*/
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.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.util.ColorUtils;
-import jalview.util.Comparison;
import java.awt.Color;
import java.util.Map;
{
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.
*
* ResidueProperties.aaIndex)
* @param colors
* colours for symbols in sequences
- * @param threshold
- * threshold for conservation shading
*/
- public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours,
- int threshold)
+ public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours)
{
symbolIndex = aaOrnaIndex;
this.colors = colours;
- this.threshold = threshold;
}
/**
}
/**
- * 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 currentColour;
-
- if (colors != null && symbolIndex != null && (threshold == 0)
- || aboveThreshold(c, j))
- {
- currentColour = colors[symbolIndex[c]];
- }
- else
- {
- currentColour = Color.white;
- }
+ Color colour = Color.white;
- if (conservationColouring)
+ if (colors != null && symbolIndex != null
+ && c < symbolIndex.length
+ && symbolIndex[c] < colors.length)
{
- currentColour = applyConservation(currentColour, j);
+ colour = colors[symbolIndex[c]];
}
- return currentColour;
+ return colour;
}
/**
- * Get the percentage threshold for this colour scheme
- *
- * @return Returns the percentage threshold
+ * Default is to call the overloaded method that ignores consensus. A colour
+ * scheme that depends on consensus (for example, Blosum62), should override
+ * this method instead.
*/
@Override
- public int getThreshold()
+ public Color findColour(char c, int j, SequenceI seq,
+ String consensusResidue, float pid)
{
- return threshold;
+ return findColour(c, j, seq);
}
/**
- * 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)
+ * Default implementation looks up the residue colour in a fixed scheme, or
+ * returns White if not found. Override this method for a colour scheme that
+ * depends on the column position or sequence.
*
+ * @param c
+ * @param j
+ * @param seq
* @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)
+ protected Color findColour(char c, int j, SequenceI seq)
{
- 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);
+ return findColour(c);
}
@Override
{
return true;
}
-
- /*
- * inspect the data context (alignment dataset) for residue type
- */
- boolean nucleotide = false;
- AnnotatedCollectionI context = ac.getContext();
- if (context != null)
- {
- if (context instanceof AlignmentI)
- {
- nucleotide = ((AlignmentI) context).isNucleotide();
- }
- else
- {
- // not sure what's going on, play safe
- return true;
- }
- }
- else if (ac instanceof AlignmentI)
+ if (ac == null)
{
- nucleotide = ((AlignmentI) ac).isNucleotide();
+ return true;
}
- else
+ /*
+ * pop-up menu on selection group before group created
+ * (no alignment context)
+ */
+ // TODO: add nucleotide flag to SequenceGroup?
+ if (ac instanceof SequenceGroup && ac.getContext() == null)
{
return true;
}
/*
+ * inspect the data context (alignment) for residue type
+ */
+ boolean nucleotide = ac.isNucleotide();
+
+ /*
* does data type match colour scheme type?
*/
return (nucleotide && 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