+++ /dev/null
-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 java.awt.Color;
-import java.util.Map;
-
-/**
- * A class that computes the colouring of an alignment (or subgroup). Currently
- * the factors that may influence residue colouring are
- * <ul>
- * <li>the colour scheme that provides a colour for each aligned residue</li>
- * <li>any threshold for colour, based on percentage identity with consensus</li>
- * <li>any graduation based on conservation of physico-chemical properties</li>
- * </ul>
- *
- * @author gmcarstairs
- *
- */
-public class CollectionColourScheme implements CollectionColourSchemeI
-{
- private ColourSchemeI colourScheme;
-
- private ProfilesI consensus;
-
- private boolean conservationColouring;
-
- private char[] conservation;
-
- private int threshold;
-
- private boolean ignoreGaps;
-
- private int inc;
-
- public CollectionColourScheme(ColourSchemeI cs)
- {
- colourScheme = cs;
- }
-
- /**
- * Default constructor
- */
- public CollectionColourScheme()
- {
- }
-
- /**
- * @see jalview.schemes.CollectionColourSchemeI#setConsensus(jalview.datamodel.ProfilesI)
- */
- @Override
- public void setConsensus(ProfilesI cons)
- {
- consensus = cons;
- }
-
- /**
- * @see jalview.schemes.CollectionColourSchemeI#conservationApplied()
- */
- @Override
- public boolean conservationApplied()
- {
- return conservationColouring;
- }
-
- /**
- * @see jalview.schemes.CollectionColourSchemeI#setConservationApplied(boolean)
- */
- @Override
- public void setConservationApplied(boolean conservationApplied)
- {
- conservationColouring = conservationApplied;
- }
-
- /**
- * @see jalview.schemes.CollectionColourSchemeI#setConservation(jalview.analysis.Conservation)
- */
- @Override
- public void setConservation(Conservation cons)
- {
- if (cons == null)
- {
- conservationColouring = false;
- conservation = null;
- }
- else
- {
- conservationColouring = true;
- conservation = cons.getConsSequence().getSequenceAsString()
- .toCharArray();
- }
-
- }
-
- /**
- * @see jalview.schemes.CollectionColourSchemeI#alignmentChanged(jalview.datamodel.AnnotatedCollectionI,
- * java.util.Map)
- */
- @Override
- public void alignmentChanged(AnnotatedCollectionI alignment,
- Map<SequenceI, SequenceCollectionI> hiddenReps)
- {
- if (colourScheme != null)
- {
- colourScheme.alignmentChanged(alignment, hiddenReps);
- }
- }
-
- /**
- * @see jalview.schemes.CollectionColourSchemeI#setThreshold(int, boolean)
- */
- @Override
- public void setThreshold(int consensusThreshold, boolean ignoreGaps)
- {
- threshold = consensusThreshold;
- this.ignoreGaps = ignoreGaps;
- }
-
- /**
- * @see jalview.schemes.CollectionColourSchemeI#setConservationInc(int)
- */
- @Override
- public void setConservationInc(int i)
- {
- inc = i;
- }
-
- /**
- * @see jalview.schemes.CollectionColourSchemeI#getConservationInc()
- */
- @Override
- public int getConservationInc()
- {
- return inc;
- }
-
- /**
- * @see jalview.schemes.CollectionColourSchemeI#getThreshold()
- */
- @Override
- public int getThreshold()
- {
- return threshold;
- }
-
- /**
- * @see jalview.schemes.CollectionColourSchemeI#findColour(char, int,
- * jalview.datamodel.SequenceI)
- */
- @Override
- public Color findColour(char symbol, int position, SequenceI seq)
- {
- /*
- * get 'base' colour
- */
- ProfileI profile = consensus == null ? null : consensus.get(position);
- String modalResidue = profile == null ? null : profile
- .getModalResidue();
- float pid = profile == null ? 0f : profile
- .getPercentageIdentity(ignoreGaps);
- Color colour = colourScheme == null ? Color.white : colourScheme
- .findColour(symbol, position, seq, modalResidue, pid);
-
- /*
- * apply PID threshold and consensus fading if in force
- */
- colour = adjustColour(symbol, position, 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;
- }
-
- /**
- * 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)
- */
- protected 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;
- }
-
- /**
- * 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
- */
- protected 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);
- }
-
- /**
- * @see jalview.schemes.CollectionColourSchemeI#getColourScheme()
- */
- @Override
- public ColourSchemeI getColourScheme()
- {
- return this.colourScheme;
- }
-
- /**
- * @see jalview.schemes.CollectionColourSchemeI#setColourScheme(jalview.schemes.ColourSchemeI)
- */
- @Override
- public void setColourScheme(ColourSchemeI cs)
- {
- colourScheme = cs;
- }
-}
git://source.jalview.org / jalview.git / blobdiff