >= threshold)
+ {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ @Override
+ public boolean conservationApplied()
+ {
+ return conservationColouring;
+ }
+
+ @Override
+ public void setConservationApplied(boolean conservationApplied)
+ {
+ conservationColouring = conservationApplied;
+ }
+
+ @Override
+ public void setConservationInc(int i)
+ {
+ inc = i;
+ }
+
+ @Override
+ public int getConservationInc()
+ {
+ return inc;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param consensus
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setConsensus(ProfilesI consensus)
+ {
+ if (consensus == null)
+ {
+ return;
+ }
+
+ this.consensus = consensus;
+ }
+
+ @Override
+ public void setConservation(Conservation cons)
+ {
+ if (cons == null)
+ {
+ conservationColouring = false;
+ conservation = null;
+ }
+ else
+ {
+ conservationColouring = true;
+ int iSize = cons.getConsSequence().getLength();
+ conservation = new char[iSize];
+ for (int i = 0; i < iSize; i++)
+ {
+ conservation[i] = cons.getConsSequence().getCharAt(i);
+ }
+ }
+
+ }
+
+ /**
+ * Applies a combination of column conservation score, and conservation
+ * percentage slider, to 'bleach' out the residue colours towards white.
+ * <p>
+ * If a column is fully conserved (identical residues, conservation score 11,
+ * shown as *), or all 10 physico-chemical properties are conserved
+ * (conservation score 10, shown as +), then the colour is left unchanged.
+ * <p>
+ * Otherwise a 'bleaching' factor is computed and applied to the colour. This
+ * is designed to fade colours for scores of 0-9 completely to white at slider
+ * positions ranging from 18% - 100% respectively.
+ *
+ * @param currentColour
+ * @param column
+ *
+ * @return bleached (or unmodified) colour
+ */
+ Color applyConservation(Color currentColour, int column)
+ {
+ if (conservation == null || conservation.length <= column)
+ {
+ return currentColour;
+ }
+ char conservationScore = conservation[column];
+
+ /*
+ * if residues are fully conserved (* or 11), or all properties
+ * are conserved (+ or 10), leave colour unchanged
+ */
+ if (conservationScore == '*' || conservationScore == '+'
+ || conservationScore == (char) 10
+ || conservationScore == (char) 11)
+ {
+ return currentColour;
+ }
+
+ if (Comparison.isGap(conservationScore))
+ {
+ return Color.white;
+ }
+
+ /*
+ * convert score 0-9 to a bleaching factor 1.1 - 0.2
+ */
+ float bleachFactor = (11 - (conservationScore - '0')) / 10f;
+
+ /*
+ * scale this up by 0-5 (percentage slider / 20)
+ * as a result, scores of: 0 1 2 3 4 5 6 7 8 9
+ * fade to white at slider value: 18 20 22 25 29 33 40 50 67 100%
+ */
+ bleachFactor *= (inc / 20f);
+
+ return ColorUtils.bleachColour(currentColour, bleachFactor);
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ }
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ try
+ {
+ return getClass().newInstance();
+ } catch (Exception q)
+ {
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_cannot_duplicate_colour_scheme",
+ new String[] { getClass().getName() }), q);
+ }
+ }
+}