/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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/>.
+ * 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 java.util.*;
-
-import java.awt.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
-import jalview.analysis.*;
+import java.awt.Color;
+import java.util.Map;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * Base class for residue-based colour schemes
*/
-public class ResidueColourScheme implements ColourSchemeI
+public abstract class ResidueColourScheme implements ColourSchemeI
{
+ public static final String NONE = "None";
- boolean conservationColouring = false;
+ public static final String USER_DEFINED = "User Defined";
- Color[] colors = null;
+ /*
+ * 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;
- int threshold = 0;
+ /*
+ * colour for residue characters as indexed by symbolIndex
+ */
+ Color[] colors = null;
/* 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;
+ protected boolean ignoreGaps = false;
/**
* Creates a new ResidueColourScheme object.
*
+ * @param final int[] index table into colors (ResidueProperties.naIndex or
+ * ResidueProperties.aaIndex)
* @param colors
- * DOCUMENT ME!
- * @param threshold
- * DOCUMENT ME!
+ * colours for symbols in sequences
*/
- public ResidueColourScheme(Color[] colours, int threshold)
+ public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours)
{
+ symbolIndex = aaOrnaIndex;
this.colors = colours;
- this.threshold = threshold;
}
/**
- * Creates a new ResidueColourScheme object.
+ * Creates a new ResidueColourScheme object with a lookup table for indexing
+ * the colour map
*/
- public ResidueColourScheme()
+ public ResidueColourScheme(int[] aaOrNaIndex)
{
+ symbolIndex = aaOrNaIndex;
}
/**
- * Find a colour without an index in a sequence
+ * Creates a new ResidueColourScheme object - default constructor for
+ * non-sequence dependent colourschemes
*/
- public Color findColour(char c)
+ public ResidueColourScheme()
{
- return colors == null ? Color.white
- : colors[ResidueProperties.aaIndex[c]];
+ symbolIndex = null;
}
- public Color findColour(char c, int j)
+ /**
+ * Find a colour without an index in a sequence
+ */
+ public Color findColour(char c)
{
- Color currentColour;
-
- if ((threshold == 0) || aboveThreshold(c, j))
- {
- currentColour = colors[ResidueProperties.aaIndex[c]];
- }
- else
- {
- currentColour = Color.white;
- }
+ Color colour = Color.white;
- if (conservationColouring)
+ if (!Comparison.isGap(c) && 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.
*/
- public int getThreshold()
+ @Override
+ public Color findColour(char c, int j, SequenceI seq,
+ String consensusResidue, float pid)
{
- return threshold;
+ return findColour(c, j, seq);
}
/**
- * DOCUMENT ME!
+ * 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 ct
- * DOCUMENT ME!
+ * @param c
+ * @param j
+ * @param seq
+ * @return
*/
- public void setThreshold(int ct, boolean ignoreGaps)
+ protected Color findColour(char c, int j, SequenceI seq)
+ {
+ return findColour(c);
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
{
- 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!
+ * 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.
*/
- public boolean aboveThreshold(char c, int j)
+ @Override
+ public boolean isApplicableTo(AnnotatedCollectionI ac)
{
- if ('a' <= c && c <= 'z')
+ if (!isPeptideSpecific() && !isNucleotideSpecific())
{
- // TO UPPERCASE !!!
- // Faster than toUpperCase
- c -= ('a' - 'A');
+ return true;
}
- if (consensus == null || consensus.length < j || consensus[j] == null)
+ /*
+ * inspect the data context (alignment) for residue type
+ */
+ boolean nucleotide = false;
+ if (ac instanceof AlignmentI)
{
- return false;
+ nucleotide = ((AlignmentI) ac).isNucleotide();
}
-
- if ((((Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1)
- && consensus[j].contains(String.valueOf(c)))
+ else
{
- if (((Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+ AnnotatedCollectionI context = ac.getContext();
+ if (context instanceof AlignmentI)
+ {
+ nucleotide = ((AlignmentI) context).isNucleotide();
+ }
+ else
{
+ // not sure what's going on, play safe
return true;
}
}
- return false;
- }
-
- public boolean conservationApplied()
- {
- return conservationColouring;
- }
-
- public void setConservationInc(int i)
- {
- inc = i;
- }
-
- public int getConservationInc()
- {
- return inc;
+ /*
+ * does data type match colour scheme type?
+ */
+ return (nucleotide && isNucleotideSpecific())
+ || (!nucleotide && isPeptideSpecific());
}
/**
- * DOCUMENT ME!
+ * Answers true if the colour scheme is normally only for peptide data
*
- * @param consensus
- * DOCUMENT ME!
+ * @return
*/
- public void setConsensus(Hashtable[] consensus)
+ public boolean isPeptideSpecific()
{
- if (consensus == null)
- {
- return;
- }
-
- this.consensus = consensus;
+ return false;
}
- public void setConservation(Conservation cons)
+ /**
+ * Answers true if the colour scheme is normally only for nucleotide data
+ *
+ * @return
+ */
+ public boolean isNucleotideSpecific()
{
- 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;
- }
-
+ return false;
}
/**
- * DOCUMENT ME!
- *
- * @param s
- * DOCUMENT ME!
- * @param i
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Default method returns true. Override this to return false in colour
+ * schemes that are not determined solely by the sequence symbol.
*/
-
- Color applyConservation(Color currentColour, int i)
+ @Override
+ public boolean isSimple()
{
-
- 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;
+ return true;
}
-
}
git://source.jalview.org / jalview.git / blobdiff