-/*\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
- /* Set when threshold colouring to either pid_gaps or pid_nogaps*/\r
- protected String ignoreGaps = "pid_gaps";\r
-\r
- /** DOCUMENT ME!! */\r
- public Hashtable [] 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 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
- /**\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
- int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();\r
-\r
- if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))\r
- {\r
- return colors[index];\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, boolean ignoreGaps)\r
- {\r
- threshold = ct;\r
- if(ignoreGaps)\r
- this.ignoreGaps = "pid_nogaps";\r
- else\r
- this.ignoreGaps = "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
- if ((((Integer) consensus[j].get("maxCount")).intValue() != -1) &&\r
- consensus[j].contains(s))\r
- {\r
- float ratio = ((Float)consensus[j].get(ignoreGaps)).floatValue();\r
-\r
- if (ratio >= threshold)\r
- {\r
- return true;\r
- }\r
- }\r
-\r
- return false;\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.AlignmentI;
+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 java.awt.Color;
+import java.util.Map;
+
+/**
+ * Base class for residue-based colour schemes
+ */
+public abstract class ResidueColourScheme implements ColourSchemeI
+{
+ public static final String NONE = "None";
+
+ public static final String USER_DEFINED = "User Defined";
+
+ /*
+ * lookup up by character value e.g. 'G' to the colors array index
+ * e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K
+ */
+ final int[] symbolIndex;
+
+ boolean conservationColouring = false;
+
+ /*
+ * colour for residue characters as indexed by symbolIndex
+ */
+ 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;
+ }
+
+ /**
+ * Returns the colour for symbol 'A'. Intended for use in a 'fixed colour'
+ * colour scheme (for example a feature colour).
+ */
+ @Override
+ public Color findColour()
+ {
+ // TODO delete this method in favour of ColorUtils.parseColourString()?
+ return findColour('A');
+ }
+
+ /**
+ * 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 colour = Color.white;
+
+ if (colors != null && symbolIndex != null)
+ {
+ colour = colors[symbolIndex[c]];
+ }
+ colour = adjustColour(c, j, colour);
+
+ return colour;
+ }
+
+ /**
+ * Adjusts colour by applying thresholding or conservation shading, if in
+ * force. That is
+ * <ul>
+ * <li>if there is a threshold set for colouring, and the residue doesn't
+ * match the consensus (or a joint consensus) residue, or the consensus score
+ * is not above the threshold, then the colour is set to white</li>
+ * <li>if conservation colouring is selected, the colour is faded by an amount
+ * depending on the conservation score for the column, and the conservation
+ * colour threshold</li>
+ * </ul>
+ *
+ * @param symbol
+ * @param column
+ * @param colour
+ * @return
+ */
+ protected Color adjustColour(char symbol, int column, Color colour)
+ {
+ if (!aboveThreshold(symbol, column))
+ {
+ colour = Color.white;
+ }
+
+ if (conservationColouring)
+ {
+ colour = applyConservation(colour, column);
+ }
+ return colour;
+ }
+
+ /**
+ * 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 (threshold == 0)
+ {
+ return true;
+ }
+ 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)
+ {
+ }
+
+ /**
+ * Answers false if the colour scheme is nucleotide or peptide specific, and
+ * the data does not match, else true. Override to modify or extend this test
+ * as required.
+ */
+ @Override
+ public boolean isApplicableTo(AnnotatedCollectionI ac)
+ {
+ if (!isPeptideSpecific() && !isNucleotideSpecific())
+ {
+ return true;
+ }
+
+ /*
+ * inspect the data context (alignment) for residue type
+ */
+ boolean nucleotide = false;
+ if (ac instanceof AlignmentI)
+ {
+ nucleotide = ((AlignmentI) ac).isNucleotide();
+ }
+ else
+ {
+ AnnotatedCollectionI context = ac.getContext();
+ if (context instanceof AlignmentI)
+ {
+ nucleotide = ((AlignmentI) context).isNucleotide();
+ }
+ else
+ {
+ // not sure what's going on, play safe
+ return true;
+ }
+ }
+
+ /*
+ * does data type match colour scheme type?
+ */
+ return (nucleotide && isNucleotideSpecific())
+ || (!nucleotide && isPeptideSpecific());
+ }
+
+ /**
+ * Answers true if the colour scheme is normally only for peptide data
+ *
+ * @return
+ */
+ public boolean isPeptideSpecific()
+ {
+ return false;
+ }
+
+ /**
+ * Answers true if the colour scheme is normally only for nucleotide data
+ *
+ * @return
+ */
+ public boolean isNucleotideSpecific()
+ {
+ return false;
+ }
+
+ /**
+ * Default method returns true. Override this to return false in colour
+ * schemes that are not determined solely by the sequence symbol.
+ */
+ @Override
+ public boolean isSimple()
+ {
+ return true;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff